02:05:2012 11:08 kareneilbeck sequence autogenerated-by: DAG-Edit version 1.417\nsaved-by: eilbeck\ndate: Tue May 11 15:18:44 PDT 2004\nversion: $Revision: 1.281 $ biosapiens protein feature ontology database of genomic structural variation SO feature annotation sequence This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi Sequence_Ontology sequence region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence sequence sequence_secondary_structure A folded sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence secondary structure sequence G_quartet G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet. URL:http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract G quartet G tetrad G-quadruplex G-quartet G-tetrad G_quadruplex guanine tetrad sequence URL:http://en.wikipedia.org/wiki/G-quadruplex http://en.wikipedia.org/wiki/G-quadruplex interior_coding_exon interior coding exon sequence satellite_DNA The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html satellite DNA sequence URL:http://en.wikipedia.org/wiki/Satellite_DNA http://en.wikipedia.org/wiki/Satellite_DNA PCR_product This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406. A region amplified by a PCR reaction. SO:ke http://purl.org/obo/owl/SO#SO_ke amplicon PCR product sequence URL:http://en.wikipedia.org/wiki/RAPD http://en.wikipedia.org/wiki/RAPD read_pair One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert. SO:ls http://purl.org/obo/owl/SO#SO_ls mate pair read-pair sequence gene_sensu_your_favorite_organism sequence gene_class sequence protein_coding protein-coding sequence non_protein_coding non protein-coding sequence scRNA_primary_transcript The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote. URL:http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html scRNA primary transcript scRNA transcript small cytoplasmic RNA small cytoplasmic RNA transcript small_cytoplasmic_RNA sequence scRNA A small non coding RNA sequence, present in the cytoplasm. SO:ke http://purl.org/obo/owl/SO#SO_ke small cytoplasmic RNA sequence INR_motif Binds TAF1, TAF2. A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element. PMID:12651739 http://purl.org/obo/owl/PMID#PMID_12651739 PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 DMp2 initiator initiator motif INR motif sequence DPE_motif Binds TAF6, TAF9. A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C). PMID:12651739:12537576 http://purl.org/obo/owl/PMID#PMID_12651739:12537576 PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 CRWMGCGWKCGCTTS downstream core promoter element DPE motif sequence BREu_motif Binds TFIIB. A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB. PMID:12651739 http://purl.org/obo/owl/PMID#PMID_12651739 PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 B-recognition element BRE motif BREu BREu motif TFIIB recognition element transcription factor B-recognition element sequence PSE_motif A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). PMID:12651739 http://purl.org/obo/owl/PMID#PMID_12651739 proximal sequence element PSE motif sequence linkage_group A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned. ISBN:038752046 http://purl.org/obo/owl/ISBN#ISBN_038752046 linkage group sequence URL:http://en.wikipedia.org/wiki/Linkage_group http://en.wikipedia.org/wiki/Linkage_group RNA_internal_loop A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge. SO:ke http://purl.org/obo/owl/SO#SO_ke RNA internal loop sequence asymmetric_RNA_internal_loop An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand. SO:ke http://purl.org/obo/owl/SO#SO_ke asymmetric RNA internal loop sequence A_minor_RNA_motif A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix. SO:ke http://purl.org/obo/owl/SO#SO_ke A minor RNA motif sequence K_turn_RNA_motif The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices. SO:ke http://purl.org/obo/owl/SO#SO_ke K turn RNA motif K-turn kink turn kink-turn motif sequence URL:http://en.wikipedia.org/wiki/K-turn http://en.wikipedia.org/wiki/K-turn sarcin_like_RNA_motif A loop in ribosomal RNA containing the sites of attack for ricin and sarcin. URL:http://www.ncbi.nlm.nih.gov/pubmed/7897662 http://www.ncbi.nlm.nih.gov/pubmed/7897662 sarcin like RNA motif sarcin/ricin domain sarcin/ricin loop sarcin/ricin RNA domain sequence symmetric_RNA_internal_loop An internal RNA loop where the extent of the loop on both stands is the same size. SO:ke http://purl.org/obo/owl/SO#SO_ke A-minor RNA motif sequence RNA_junction_loop RNA junction loop sequence RNA_hook_turn hook turn hook-turn motif RNA hook turn sequence base_pair base pair sequence URL:http://en.wikipedia.org/wiki/Base_pair http://en.wikipedia.org/wiki/Base_pair WC_base_pair The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation. PMID:12177293 http://purl.org/obo/owl/PMID#PMID_12177293 canonical base pair Watson Crick base pair Watson-Crick base pair Watson-Crick pair WC base pair sequence sugar_edge_base_pair A type of non-canonical base-pairing. PMID:12177293 http://purl.org/obo/owl/PMID#PMID_12177293 sugar edge base pair sequence aptamer DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. URL:http://aptamer.icmb.utexas.edu http://aptamer.icmb.utexas.edu sequence URL:http://en.wikipedia.org/wiki/Aptamer http://en.wikipedia.org/wiki/Aptamer DNA_aptamer DNA molecules that have been selected from random pools based on their ability to bind other molecules. http:aptamer.icmb.utexas.edu http://purl.org/obo/owl/http#http_aptamer.icmb.utexas.edu DNA aptamer sequence RNA_aptamer RNA molecules that have been selected from random pools based on their ability to bind other molecules. URL:http://aptamer.icmb.utexas.edu http://aptamer.icmb.utexas.edu RNA aptamer sequence morpholino_oligo Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. URL:http://www.gene-tools.com/ http://www.gene-tools.com/ morphant morpholino morpholino oligo sequence riboswitch A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites. PMID:2820954 http://purl.org/obo/owl/PMID#PMID_2820954 riboswitch RNA sequence URL:http://en.wikipedia.org/wiki/Riboswitch http://en.wikipedia.org/wiki/Riboswitch matrix_attachment_site A DNA region that is required for the binding of chromatin to the nuclear matrix. SO:ma http://purl.org/obo/owl/SO#SO_ma MAR matrix association region matrix attachment region matrix attachment site nuclear matrix association region nuclear matrix attachment site S/MAR S/MAR element scaffold attachment site scaffold matrix attachment region SMAR sequence URL:http://en.wikipedia.org/wiki/Matrix_attachment_site http://en.wikipedia.org/wiki/Matrix_attachment_site locus_control_region A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene. SO:ma http://purl.org/obo/owl/SO#SO_ma LCR locus control element locus control region sequence URL:http://en.wikipedia.org/wiki/Locus_control_region http://en.wikipedia.org/wiki/Locus_control_region match_set A collection of match parts. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence match_part A part of a match, for example an hsp from blast is a match_part. SO:ke http://purl.org/obo/owl/SO#SO_ke match part sequence genomic_clone A clone of a DNA region of a genome. SO:ma http://purl.org/obo/owl/SO#SO_ma genomic clone sequence sequence_operation An operation that can be applied to a sequence, that results in a change. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence operation sequence pseudogene_attribute An attribute of a pseudogene (SO:0000336). SO:ma http://purl.org/obo/owl/SO#SO_ma pseudogene attribute sequence processed_pseudogene Please not the synonym R psi M uses the spelled out form of the greek letter. A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail. SO:xp http://purl.org/obo/owl/SO#SO_xp processed pseudogene pseudogene by reverse transcription R psi G retropseudogene sequence pseudogene_by_unequal_crossing_over A pseudogene caused by unequal crossing over at recombination. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogene by unequal crossing over sequence delete To remove a subsection of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence insert To insert a subsection of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence invert To invert a subsection of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence substitute To substitute a subsection of sequence for another. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence translocate To translocate a subsection of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence gene_part A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence probe A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/Hybridization_probe http://en.wikipedia.org/wiki/Hybridization_probe assortment_derived_deficiency assortment-derived_deficiency sequence sequence_variant_affecting_regulatory_region OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. A sequence_variant_effect which changes the regulatory region of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation affecting regulatory region sequence variant affecting regulatory region sequence aneuploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Aneuploid http://en.wikipedia.org/wiki/Aneuploid hyperploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Hyperploid http://en.wikipedia.org/wiki/Hyperploid hypoploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Hypoploid http://en.wikipedia.org/wiki/Hypoploid operator A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. SO:ma http://purl.org/obo/owl/SO#SO_ma operator segment sequence URL:http://en.wikipedia.org/wiki/Operator_(biology)#Operator http://en.wikipedia.org/wiki/Operator_(biology)#Operator assortment_derived_aneuploid assortment-derived_aneuploid sequence nuclease_binding_site A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease. SO:cb http://purl.org/obo/owl/SO#SO_cb nuclease binding site sequence compound_chromosome_arm FLAG - this term is should probably be a part of rather than an is_a. compound chromosome arm sequence restriction_enzyme_binding_site A region of a molecule that binds to a restriction enzyme. A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme. SO:cb http://purl.org/obo/owl/SO#SO_cb restriction endonuclease binding site restriction enzyme binding site sequence deficient_intrachromosomal_transposition An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual deficient intrachromosomal transposition sequence deficient_interchromosomal_transposition An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. SO:ke http://purl.org/obo/owl/SO#SO_ke deficient interchromosomal transposition sequence gene_by_transcript_attribute This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004. sequence free_chromosome_arm A chromosome structure variation whereby an arm exists as an individual chromosome element. SO:ke http://purl.org/obo/owl/SO#SO_ke free chromosome arm sequence gene_by_polyadenylation_attribute sequence gene_to_gene_feature gene to gene feature sequence overlapping An attribute describing a gene that has a sequence that overlaps the sequence of another gene. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence inside_intron An attribute to describe a gene when it is located within the intron of another gene. SO:ke http://purl.org/obo/owl/SO#SO_ke inside intron sequence inside_intron_antiparallel An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand. SO:ke http://purl.org/obo/owl/SO#SO_ke inside intron antiparallel sequence inside_intron_parallel An attribute to describe a gene when it is located within the intron of another gene and on the same strand. SO:ke http://purl.org/obo/owl/SO#SO_ke inside intron parallel sequence end_overlapping_gene sequence five_prime_three_prime_overlap An attribute to describe a gene when the five prime region overlaps with another gene's 3' region. SO:ke http://purl.org/obo/owl/SO#SO_ke five prime-three prime overlap sequence five_prime_five_prime_overlap An attribute to describe a gene when the five prime region overlaps with another gene's five prime region. SO:ke http://purl.org/obo/owl/SO#SO_ke five prime-five prime overlap sequence three_prime_three_prime_overlap An attribute to describe a gene when the 3' region overlaps with another gene's 3' region. SO:ke http://purl.org/obo/owl/SO#SO_ke three prime-three prime overlap sequence three_prime_five_prime_overlap An attribute to describe a gene when the 3' region overlaps with another gene's 5' region. SO:ke http://purl.org/obo/owl/SO#SO_ke 5' 3' overlap three prime five prime overlap sequence antisense A region sequence that is complementary to a sequence of messenger RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Antisense http://en.wikipedia.org/wiki/Antisense polycistronic_transcript A transcript that is polycistronic. SO:xp http://purl.org/obo/owl/SO#SO_xp polycistronic transcript sequence dicistronic_transcript A transcript that is dicistronic. SO:ke http://purl.org/obo/owl/SO#SO_ke dicistronic transcript sequence operon_member operon member sequence gene_array_member gene array member sequence processed_transcript_attribute sequence macronuclear_sequence macronuclear sequence sequence micronuclear_sequence micronuclear sequence sequence gene_by_genome_location sequence gene_by_organelle_of_genome sequence nuclear_gene A gene from nuclear sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp nuclear gene sequence URL:http://en.wikipedia.org/wiki/Nuclear_gene http://en.wikipedia.org/wiki/Nuclear_gene mt_gene A gene located in mitochondrial sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp mitochondrial gene mt gene sequence URL:http://en.wikipedia.org/wiki/Mitochondrial_gene http://en.wikipedia.org/wiki/Mitochondrial_gene kinetoplast_gene A gene located in kinetoplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp kinetoplast gene sequence plastid_gene A gene from plastid sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp plastid gene sequence apicoplast_gene A gene from apicoplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp apicoplast gene sequence ct_gene A gene from chloroplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp chloroplast gene ct gene sequence chromoplast_gene A gene from chromoplast_sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp chromoplast gene sequence cyanelle_gene A gene from cyanelle sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp cyanelle gene sequence leucoplast_gene A plastid gene from leucoplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp leucoplast gene sequence proplastid_gene A gene from proplastid sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke proplastid gene sequence nucleomorph_gene A gene from nucleomorph sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp nucleomorph gene sequence plasmid_gene A gene from plasmid sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp plasmid gene sequence proviral_gene A gene from proviral sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp proviral gene sequence endogenous_retroviral_gene A proviral gene with origin endogenous retrovirus. SO:xp http://purl.org/obo/owl/SO#SO_xp endogenous retroviral gene sequence transposable_element A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. URL:http://www.sci.sdsu.edu/~smaloy/Glossary/T.html http://www.sci.sdsu.edu/~smaloy/Glossary/T.html transposable element transposon sequence URL:http://en.wikipedia.org/wiki/Transposable_element http://en.wikipedia.org/wiki/Transposable_element expressed_sequence_match A match to an EST or cDNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke expressed sequence match sequence clone_insert_end The end of the clone insert. SO:ke http://purl.org/obo/owl/SO#SO_ke clone insert end sequence polypeptide This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute. A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. SO:ma http://purl.org/obo/owl/SO#SO_ma protein sequence SO:0000358 URL:http://en.wikipedia.org/wiki/Polypeptide http://en.wikipedia.org/wiki/Polypeptide chromosome_arm A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. URL:http://www.medterms.com/script/main/art.asp?articlekey=5152 http://www.medterms.com/script/main/art.asp?articlekey=5152 chromosome arm sequence non_capped_primary_transcript sequence sequencing_primer sequencing primer sequence mRNA_with_frameshift An mRNA with a frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp frameshifted mRNA mRNA with frameshift sequence sequence_variant_obs A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. SO:ke http://purl.org/obo/owl/SO#SO_ke mutation sequence sequence_feature An extent of biological sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke located sequence feature located_sequence_feature sequence feature sequence transposable_element_gene A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast. SO:ke http://purl.org/obo/owl/SO#SO_ke transposable element gene sequence primer An oligo to which new deoxyribonucleotides can be added by DNA polymerase. SO:ke http://purl.org/obo/owl/SO#SO_ke DNA primer primer oligonucleotide primer polynucleotide primer sequence sequence URL:http://en.wikipedia.org/wiki/Primer_(molecular_biology) http://en.wikipedia.org/wiki/Primer_(molecular_biology) proviral_region A viral sequence which has integrated into a host genome. SO:ke http://purl.org/obo/owl/SO#SO_ke proviral region proviral sequence sequence methylated_C A methylated deoxy-cytosine. SO:ke http://purl.org/obo/owl/SO#SO_ke methylated C methylated cytosine methylated cytosine base methylated cytosine residue sequence transcript_feature sequence edited An attribute describing a sequence that is modified by editing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence transcript_with_readthrough_stop_codon sequence transcript_with_translational_frameshift A transcript with a translational frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp transcript with translational frameshift sequence regulated An attribute to describe a sequence that is regulated. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence protein_coding_primary_transcript May contain introns. A primary transcript that, at least in part, encodes one or more proteins. SO:ke http://purl.org/obo/owl/SO#SO_ke pre mRNA protein coding primary transcript sequence forward_primer This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A single stranded oligo used for polymerase chain reaction. URL:http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php DNA forward primer forward DNA primer forward primer forward primer oligo forward primer oligonucleotide forward primer polynucleotide forward primer sequence sequence RNA_sequence_secondary_structure A folded RNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke RNA sequence secondary structure sequence transcriptionally_regulated By:<protein_id>. An attribute describing a gene that is regulated at transcription. SO:ma http://purl.org/obo/owl/SO#SO_ma transcriptionally regulated sequence transcriptionally_constitutive Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate. SO:ke http://purl.org/obo/owl/SO#SO_ke transcriptionally constitutive sequence transcriptionally_induced An inducer molecule is required for transcription to occur. SO:ke http://purl.org/obo/owl/SO#SO_ke transcriptionally induced sequence transcriptionally_repressed A repressor molecule is required for transcription to stop. SO:ke http://purl.org/obo/owl/SO#SO_ke transcriptionally repressed sequence silenced_gene A gene that is silenced. SO:xp http://purl.org/obo/owl/SO#SO_xp silenced gene sequence gene_silenced_by_DNA_modification A gene that is silenced by DNA modification. SO:xp http://purl.org/obo/owl/SO#SO_xp gene silenced by DNA modification sequence gene_silenced_by_DNA_methylation A gene that is silenced by DNA methylation. SO:xp http://purl.org/obo/owl/SO#SO_xp gene silenced by DNA methylation methylation-silenced gene sequence post_translationally_regulated An attribute describing a gene that is regulated after it has been translated. SO:ke http://purl.org/obo/owl/SO#SO_ke post translationally regulated post-translationally regulated sequence translationally_regulated An attribute describing a gene that is regulated as it is translated. SO:ke http://purl.org/obo/owl/SO#SO_ke translationally regulated sequence reverse_primer This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A single stranded oligo used for polymerase chain reaction. URL:http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php DNA reverse primer reverse DNA primer reverse primer reverse primer oligo reverse primer oligonucleotide reverse primer sequence sequence epigenetically_modified This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones. SO:ke http://purl.org/obo/owl/SO#SO_ke epigenetically modified sequence genomically_imprinted Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin. SO:ke http://purl.org/obo/owl/SO#SO_ke genomically imprinted imprinted sequence http:http://en.wikipedia.org/wiki/Genomic_imprinting http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Genomic_imprinting maternally_imprinted The maternal copy of the gene is modified, rendering it transcriptionally silent. SO:ke http://purl.org/obo/owl/SO#SO_ke maternally imprinted sequence paternally_imprinted The paternal copy of the gene is modified, rendering it transcriptionally silent. SO:ke http://purl.org/obo/owl/SO#SO_ke paternally imprinted sequence allelically_excluded Examples are x-inactivation and immunoglobulin formation. Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell. SO:ke http://purl.org/obo/owl/SO#SO_ke allelically excluded sequence gene_rearranged_at_DNA_level An epigenetically modified gene, rearranged at the DNA level. SO:xp http://purl.org/obo/owl/SO#SO_xp gene rearranged at DNA level sequence ribosome_entry_site Region in mRNA where ribosome assembles. SO:ke http://purl.org/obo/owl/SO#SO_ke ribosome entry site sequence attenuator A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. SO:as http://purl.org/obo/owl/SO#SO_as attenuator sequence sequence URL:http://en.wikipedia.org/wiki/Attenuator http://en.wikipedia.org/wiki/Attenuator terminator The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html terminator sequence sequence URL:http://en.wikipedia.org/wiki/Terminator_(genetics) http://en.wikipedia.org/wiki/Terminator_(genetics) DNA_sequence_secondary_structure A folded DNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke DNA sequence secondary structure sequence assembly_component A region of known length which may be used to manufacture a longer region. SO:ke http://purl.org/obo/owl/SO#SO_ke assembly component sequence primary_transcript_attribute sequence recoded_codon A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough. SO:xp http://purl.org/obo/owl/SO#SO_xp recoded codon sequence capped An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence exon This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Exon http://en.wikipedia.org/wiki/Exon supercontig One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. SO:ls http://purl.org/obo/owl/SO#SO_ls scaffold sequence contig A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. SO:ls http://purl.org/obo/owl/SO#SO_ls sequence URL:http://en.wikipedia.org/wiki/Contig http://en.wikipedia.org/wiki/Contig read A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. SO:rd http://purl.org/obo/owl/SO#SO_rd sequence clone A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence http:http://en.wikipedia.org/wiki/Clone_(genetics) http://purl.org/obo/owl/http#http_http://en.wikipedia.org/wiki/Clone_(genetics) YAC This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells. SO:ma http://purl.org/obo/owl/SO#SO_ma yeast artificial chromosome sequence BAC This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host. SO:ma http://purl.org/obo/owl/SO#SO_ma bacterial artificial chromosome sequence PAC This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome. The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. URL:http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome P1 P1 artificial chromosome sequence URL:http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome plasmid This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. SO:ma http://purl.org/obo/owl/SO#SO_ma plasmid sequence sequence cosmid Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites. SO:ma http://purl.org/obo/owl/SO#SO_ma cosmid vector sequence URL:http://en.wikipedia.org/wiki/Cosmid http://en.wikipedia.org/wiki/Cosmid phagemid A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids. SO:ma http://purl.org/obo/owl/SO#SO_ma phagemid vector sequence URL:http://en.wikipedia.org/wiki/Phagemid http://en.wikipedia.org/wiki/Phagemid fosmid Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996. A cloning vector that utilizes the E. coli F factor. SO:ma http://purl.org/obo/owl/SO#SO_ma fosmid vector sequence URL:http://en.wikipedia.org/wiki/Fosmid http://en.wikipedia.org/wiki/Fosmid deletion The point at which one or more contiguous nucleotides were excised. SO:ke http://purl.org/obo/owl/SO#SO_ke deleted_sequence nucleotide deletion nucleotide_deletion sequence SO:1000033 URL:http://en.wikipedia.org/wiki/Nucleotide_deletion http://en.wikipedia.org/wiki/Nucleotide_deletion loinc:LA6692-3 http://purl.org/obo/owl/loinc#loinc_LA6692-3 lambda_clone A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. ISBN:0-1767-2380-8 http://purl.org/obo/owl/ISBN#ISBN_0-1767-2380-8 sequence methylated_A A modified RNA base in which adenine has been methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke methylated A methylated adenine methylated adenine base methylated adenine residue sequence splice_site With spliceosomal introns, the splice sites bind the spliceosomal machinery. Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. SO:cjm http://purl.org/obo/owl/SO#SO_cjm SO:ke http://purl.org/obo/owl/SO#SO_ke splice site sequence URL:http://en.wikipedia.org/wiki/Splice_site http://en.wikipedia.org/wiki/Splice_site five_prime_cis_splice_site Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron. URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html SO:cjm http://purl.org/obo/owl/SO#SO_cjm SO:ke http://purl.org/obo/owl/SO#SO_ke 5' splice site donor donor splice site five prime splice site splice donor site sequence three_prime_cis_splice_site Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron. URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html SO:cjm http://purl.org/obo/owl/SO#SO_cjm SO:ke http://purl.org/obo/owl/SO#SO_ke 3' splice site acceptor acceptor splice site splice acceptor site three prime splice site sequence enhancer An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO. A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html sequence URL:http://en.wikipedia.org/wiki/Enhancer_(genetics) http://en.wikipedia.org/wiki/Enhancer_(genetics) enhancer_bound_by_factor An enhancer bound by a factor. SO:xp http://purl.org/obo/owl/SO#SO_xp enhancer bound by factor sequence promoter This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery. SO:regcreative http://purl.org/obo/owl/SO#SO_regcreative promoter sequence sequence URL:http://en.wikipedia.org/wiki/Promoter http://en.wikipedia.org/wiki/Promoter restriction_enzyme_cut_site A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence RNApol_I_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke pol I promoter polymerase I promoter RNA polymerase A promoter RNApol I promoter sequence RNApol_II_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke pol II promoter polymerase II promoter RNA polymerase B promoter RNApol II promoter sequence RNApol_III_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke pol III promoter polymerase III promoter RNA polymerase C promoter RNApol III promoter sequence CAAT_signal Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html CAAT box CAAT signal CAAT-box sequence URL:http://en.wikipedia.org/wiki/CAAT_box http://en.wikipedia.org/wiki/CAAT_box GC_rich_promoter_region A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html GC rich promoter region GC-rich region sequence TATA_box Binds TBP. A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T). URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html PMID:16858867 http://purl.org/obo/owl/PMID#PMID_16858867 Goldstein-Hogness box TATA box sequence URL:http://en.wikipedia.org/wiki/TATA_box http://en.wikipedia.org/wiki/TATA_box minus_10_signal A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html -10 signal minus 10 signal Pribnow box Pribnow Schaller box Pribnow-Schaller box sequence URL:http://en.wikipedia.org/wiki/Pribnow_box http://en.wikipedia.org/wiki/Pribnow_box minus_35_signal A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html -35 signal minus 35 signal sequence cross_genome_match A nucleotide match against a sequence from another organism. SO:ma http://purl.org/obo/owl/SO#SO_ma cross genome match sequence operon This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/Operon http://en.wikipedia.org/wiki/Operon clone_insert_start The start of the clone insert. SO:ke http://purl.org/obo/owl/SO#SO_ke clone insert start sequence retrotransposon A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase. URL:http://www.dddmag.com/Glossary.aspx#r http://www.dddmag.com/Glossary.aspx#r class I class I transposon retrotransposon element sequence URL:http://en.wikipedia.org/wiki/Retrotransposon http://en.wikipedia.org/wiki/Retrotransposon translated_nucleotide_match A match against a translated sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke translated nucleotide match sequence DNA_transposon A transposon where the mechanism of transposition is via a DNA intermediate. SO:ke http://purl.org/obo/owl/SO#SO_ke class II class II transposon DNA transposon sequence non_transcribed_region A region of the gene which is not transcribed. SO:ke http://purl.org/obo/owl/SO#SO_ke non transcribed region non-transcribed sequence nontranscribed region nontranscribed sequence sequence U2_intron May have either GT-AG or AT-AG 5' and 3' boundaries. A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs. PMID:9428511 http://purl.org/obo/owl/PMID#PMID_9428511 U2 intron sequence primary_transcript A transcript that in its initial state requires modification to be functional. SO:ma http://purl.org/obo/owl/SO#SO_ma precursor RNA primary transcript sequence URL:http://en.wikipedia.org/wiki/Primary_transcript http://en.wikipedia.org/wiki/Primary_transcript LTR_retrotransposon A retrotransposon flanked by long terminal repeat sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke long terminal repeat retrotransposon LTR retrotransposon sequence repeat_family A group of characterized repeat sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence intron This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html sequence URL:http://en.wikipedia.org/wiki/Intron http://en.wikipedia.org/wiki/Intron non_LTR_retrotransposon A retrotransposon without long terminal repeat sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke non LTR retrotransposon sequence five_prime_intron 5' intron 5' intron sequence five prime intron sequence interior_intron interior intron sequence three_prime_intron 3' intron 3' intron sequence three prime intron sequence RFLP_fragment A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme. GOC:pj http://purl.org/obo/owl/GOC#GOC_pj restriction fragment length polymorphism RFLP RFLP fragment sequence URL:http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism LINE_element A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats. URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html LINE LINE element Long interspersed element Long interspersed nuclear element sequence coding_exon An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon). SO:ke http://purl.org/obo/owl/SO#SO_ke coding exon sequence five_prime_coding_exon_coding_region The sequence of the five_prime_coding_exon that codes for protein. SO:cjm http://purl.org/obo/owl/SO#SO_cjm five prime exon coding region sequence three_prime_coding_exon_coding_region The sequence of the three_prime_coding_exon that codes for protein. SO:cjm http://purl.org/obo/owl/SO#SO_cjm three prime exon coding region sequence noncoding_exon An exon that does not contain any codons. SO:ke http://purl.org/obo/owl/SO#SO_ke noncoding exon sequence translocation A region of nucleotide sequence that has translocated to a new position. SO:ke http://purl.org/obo/owl/SO#SO_ke transchr URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ translocated sequence sequence five_prime_coding_exon The 5' most coding exon. SO:ke http://purl.org/obo/owl/SO#SO_ke 5' coding exon five prime coding exon sequence interior_exon An exon that is bounded by 5' and 3' splice sites. PMID:10373547 http://purl.org/obo/owl/PMID#PMID_10373547 interior exon sequence three_prime_coding_exon The coding exon that is most 3-prime on a given transcript. SO:ma http://purl.org/obo/owl/SO#SO_ma 3' coding exon three prime coding exon sequence UTR Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. SO:ke http://purl.org/obo/owl/SO#SO_ke untranslated region sequence five_prime_UTR A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html 5' UTR five prime UTR five_prime_untranslated_region sequence URL:http://en.wikipedia.org/wiki/5'_UTR http://en.wikipedia.org/wiki/5'_UTR three_prime_UTR A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html three prime untranslated region three prime UTR sequence URL:http://en.wikipedia.org/wiki/Three_prime_untranslated_region http://en.wikipedia.org/wiki/Three_prime_untranslated_region SINE_element A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element. SO:ke http://purl.org/obo/owl/SO#SO_ke Short interspersed element Short interspersed nuclear element SINE element sequence URL:http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element simple_sequence_length_variation simple sequence length polymorphism simple sequence length variation SSLP sequence terminal_inverted_repeat_element A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long. URL:http://www.genetics.org/cgi/reprint/156/4/1983.pdf http://www.genetics.org/cgi/reprint/156/4/1983.pdf terminal inverted repeat element TIR element sequence rRNA_primary_transcript A primary transcript encoding a ribosomal RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke ribosomal RNA primary transcript rRNA primary transcript sequence tRNA_primary_transcript A primary transcript encoding a transfer RNA (SO:0000253). SO:ke http://purl.org/obo/owl/SO#SO_ke tRNA primary transcript sequence alanine_tRNA_primary_transcript A primary transcript encoding alanyl tRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke alanine tRNA primary transcript sequence arginine_tRNA_primary_transcript A primary transcript encoding arginyl tRNA (SO:0000255). SO:ke http://purl.org/obo/owl/SO#SO_ke arginine tRNA primary transcript sequence asparagine_tRNA_primary_transcript A primary transcript encoding asparaginyl tRNA (SO:0000256). SO:ke http://purl.org/obo/owl/SO#SO_ke asparagine tRNA primary transcript sequence aspartic_acid_tRNA_primary_transcript A primary transcript encoding aspartyl tRNA (SO:0000257). SO:ke http://purl.org/obo/owl/SO#SO_ke aspartic acid tRNA primary transcript sequence cysteine_tRNA_primary_transcript A primary transcript encoding cysteinyl tRNA (SO:0000258). SO:ke http://purl.org/obo/owl/SO#SO_ke cysteine tRNA primary transcript sequence glutamic_acid_tRNA_primary_transcript A primary transcript encoding glutaminyl tRNA (SO:0000260). SO:ke http://purl.org/obo/owl/SO#SO_ke glutamic acid tRNA primary transcript sequence glutamine_tRNA_primary_transcript A primary transcript encoding glutamyl tRNA (SO:0000260). SO:ke http://purl.org/obo/owl/SO#SO_ke glutamine tRNA primary transcript sequence glycine_tRNA_primary_transcript A primary transcript encoding glycyl tRNA (SO:0000263). SO:ke http://purl.org/obo/owl/SO#SO_ke glycine tRNA primary transcript sequence histidine_tRNA_primary_transcript A primary transcript encoding histidyl tRNA (SO:0000262). SO:ke http://purl.org/obo/owl/SO#SO_ke histidine tRNA primary transcript sequence isoleucine_tRNA_primary_transcript A primary transcript encoding isoleucyl tRNA (SO:0000263). SO:ke http://purl.org/obo/owl/SO#SO_ke isoleucine tRNA primary transcript sequence leucine_tRNA_primary_transcript A primary transcript encoding leucyl tRNA (SO:0000264). SO:ke http://purl.org/obo/owl/SO#SO_ke leucine tRNA primary transcript sequence lysine_tRNA_primary_transcript A primary transcript encoding lysyl tRNA (SO:0000265). SO:ke http://purl.org/obo/owl/SO#SO_ke lysine tRNA primary transcript sequence methionine_tRNA_primary_transcript A primary transcript encoding methionyl tRNA (SO:0000266). SO:ke http://purl.org/obo/owl/SO#SO_ke methionine tRNA primary transcript sequence phenylalanine_tRNA_primary_transcript A primary transcript encoding phenylalanyl tRNA (SO:0000267). SO:ke http://purl.org/obo/owl/SO#SO_ke phenylalanine tRNA primary transcript sequence proline_tRNA_primary_transcript A primary transcript encoding prolyl tRNA (SO:0000268). SO:ke http://purl.org/obo/owl/SO#SO_ke proline tRNA primary transcript sequence serine_tRNA_primary_transcript A primary transcript encoding seryl tRNA (SO:000269). SO:ke http://purl.org/obo/owl/SO#SO_ke serine tRNA primary transcript sequence threonine_tRNA_primary_transcript A primary transcript encoding threonyl tRNA (SO:000270). SO:ke http://purl.org/obo/owl/SO#SO_ke threonine tRNA primary transcript sequence tryptophan_tRNA_primary_transcript A primary transcript encoding tryptophanyl tRNA (SO:000271). SO:ke http://purl.org/obo/owl/SO#SO_ke tryptophan tRNA primary transcript sequence tyrosine_tRNA_primary_transcript A primary transcript encoding tyrosyl tRNA (SO:000272). SO:ke http://purl.org/obo/owl/SO#SO_ke tyrosine tRNA primary transcript sequence valine_tRNA_primary_transcript A primary transcript encoding valyl tRNA (SO:000273). SO:ke http://purl.org/obo/owl/SO#SO_ke valine tRNA primary transcript sequence snRNA_primary_transcript A primary transcript encoding a small nuclear RNA (SO:0000274). SO:ke http://purl.org/obo/owl/SO#SO_ke snRNA primary transcript sequence snoRNA_primary_transcript A primary transcript encoding a small nucleolar mRNA (SO:0000275). SO:ke http://purl.org/obo/owl/SO#SO_ke snoRNA primary transcript sequence mature_transcript A processed transcript cannot contain introns. A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. SO:ke http://purl.org/obo/owl/SO#SO_ke mature transcript sequence URL:http://en.wikipedia.org/wiki/Mature_transcript http://en.wikipedia.org/wiki/Mature_transcript mRNA An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. SO:ma http://purl.org/obo/owl/SO#SO_ma messenger RNA sequence URL:http://en.wikipedia.org/wiki/MRNA http://en.wikipedia.org/wiki/MRNA TF_binding_site A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]. SO:ke http://purl.org/obo/owl/SO#SO_ke TF binding site transcription factor binding site sequence ORF The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. SGD:rb http://purl.org/obo/owl/SGD#SGD_rb SO:ma http://purl.org/obo/owl/SO#SO_ma open reading frame sequence transcript_attribute transcript attribute sequence foldback_element A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats. URL:http://www.genetics.org/cgi/reprint/156/4/1983.pdf http://www.genetics.org/cgi/reprint/156/4/1983.pdf foldback element long inverted repeat element LVR element sequence flanking_region The sequences extending on either side of a specific region. SO:ke http://purl.org/obo/owl/SO#SO_ke flanking region sequence chromosome_variation chromosome variation sequence internal_UTR A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal. SO:cjm http://purl.org/obo/owl/SO#SO_cjm internal UTR sequence untranslated_region_polycistronic_mRNA The untranslated sequence separating the 'cistrons' of multicistronic mRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke untranslated region polycistronic mRNA sequence internal_ribosome_entry_site Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation. SO:ke http://purl.org/obo/owl/SO#SO_ke internal ribosomal entry sequence internal ribosomal entry site internal ribosome entry sequence internal ribosome entry site IRES sequence URL:http://en.wikipedia.org/wiki/Internal_ribosome_entry_site http://en.wikipedia.org/wiki/Internal_ribosome_entry_site four_cutter_restriction_site 4-cutter_restriction_site four-cutter_restriction_sit sequence mRNA_by_polyadenylation_status sequence polyadenylated A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence mRNA_not_polyadenylated sequence sequence_length_variation sequence length variation sequence six_cutter_restriction_site 6-cutter_restriction_site six-cutter_restriction_site sequence modified_RNA_base_feature A post_transcriptionally modified base. SO:ke http://purl.org/obo/owl/SO#SO_ke modified RNA base feature sequence eight_cutter_restriction_site 8-cutter_restriction_site eight-cutter_restriction_site sequence rRNA RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html ISBN:0198506732 http://purl.org/obo/owl/ISBN#ISBN_0198506732 ribosomal ribonucleic acid ribosomal RNA sequence URL:http://en.wikipedia.org/wiki/RRNA http://en.wikipedia.org/wiki/RRNA tRNA This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005 ISBN:0198506732 http://purl.org/obo/owl/ISBN#ISBN_0198506732 transfer ribonucleic acid transfer RNA sequence URL:http://en.wikipedia.org/wiki/TRNA http://en.wikipedia.org/wiki/TRNA alanyl_tRNA A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke alanyl tRNA alanyl-transfer ribonucleic acid alanyl-transfer RNA sequence rRNA_small_subunit_primary_transcript A primary transcript encoding a small ribosomal subunit RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke rRNA small subunit primary transcript sequence asparaginyl_tRNA A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke asparaginyl tRNA asparaginyl-transfer ribonucleic acid asparaginyl-transfer RNA sequence aspartyl_tRNA A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke aspartyl tRNA aspartyl-transfer ribonucleic acid aspartyl-transfer RNA sequence cysteinyl_tRNA A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke cysteinyl tRNA cysteinyl-transfer ribonucleic acid cysteinyl-transfer RNA sequence glutaminyl_tRNA A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke glutaminyl tRNA glutaminyl-transfer ribonucleic acid glutaminyl-transfer RNA sequence glutamyl_tRNA A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke glutamyl tRNA glutamyl-transfer ribonucleic acid glutamyl-transfer RNA sequence glycyl_tRNA A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke glycyl tRNA glycyl-transfer ribonucleic acid glycyl-transfer RNA sequence histidyl_tRNA A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke histidyl tRNA histidyl-transfer ribonucleic acid histidyl-transfer RNA sequence isoleucyl_tRNA A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke isoleucyl tRNA isoleucyl-transfer ribonucleic acid isoleucyl-transfer RNA sequence leucyl_tRNA A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke leucyl tRNA leucyl-transfer ribonucleic acid leucyl-transfer RNA sequence lysyl_tRNA A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke lysyl tRNA lysyl-transfer ribonucleic acid lysyl-transfer RNA sequence methionyl_tRNA A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke methionyl tRNA methionyl-transfer ribonucleic acid methionyl-transfer RNA sequence phenylalanyl_tRNA A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke phenylalanyl tRNA phenylalanyl-transfer ribonucleic acid phenylalanyl-transfer RNA sequence prolyl_tRNA A tRNA sequence that has a proline anticodon, and a 3' proline binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke prolyl tRNA prolyl-transfer ribonucleic acid prolyl-transfer RNA sequence seryl_tRNA A tRNA sequence that has a serine anticodon, and a 3' serine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke seryl tRNA seryl-transfer ribonucleic acid seryl-transfer RNA sequence threonyl_tRNA A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke threonyl tRNA threonyl-transfer ribonucleic acid threonyl-transfer RNA sequence tryptophanyl_tRNA A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke tryptophanyl tRNA tryptophanyl-transfer ribonucleic acid tryptophanyl-transfer RNA sequence tyrosyl_tRNA A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke tyrosyl tRNA tyrosyl-transfer ribonucleic acid tyrosyl-transfer RNA sequence valyl_tRNA A tRNA sequence that has a valine anticodon, and a 3' valine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke valyl tRNA valyl-transfer ribonucleic acid valyl-transfer RNA sequence snRNA This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A small nuclear RNA molecule involved in pre-mRNA splicing and processing. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html PMID:11733745 http://purl.org/obo/owl/PMID#PMID_11733745 WB:ems http://purl.org/obo/owl/WB#WB_ems small nuclear RNA sequence URL:http://en.wikipedia.org/wiki/SnRNA http://en.wikipedia.org/wiki/SnRNA snoRNA A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA. GOC:kgc http://purl.org/obo/owl/GOC#GOC_kgc small nucleolar RNA sequence URL:http://en.wikipedia.org/wiki/SnoRNA http://en.wikipedia.org/wiki/SnoRNA miRNA Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. PMID:12592000 http://purl.org/obo/owl/PMID#PMID_12592000 micro RNA microRNA sequence URL:http://en.wikipedia.org/wiki/MiRNA http://en.wikipedia.org/wiki/MiRNA bound_by_factor Formerly called transcript_by_bound_factor. An attribute describing a sequence that is bound by another molecule. SO:ke http://purl.org/obo/owl/SO#SO_ke bound by factor sequence transcript_bound_by_nucleic_acid Formerly called transcript_by_bound_nucleic_acid. A transcript that is bound by a nucleic acid. SO:xp http://purl.org/obo/owl/SO#SO_xp transcript bound by nucleic acid sequence transcript_bound_by_protein Formerly called transcript_by_bound_protein. A transcript that is bound by a protein. SO:xp http://purl.org/obo/owl/SO#SO_xp transcript bound by protein sequence engineered_gene A gene that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered gene sequence engineered_foreign_gene A gene that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered foreign gene sequence mRNA_with_minus_1_frameshift An mRNA with a minus 1 frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp mRNA with minus 1 frameshift sequence engineered_foreign_transposable_element_gene A transposable_element that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered foreign transposable element gene sequence type_I_enzyme_restriction_site The recognition site is bipartite and interrupted. URL:http://www.promega.com http://www.promega.com sequence foreign_gene A gene that is foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp foreign gene sequence long_terminal_repeat A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html direct terminal repeat long terminal repeat LTR sequence URL:http://en.wikipedia.org/wiki/Long_terminal_repeat http://en.wikipedia.org/wiki/Long_terminal_repeat fusion_gene A gene that is a fusion. SO:xp http://purl.org/obo/owl/SO#SO_xp fusion gene sequence URL:http://en.wikipedia.org/wiki/Fusion_gene http://en.wikipedia.org/wiki/Fusion_gene engineered_fusion_gene A fusion gene that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered fusion gene sequence microsatellite A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem. URL:http://www.informatics.jax.org/silver/glossary.shtml http://www.informatics.jax.org/silver/glossary.shtml microsatellite locus microsatellite marker VNTR sequence URL:http://en.wikipedia.org/wiki/Microsatellite http://en.wikipedia.org/wiki/Microsatellite dinucleotide_repeat_microsatellite_feature dinucleotide repeat microsatellite dinucleotide repeat microsatellite feature dinucleotide repeat microsatellite locus dinucleotide repeat microsatellite marker sequence trinucleotide_repeat_microsatellite_feature dinucleotide repeat microsatellite marker rinucleotide repeat microsatellite trinucleotide repeat microsatellite feature trinucleotide repeat microsatellite locus sequence repetitive_element sequence engineered_foreign_repetitive_element A repetitive element that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered foreign repetitive element sequence inverted_repeat The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC. SO:ke http://purl.org/obo/owl/SO#SO_ke inverted repeat inverted repeat sequence sequence URL:http://en.wikipedia.org/wiki/Inverted_repeat http://en.wikipedia.org/wiki/Inverted_repeat U12_intron May have either GT-AC or AT-AC 5' and 3' boundaries. A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs. PMID:9428511 http://purl.org/obo/owl/PMID#PMID_9428511 U12 intron U12-dependent intron sequence origin_of_replication The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html ori origin of replication sequence URL:http://en.wikipedia.org/wiki/Origin_of_replication http://en.wikipedia.org/wiki/Origin_of_replication D_loop Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html D-loop displacement loop sequence URL:http://en.wikipedia.org/wiki/D_loop http://en.wikipedia.org/wiki/D_loop recombination_feature recombination feature sequence specific_recombination_site specific recombination site sequence recombination_feature_of_rearranged_gene recombination feature of rearranged gene sequence vertebrate_immune_system_gene_recombination_feature vertebrate immune system gene recombination feature sequence J_gene_recombination_feature Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J gene recombination feature J-RS sequence clip Part of the primary transcript that is clipped off during processing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence type_II_enzyme_restriction_site The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site. URL:http://www.promega.com http://www.promega.com sequence modified_base Modified base:<modified_base>. A modified nucleotide, i.e. a nucleotide other than A, T, C. G. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html modified base site sequence methylated_base_feature A nucleotide modified by methylation. SO:ke http://purl.org/obo/owl/SO#SO_ke methylated base feature sequence CpG_island Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. SO:rd http://purl.org/obo/owl/SO#SO_rd CG island CpG island sequence URL:http://en.wikipedia.org/wiki/CpG_island http://en.wikipedia.org/wiki/CpG_island sequence_feature_locating_method sequence computed_feature sequence predicted_ab_initio_computation sequence computed_feature_by_similarity similar to:<sequence_id> . SO:ma http://purl.org/obo/owl/SO#SO_ma sequence experimentally_determined Attribute to describe a feature that has been experimentally verified. SO:ke http://purl.org/obo/owl/SO#SO_ke experimentally determined sequence stem_loop A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html RNA_hairpin_loop stem loop stem-loop sequence SO:0000019 URL:http://en.wikipedia.org/wiki/Stem_loop http://en.wikipedia.org/wiki/Stem_loop direct_repeat A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA. SO:ke http://purl.org/obo/owl/SO#SO_ke direct repeat sequence URL:http://en.wikipedia.org/wiki/Direct_repeat http://en.wikipedia.org/wiki/Direct_repeat TSS The first base where RNA polymerase begins to synthesize the RNA transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke transcription start site sequence CDS A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. SO:ma http://purl.org/obo/owl/SO#SO_ma coding sequence sequence cDNA_clone This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host. URL:http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html cDNA clone sequence start_codon First codon to be translated by a ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke initiation codon start codon sequence URL:http://en.wikipedia.org/wiki/Start_codon http://en.wikipedia.org/wiki/Start_codon stop_codon In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. SO:ke http://purl.org/obo/owl/SO#SO_ke stop codon sequence URL:http://en.wikipedia.org/wiki/Stop_codon http://en.wikipedia.org/wiki/Stop_codon intronic_splice_enhancer Sequences within the intron that modulate splice site selection for some introns. SO:ke http://purl.org/obo/owl/SO#SO_ke intronic splice enhancer sequence mRNA_with_plus_1_frameshift An mRNA with a plus 1 frameshift. SO:ke http://purl.org/obo/owl/SO#SO_ke mRNA with plus 1 frameshift sequence nuclease_hypersensitive_site nuclease hypersensitive site sequence coding_start The first base to be translated into protein. SO:ke http://purl.org/obo/owl/SO#SO_ke coding start translation initiation site translation start sequence tag A nucleotide sequence that may be used to identify a larger sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence rRNA_large_subunit_primary_transcript A primary transcript encoding a large ribosomal subunit RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke rRNA large subunit primary transcript sequence SAGE_tag A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=7570003&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=7570003&amp;dopt=Abstract SAGE tag sequence coding_end The last base to be translated into protein. It does not include the stop codon. SO:ke http://purl.org/obo/owl/SO#SO_ke coding end translation termination site translation_end sequence microarray_oligo microarray oligo microarray oligonucleotide sequence mRNA_with_plus_2_frameshift An mRNA with a plus 2 frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp mRNA with plus 2 frameshift sequence conserved_region Region of sequence similarity by descent from a common ancestor. SO:ke http://purl.org/obo/owl/SO#SO_ke conserved region sequence URL:http://en.wikipedia.org/wiki/Conserved_region http://en.wikipedia.org/wiki/Conserved_region STS Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. URL:http://www.biospace.com http://www.biospace.com sequence tag site sequence coding_conserved_region Coding region of sequence similarity by descent from a common ancestor. SO:ke http://purl.org/obo/owl/SO#SO_ke coding conserved region sequence exon_junction The boundary between two exons in a processed transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke exon junction sequence nc_conserved_region Non-coding region of sequence similarity by descent from a common ancestor. SO:ke http://purl.org/obo/owl/SO#SO_ke nc conserved region noncoding conserved region sequence mRNA_with_minus_2_frameshift A mRNA with a minus 2 frameshift. SO:ke http://purl.org/obo/owl/SO#SO_ke mRNA with minus 2 frameshift sequence pseudogene A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html sequence URL:http://en.wikipedia.org/wiki/Pseudogene http://en.wikipedia.org/wiki/Pseudogene RNAi_reagent A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. SO:rd http://purl.org/obo/owl/SO#SO_rd RNAi reagent sequence MITE A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins. URL:http://www.pnas.org/cgi/content/full/97/18/10083 http://www.pnas.org/cgi/content/full/97/18/10083 miniature inverted repeat transposable element sequence recombination_hotspot A region in a genome which promotes recombination. SO:rd http://purl.org/obo/owl/SO#SO_rd recombination hotspot sequence URL:http://en.wikipedia.org/wiki/Recombination_hotspot http://en.wikipedia.org/wiki/Recombination_hotspot chromosome This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/Chromosome http://en.wikipedia.org/wiki/Chromosome chromosome_band A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. SO:ma http://purl.org/obo/owl/SO#SO_ma chromosome band cytoband cytological band sequence URL:http://en.wikipedia.org/wiki/Cytological_band http://en.wikipedia.org/wiki/Cytological_band site_specific_recombination_target_region site specific recombination target region sequence match A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence splice_enhancer Region of a transcript that regulates splicing. SO:ke http://purl.org/obo/owl/SO#SO_ke splice enhancer sequence EST This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long. SO:ke http://purl.org/obo/owl/SO#SO_ke expressed sequence tag sequence loxP_site Cre-recombination target region loxP site sequence nucleotide_match A match against a nucleotide sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke nucleotide match sequence nucleic_acid An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. CHEBI:33696 http://purl.org/obo/owl/CHEBI#CHEBI_33696 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb nucleic acid sequence URL:http://en.wikipedia.org/wiki/Nucleic_acid http://en.wikipedia.org/wiki/Nucleic_acid protein_match A match against a protein sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke protein match sequence FRT_site An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid. SO:ma http://purl.org/obo/owl/SO#SO_ma FLP recombination target region FRT site sequence synthetic_sequence An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence. SO:ma http://purl.org/obo/owl/SO#SO_ma synthetic sequence sequence DNA An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence sequence_assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence assembly sequence URL:http://en.wikipedia.org/wiki/Sequence_assembly http://en.wikipedia.org/wiki/Sequence_assembly group_1_intron_homing_endonuclease_target_region A region of intronic nucleotide sequence targeted by a nuclease enzyme. SO:ke http://purl.org/obo/owl/SO#SO_ke group 1 intron homing endonuclease target region sequence haplotype_block A region of the genome which is co-inherited as the result of the lack of historic recombination within it. SO:ma http://purl.org/obo/owl/SO#SO_ma haplotype block sequence RNA This term is mapped to MGED. Do not obsolete without consulting MGED ontology. An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence flanked An attribute describing a region that is bounded either side by a particular kind of region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence floxed An attribute describing sequence that is flanked by Lox-P sites. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Floxed http://en.wikipedia.org/wiki/Floxed codon A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS. URL:http://www.everythingbio.com/glos/definition.php?word=codon http://www.everythingbio.com/glos/definition.php?word=codon SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Codon http://en.wikipedia.org/wiki/Codon FRT_flanked An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT. SO:ke http://purl.org/obo/owl/SO#SO_ke FRT flanked sequence invalidated_by_chimeric_cDNA A cDNA clone constructed from more than one mRNA. Usually an experimental artifact. SO:ma http://purl.org/obo/owl/SO#SO_ma invalidated by chimeric cDNA sequence floxed_gene A transgene that is floxed. SO:xp http://purl.org/obo/owl/SO#SO_xp floxed gene sequence transposable_element_flanking_region The region of sequence surrounding a transposable element. SO:ke http://purl.org/obo/owl/SO#SO_ke transposable element flanking region sequence integron A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. SO:as http://purl.org/obo/owl/SO#SO_as sequence URL:http://en.wikipedia.org/wiki/Integron http://en.wikipedia.org/wiki/Integron insertion_site The junction where an insertion occurred. SO:ke http://purl.org/obo/owl/SO#SO_ke insertion site sequence attI_site A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place. SO:as http://purl.org/obo/owl/SO#SO_as attI site sequence transposable_element_insertion_site The junction in a genome where a transposable_element has inserted. SO:ke http://purl.org/obo/owl/SO#SO_ke transposable element insertion site sequence integrase_coding_region sequence small_regulatory_ncRNA A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. SO:ma http://purl.org/obo/owl/SO#SO_ma small regulatory ncRNA sequence conjugative_transposon A transposon that encodes function required for conjugation. URL:http://www.sci.sdsu.edu/~smaloy/Glossary/C.html http://www.sci.sdsu.edu/~smaloy/Glossary/C.html conjugative transposon sequence enzymatic_RNA This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb enzymatic RNA sequence recombinationally_inverted_gene A recombinationally rearranged gene by inversion. SO:xp http://purl.org/obo/owl/SO#SO_xp recombinationally inverted gene sequence ribozyme An RNA with catalytic activity. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/Ribozyme http://en.wikipedia.org/wiki/Ribozyme rRNA_5_8S 5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002 5.8S LSU rRNA 5.8S ribosomal RNA 5.8S rRNA rRNA 5 8S sequence URL:http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA RNA_6S A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013 6S RNA RNA 6S sequence URL:http://en.wikipedia.org/wiki/6S_RNA http://en.wikipedia.org/wiki/6S_RNA CsrB_RsmB_RNA An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018 CsrB RsmB RNA CsrB-RsmB RNA sequence DsrA_RNA DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014 DsrA RNA sequence URL:http://en.wikipedia.org/wiki/DsrA_RNA http://en.wikipedia.org/wiki/DsrA_RNA GcvB_RNA A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022 GcvB RNA sequence URL:http://en.wikipedia.org/wiki/GcvB_RNA http://en.wikipedia.org/wiki/GcvB_RNA hammerhead_ribozyme A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs. PMID:2436805 http://purl.org/obo/owl/PMID#PMID_2436805 hammerhead ribozyme sequence URL:http://en.wikipedia.org/wiki/Hammerhead_ribozyme http://en.wikipedia.org/wiki/Hammerhead_ribozyme group_IIA_intron group IIA intron sequence group_IIB_intron group IIB intron sequence MicF_RNA A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033 MicF RNA sequence URL:http://en.wikipedia.org/wiki/MicF_RNA http://en.wikipedia.org/wiki/MicF_RNA OxyS_RNA A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035 OxyS RNA sequence URL:http://en.wikipedia.org/wiki/OxyS_RNA http://en.wikipedia.org/wiki/OxyS_RNA RNase_MRP_RNA The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030 RNase MRP RNA sequence RNase_P_RNA The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010 RNase P RNA sequence RprA_RNA Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034 RprA RNA sequence URL:http://en.wikipedia.org/wiki/RprA_RNA http://en.wikipedia.org/wiki/RprA_RNA RRE_RNA The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036 RRE RNA sequence spot_42_RNA A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021 spot-42 RNA sequence URL:http://en.wikipedia.org/wiki/Spot_42_RNA http://en.wikipedia.org/wiki/Spot_42_RNA telomerase_RNA The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025 telomerase RNA sequence URL:http://en.wikipedia.org/wiki/Telomerase_RNA http://en.wikipedia.org/wiki/Telomerase_RNA U1_snRNA U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003 small nuclear RNA U1 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U1 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U1 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U1 snRNA sequence URL:http://en.wikipedia.org/wiki/U1_snRNA http://en.wikipedia.org/wiki/U1_snRNA U2_snRNA U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004 small nuclear RNA U2 RSC:CB http://purl.org/obo/owl/RSC#RSC_CB snRNA U2 RSC:CB http://purl.org/obo/owl/RSC#RSC_CB U2 small nuclear RNA RSC:CB http://purl.org/obo/owl/RSC#RSC_CB U2 snRNA sequence URL:http://en.wikipedia.org/wiki/U2_snRNA http://en.wikipedia.org/wiki/U2_snRNA U4_snRNA U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015 small nuclear RNA U4 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U4 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U4 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U4 snRNA sequence URL:http://en.wikipedia.org/wiki/U4_snRNA http://en.wikipedia.org/wiki/U4_snRNA U4atac_snRNA An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397). PMID:=12409455 http://purl.org/obo/owl/PMID#PMID_=12409455 small nuclear RNA U4atac RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U4atac RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U4atac small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U4atac snRNA sequence U5_snRNA U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020 small nuclear RNA U5 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U5 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U5 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U5 snRNA sequence URL:http://en.wikipedia.org/wiki/U5_snRNA http://en.wikipedia.org/wiki/U5_snRNA U6_snRNA U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015 small nuclear RNA U6 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U6 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U6 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U6 snRNA sequence URL:http://en.wikipedia.org/wiki/U6_snRNA http://en.wikipedia.org/wiki/U6_snRNA U6atac_snRNA U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394). URL:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&amp;db=pubmed&amp;list_uids=12409455&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&amp;db=pubmed&amp;list_uids=12409455&amp;dopt=Abstract snRNA U6atac RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U6atac small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U6atac snRNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence U11_snRNA U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence. PMID:9622129 http://purl.org/obo/owl/PMID#PMID_9622129 small nuclear RNA U11 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U11 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U11 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U11 snRNA sequence URL:http://en.wikipedia.org/wiki/U11_snRNA http://en.wikipedia.org/wiki/U11_snRNA U12_snRNA The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007 small nuclear RNA U12 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb snRNA U12 RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U12 small nuclear RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb U12 snRNA sequence URL:http://en.wikipedia.org/wiki/U12_snRNA http://en.wikipedia.org/wiki/U12_snRNA sequence_attribute An attribute describes a quality of sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence attribute sequence gene_attribute gene attribute sequence enhancer_attribute sequence U14_snoRNA An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016 PMID:2551119 http://purl.org/obo/owl/PMID#PMID_2551119 small nucleolar RNA U14 snoRNA U14 U14 small nucleolar RNA U14 snoRNA sequence SO:0005839 vault_RNA A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006 vault RNA sequence URL:http://en.wikipedia.org/wiki/Vault_RNA http://en.wikipedia.org/wiki/Vault_RNA Y_RNA Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019 Y RNA sequence URL:http://en.wikipedia.org/wiki/Y_RNA http://en.wikipedia.org/wiki/Y_RNA twintron An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed. PMID:1899376 http://purl.org/obo/owl/PMID#PMID_1899376 PMID:7823908 http://purl.org/obo/owl/PMID#PMID_7823908 sequence URL:http://en.wikipedia.org/wiki/Twintron http://en.wikipedia.org/wiki/Twintron rRNA_18S A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke 18S ribosomal RNA 18S rRNA rRNA 18S sequence URL:http://en.wikipedia.org/wiki/18S_ribosomal_RNA http://en.wikipedia.org/wiki/18S_ribosomal_RNA site The interbase position where something (eg an aberration) occurred. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence binding_site See GO:0005488 : binding. A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR SO:ke http://purl.org/obo/owl/SO#SO_ke binding_or_interaction_site site sequence BS:00033 URL:http://en.wikipedia.org/wiki/Binding_site http://en.wikipedia.org/wiki/Binding_site protein_binding_site See GO:0042277 : peptide binding. A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. SO:ke http://purl.org/obo/owl/SO#SO_ke protein binding site sequence rescue_region A region that rescues. SO:xp http://purl.org/obo/owl/SO#SO_xp rescue fragment rescue region rescue segment sequence restriction_fragment A region of polynucleotide sequence produced by digestion with a restriction endonuclease. SO:ke http://purl.org/obo/owl/SO#SO_ke restriction fragment sequence URL:http://en.wikipedia.org/wiki/Restriction_fragment http://en.wikipedia.org/wiki/Restriction_fragment sequence_difference A region where the sequence differs from that of a specified sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence difference sequence invalidated_by_genomic_contamination An attribute to describe a feature that is invalidated due to genomic contamination. SO:ke http://purl.org/obo/owl/SO#SO_ke invalidated by genomic contamination sequence invalidated_by_genomic_polyA_primed_cDNA An attribute to describe a feature that is invalidated due to polyA priming. SO:ke http://purl.org/obo/owl/SO#SO_ke invalidated by genomic polyA primed cDNA sequence invalidated_by_partial_processing An attribute to describe a feature that is invalidated due to partial processing. SO:ke http://purl.org/obo/owl/SO#SO_ke invalidated by partial processing sequence polypeptide_domain Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains. A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR ca_bind uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type DNA_bind uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type domain uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type np_bind uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type polypeptide domain polypeptide_structural_domain structural domain zn_fing uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type sequence BS:00012 BS:00134 SO:0001069 signal_peptide Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence. The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html signal uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type signal peptide signal peptide coding sequence sequence BS:00159 URL:http://en.wikipedia.org/wiki/Signal_peptide http://en.wikipedia.org/wiki/Signal_peptide mature_protein_region This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification. The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html SO:cb http://purl.org/obo/owl/SO#SO_cb chain uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type mature peptide mature protein region sequence BS:00149 five_prime_terminal_inverted_repeat 5' TIR five prime terminal inverted repeat sequence three_prime_terminal_inverted_repeat 3' TIR three prime terminal inverted repeat sequence U5_LTR_region U5 long terminal repeat region U5 LTR region sequence R_LTR_region R long terminal repeat region R LTR region sequence U3_LTR_region U3 long terminal repeat region U3 LTR region sequence five_prime_LTR 5' long terminal repeat 5' LTR five prime LTR sequence three_prime_LTR 3' long terminal repeat 3' LTR three prime LTR sequence R_five_prime_LTR_region R 5' long term repeat region R five prime LTR region sequence U5_five_prime_LTR_region U5 5' long terminal repeat region U5 five prime LTR region sequence U3_five_prime_LTR_region U3 5' long term repeat region U3 five prime LTR region sequence R_three_prime_LTR_region R 3' long terminal repeat region R three prime LTR region sequence U3_three_prime_LTR_region U3 3' long terminal repeat region U3 three prime LTR region sequence U5_three_prime_LTR_region U5 3' long terminal repeat region U5 three prime LTR region sequence non_LTR_retrotransposon_polymeric_tract A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon. SO:ke http://purl.org/obo/owl/SO#SO_ke non LTR retrotransposon polymeric tract sequence target_site_duplication A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion. URL:http://www.koko.gov.my/CocoaBioTech/Glossaryt.html http://www.koko.gov.my/CocoaBioTech/Glossaryt.html target site duplication sequence RR_tract A polypurine tract within an LTR_retrotransposon. SO:ke http://purl.org/obo/owl/SO#SO_ke LTR retrotransposon poly purine tract RR tract sequence ARS A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. SO:ma http://purl.org/obo/owl/SO#SO_ma autonomously replicating sequence sequence assortment_derived_duplication sequence gene_not_polyadenylated sequence inverted_ring_chromosome inverted ring chromosome sequence vector_replicon This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A replicon that has been modified to act as a vector for foreign sequence. SO:ma http://purl.org/obo/owl/SO#SO_ma vector vector replicon sequence URL:http://en.wikipedia.org/wiki/Vector_(molecular_biology) http://en.wikipedia.org/wiki/Vector_(molecular_biology) ss_oligo This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A single stranded oligonucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke single strand oligo single strand oligonucleotide single stranded oligonucleotide ss oligo ss oligonucleotide sequence ds_oligo This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A double stranded oligonucleotide. SO:ke http://purl.org/obo/owl/SO#SO_ke double stranded oligonucleotide ds oligo ds-oligonucleotide sequence polymer_attribute An attribute to describe the kind of biological sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke polymer attribute sequence three_prime_noncoding_exon Non-coding exon in the 3' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke three prime noncoding exon sequence five_prime_noncoding_exon Non-coding exon in the 5' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke 5' nc exon 5' non coding exon five prime noncoding exon sequence UTR_intron Intron located in the untranslated region. SO:ke http://purl.org/obo/owl/SO#SO_ke UTR intron sequence five_prime_UTR_intron An intron located in the 5' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke five prime UTR intron sequence three_prime_UTR_intron An intron located in the 3' UTR. SO:ke http://purl.org/obo/owl/SO#SO_ke three prime UTR intron sequence random_sequence A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components. SO:ma http://purl.org/obo/owl/SO#SO_ma random sequence sequence interband A light region between two darkly staining bands in a polytene chromosome. SO:ma http://purl.org/obo/owl/SO#SO_ma chromosome interband sequence gene_with_polyadenylated_mRNA A gene that encodes a polyadenylated mRNA. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with polyadenylated mRNA sequence transgene_attribute sequence chromosomal_transposition A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. FB:reference_manual http://purl.org/obo/owl/FB#FB_reference_manual SO:ke http://purl.org/obo/owl/SO#SO_ke chromosomal transposition transposition sequence rasiRNA A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. URL:http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284 http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284 repeat associated small interfering RNA sequence URL:http://en.wikipedia.org/wiki/RasiRNA http://en.wikipedia.org/wiki/RasiRNA gene_with_mRNA_with_frameshift A gene that encodes an mRNA with a frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with mRNA with frameshift sequence recombinationally_rearranged_gene A gene that is recombinationally rearranged. SO:ke http://purl.org/obo/owl/SO#SO_ke recombinationally rearranged gene sequence interchromosomal_duplication A chromosome duplication involving an insertion from another chromosome. SO:ke http://purl.org/obo/owl/SO#SO_ke interchromosomal duplication sequence D_gene_segment Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D gene D-GENE sequence gene_with_trans_spliced_transcript A gene with a transcript that is trans-spliced. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with trans spliced transcript sequence vertebrate_immunoglobulin_T_cell_receptor_segment I am using the term segment instead of gene here to avoid confusion with the region 'gene'. vertebrate immunoglobulin T cell receptor segment vertebrate_immunoglobulin/T-cell receptor gene sequence inversion_derived_bipartite_deficiency A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived bipartite deficiency sequence pseudogenic_region A non-functional descendent of a functional entity. SO:cjm http://purl.org/obo/owl/SO#SO_cjm pseudogenic region sequence encodes_alternately_spliced_transcripts A gene that encodes more than one transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke encodes alternately spliced transcripts sequence decayed_exon A non-functional descendant of an exon. SO:ke http://purl.org/obo/owl/SO#SO_ke decayed exon sequence inversion_derived_deficiency_plus_duplication A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived deficiency plus duplication sequence V_gene_segment Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V gene V-GENE variable_gene sequence post_translationally_regulated_by_protein_stability An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein. SO:ke http://purl.org/obo/owl/SO#SO_ke post translationally regulated by protein stability post-translationally regulated by protein stability sequence golden_path_fragment One of the pieces of sequence that make up a golden path. SO:rd http://purl.org/obo/owl/SO#SO_rd golden path fragment sequence post_translationally_regulated_by_protein_modification An attribute describing a gene sequence where the resulting protein is modified to regulate it. SO:ke http://purl.org/obo/owl/SO#SO_ke post translationally regulated by protein modification post-translationally regulated by protein modification sequence J_gene_segment Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J gene J-GENE sequence autoregulated The gene product is involved in its own transcriptional regulation. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence tiling_path A set of regions which overlap with minimal polymorphism to form a linear sequence. SO:cjm http://purl.org/obo/owl/SO#SO_cjm tiling path sequence negatively_autoregulated The gene product is involved in its own transcriptional regulation where it decreases transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke negatively autoregulated sequence tiling_path_fragment A piece of sequence that makes up a tiling_path (SO:0000472). SO:ke http://purl.org/obo/owl/SO#SO_ke tiling path fragment sequence positively_autoregulated The gene product is involved in its own transcriptional regulation, where it increases transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke positively autoregulated sequence contig_read A DNA sequencer read which is part of a contig. SO:ke http://purl.org/obo/owl/SO#SO_ke contig read sequence polycistronic_gene A gene that is polycistronic. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence C_gene_segment Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205). URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# C gene C_GENE constant gene sequence trans_spliced_transcript A transcript that is trans-spliced. SO:xp http://purl.org/obo/owl/SO#SO_xp trans spliced transcript trans-spliced transcript sequence tiling_path_clone A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly. SO:ke http://purl.org/obo/owl/SO#SO_ke tiling path clone sequence terminal_inverted_repeat An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon. SO:ke http://purl.org/obo/owl/SO#SO_ke terminal inverted repeat TIR sequence vertebrate_immunoglobulin_T_cell_receptor_gene_cluster vertebrate immunoglobulin T cell receptor gene cluster vertebrate_immunoglobulin/T-cell receptor gene cluster sequence nc_primary_transcript A primary transcript that is never translated into a protein. SO:ke http://purl.org/obo/owl/SO#SO_ke nc primary transcript noncoding primary transcript sequence three_prime_coding_exon_noncoding_region The sequence of the 3' exon that is not coding. SO:ke http://purl.org/obo/owl/SO#SO_ke three prime coding exon noncoding region three_prime_exon_noncoding_region sequence DJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (DJ)-J-CLUSTER DJ J cluster sequence five_prime_coding_exon_noncoding_region The sequence of the 5' exon preceding the start codon. SO:ke http://purl.org/obo/owl/SO#SO_ke five prime coding exon noncoding region five_prime_exon_noncoding_region sequence VDJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VDJ)-J-C-CLUSTER VDJ J C cluster sequence VDJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VDJ)-J-CLUSTER VDJ J cluster sequence VJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VJ)-C-CLUSTER VJ C cluster sequence VJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VJ)-J-C-CLUSTER VJ J C cluster sequence VJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VJ)-J-CLUSTER VJ J cluster sequence D_gene_recombination_feature D gene recombination feature sequence three_prime_D_heptamer 7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 3'D-HEPTAMER three prime D heptamer sequence three_prime_D_nonamer A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 3'D-NOMAMER three prime D nonamer sequence three_prime_D_spacer A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 3'D-SPACER three prime D spacer sequence five_prime_D_heptamer 7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 5'D-HEPTAMER five prime D heptamer sequence five_prime_D_nonamer 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 5'D-NONAMER five prime D nonamer sequence five_prime_D_spacer 12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 5'-SPACER five prime D spacer five prime D-spacer sequence virtual_sequence A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. SO:ke http://purl.org/obo/owl/SO#SO_ke virtual sequence sequence Hoogsteen_base_pair A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds. PMID:12177293 http://purl.org/obo/owl/PMID#PMID_12177293 Hoogsteen base pair sequence URL:http://en.wikipedia.org/wiki/Hoogsteen_base_pair http://en.wikipedia.org/wiki/Hoogsteen_base_pair reverse_Hoogsteen_base_pair A type of non-canonical base-pairing. SO:ke http://purl.org/obo/owl/SO#SO_ke reverse Hoogsteen base pair sequence transcribed_region This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being. A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence alternately_spliced_gene_encodeing_one_transcript sequence D_DJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D DJ C cluster D-(DJ)-C-CLUSTER sequence D_DJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D DJ cluster D-(DJ)-CLUSTER sequence D_DJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D DJ J C cluster D-(DJ)-J-C-CLUSTER sequence pseudogenic_exon This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. A non functional descendant of an exon, part of a pseudogene. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogenic exon sequence D_DJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D DJ J cluster D-(DJ)-J-CLUSTER sequence D_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D J C cluster D-J-C-CLUSTER sequence VD_gene_segment Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205). URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V_D_GENE VD gene sequence J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J C cluster J-C-CLUSTER sequence inversion_derived_deficiency_plus_aneuploid A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived deficiency plus aneuploid sequence J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J cluster J-CLUSTER sequence J_nonamer 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J nonamer J-NONAMER sequence J_heptamer 7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J heptamer J-HEPTAMER sequence pseudogenic_transcript This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. A non functional descendant of a transcript, part of a pseudogene. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogenic transcript sequence J_spacer 12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# J spacer J-SPACER sequence V_DJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V DJ cluster V-(DJ)-CLUSTER sequence V_DJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V DJ J cluster V-(DJ)-J-CLUSTER sequence V_VDJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VDJ C cluster V-(VDJ)-C-CLUSTER sequence V_VDJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VDJ cluster V-(VDJ)-CLUSTER sequence V_VDJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VDJ J cluster V-(VDJ)-J-CLUSTER sequence V_VJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VJ C cluster V-(VJ)-C-CLUSTER sequence V_VJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VJ cluster V-(VJ)-CLUSTER sequence V_VJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VJ J cluster V-(VJ)-J-CLUSTER sequence V_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V cluster V-CLUSTER sequence V_D_DJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D DJ C cluster V-D-(DJ)-C-CLUSTER sequence V_D_DJ_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D DJ cluster V-D-(DJ)-CLUSTER sequence V_D_DJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D DJ J C cluster V-D-(DJ)-J-C-CLUSTER sequence V_D_DJ_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D DJ J cluster V-D-(DJ)-J-CLUSTER sequence V_D_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D J C cluster V-D-J-C-CLUSTER sequence V_D_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V D J cluster V-D-J-CLUSTER sequence V_heptamer 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V heptamer V-HEPTAMER sequence V_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V J cluster V-J-CLUSTER sequence V_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V J C cluster V-J-C-CLUSTER sequence V_nonamer 9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V nonamer V-NONAMER sequence V_spacer 12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V spacer V-SPACER sequence V_gene_recombination_feature Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V gene recombination feature V-RS sequence DJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (DJ)-C-CLUSTER DJ C cluster sequence DJ_J_C_cluster Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (DJ)-J-C-CLUSTER DJ J C cluster sequence VDJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# (VDJ)-C-CLUSTER VDJ C cluster sequence V_DJ_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V DJ C cluster V-(DJ)-C-CLUSTER sequence alternately_spliced_gene_encoding_greater_than_one_transcript sequence helitron A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. URL:http://www.pnas.org/cgi/content/full/100/11/6569 http://www.pnas.org/cgi/content/full/100/11/6569 ISCR sequence URL:http://en.wikipedia.org/wiki/Helitron http://en.wikipedia.org/wiki/Helitron recoding_pseudoknot The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding. URL:http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937 recoding pseudoknot sequence designed_sequence designed sequence sequence inversion_derived_bipartite_duplication A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived bipartite duplication sequence gene_with_edited_transcript A gene that encodes a transcript that is edited. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with edited transcript sequence inversion_derived_duplication_plus_aneuploid A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived duplication plus aneuploid sequence aneuploid_chromosome Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila. A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking. SO:ke http://purl.org/obo/owl/SO#SO_ke aneuploid chromosome sequence polyA_signal_sequence The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html poly(A) signal polyA signal sequence polyadenylation termination signal sequence Shine_Dalgarno_sequence Not found in Eukaryotic sequence. A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex. SO:jh http://purl.org/obo/owl/SO#SO_jh five prime ribosome binding site RBS Shine Dalgarno sequence Shine-Dalgarno sequence sequence URL:http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence polyA_site The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html polyA cleavage site polyA junction polyA site polyA_junction polyadenylation site sequence SO:0001430 assortment_derived_deficiency_plus_duplication sequence five_prime_clip 5' most region of a precursor transcript that is clipped off during processing. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html 5' clip five prime clip sequence five_prime_D_recombination_signal_sequence Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 5'RS five prime D recombination signal sequence five prime D-recombination signal sequence sequence three_prime_clip 3'-most region of a precursor transcript that is clipped off during processing. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html 3'-clip three prime clip sequence C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# C cluster C-CLUSTER sequence D_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D cluster D-CLUSTER sequence D_J_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D J cluster D-J-CLUSTER sequence heptamer_of_recombination_feature_of_vertebrate_immune_system_gene Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# HEPTAMER heptamer of recombination feature of vertebrate immune system gene sequence nonamer_of_recombination_feature_of_vertebrate_immune_system_gene nonamer of recombination feature of vertebrate immune system gene sequence vertebrate_immune_system_gene_recombination_spacer vertebrate immune system gene recombination spacer sequence V_DJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V DJ J C cluster V-(DJ)-J-C-CLUSTER sequence V_VDJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VDJ J C cluster V-(VDJ)-J-C-CLUSTER sequence V_VJ_J_C_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V VJ J C cluster V-(VJ)-J-C-CLUSTER sequence inversion_derived_aneuploid_chromosome A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion. FB:km http://purl.org/obo/owl/FB#FB_km inversion derived aneuploid chromosome sequence bidirectional_promoter bidirectional promoter sequence retrotransposed GO:0003964 RNA-directed DNA polymerase activity. An attribute of a feature that occurred as the product of a reverse transcriptase mediated event. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence SO:0100042 URL:http://en.wikipedia.org/wiki/Retrotransposed http://en.wikipedia.org/wiki/Retrotransposed three_prime_D_recombination_signal_sequence Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# 3'D-RS three prime D recombination signal sequence three_prime_D-recombination_signal_sequence sequence miRNA_encoding miRNA encoding sequence DJ_gene_segment Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment. URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# D-J-GENE DJ gene sequence rRNA_encoding rRNA encoding sequence VDJ_gene_segment Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V-D-J-GENE VDJ gene sequence scRNA_encoding scRNA encoding sequence VJ_gene_segment Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). URL:http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7# V-J-GENE VJ gene sequence centromere A region of chromosome where the spindle fibers attach during mitosis and meiosis. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Centromere http://en.wikipedia.org/wiki/Centromere snoRNA_encoding snoRNA encoding sequence edited_transcript_feature A locatable feature on a transcript that is edited. SO:ma http://purl.org/obo/owl/SO#SO_ma edited transcript feature sequence methylation_guide_snoRNA_primary_transcript A primary transcript encoding a methylation guide small nucleolar RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke methylation guide snoRNA primary transcript sequence cap A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA. URL:http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html sequence URL:http://en.wikipedia.org/wiki/5%27_cap http://en.wikipedia.org/wiki/5%27_cap rRNA_cleavage_snoRNA_primary_transcript A primary transcript encoding an rRNA cleavage snoRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke rRNA cleavage snoRNA primary transcript sequence pre_edited_region The region of a transcript that will be edited. URL:http://dna.kdna.ucla.edu/rna/index.aspx http://dna.kdna.ucla.edu/rna/index.aspx pre edited region pre-edited region sequence tmRNA A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023 10Sa RNA ssrA sequence URL:http://en.wikipedia.org/wiki/TmRNA http://en.wikipedia.org/wiki/TmRNA C_D_box_snoRNA_encoding C/D box snoRNA encoding sequence tmRNA_primary_transcript A primary transcript encoding a tmRNA (SO:0000584). SO:ke http://purl.org/obo/owl/SO#SO_ke 10Sa RNA primary transcript ssrA RNA primary transcript tmRNA primary transcript sequence group_I_intron GO:0000372. Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028 group I intron sequence URL:http://en.wikipedia.org/wiki/Group_I_intron http://en.wikipedia.org/wiki/Group_I_intron autocatalytically_spliced_intron A self spliced intron. SO:ke http://purl.org/obo/owl/SO#SO_ke autocatalytically spliced intron sequence SRP_RNA_primary_transcript A primary transcript encoding a signal recognition particle RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke SRP RNA primary transcript sequence SRP_RNA The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017 7S RNA signal recognition particle RNA SRP RNA sequence pseudoknot A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop. RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence URL:http://en.wikipedia.org/wiki/Pseudoknot http://en.wikipedia.org/wiki/Pseudoknot H_pseudoknot A pseudoknot which contains two stems and at least two loops. URL:http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=10334330&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=10334330&amp;dopt=Abstract classical pseudoknot H pseudoknot H-pseudoknot H-type pseudoknot hairpin-type pseudoknot sequence C_D_box_snoRNA Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'. URL:http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html box C/D snoRNA C D box snoRNA C/D box snoRNA sequence H_ACA_box_snoRNA Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains. URL:http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html box H/ACA snoRNA H ACA box snoRNA H/ACA box snoRNA sequence C_D_box_snoRNA_primary_transcript A primary transcript encoding a small nucleolar RNA of the box C/D family. SO:ke http://purl.org/obo/owl/SO#SO_ke C/D box snoRNA primary transcript sequence H_ACA_box_snoRNA_primary_transcript A primary transcript encoding a small nucleolar RNA of the box H/ACA family. SO:ke http://purl.org/obo/owl/SO#SO_ke H ACA box snoRNA primary transcript sequence transcript_edited_by_U_insertion/deletion The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. URL:http://www.rna.ucla.edu/index.html http://www.rna.ucla.edu/index.html sequence edited_by_C_insertion_and_dinucleotide_insertion transcript_edited_by_C-insertion_and_dinucleotide_insertion sequence edited_by_C_to_U_substitution sequence edited_by_A_to_I_substitution sequence edited_by_G_addition sequence guide_RNA A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA. URL:http://www.rna.ucla.edu/index.html http://www.rna.ucla.edu/index.html gRNA guide RNA sequence URL:http://en.wikipedia.org/wiki/Guide_RNA http://en.wikipedia.org/wiki/Guide_RNA group_II_intron GO:0000373. Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny. URL:http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml group II intron sequence URL:http://en.wikipedia.org/wiki/Group_II_intron http://en.wikipedia.org/wiki/Group_II_intron editing_block Edited mRNA sequence mediated by a single guide RNA (SO:0000602). URL:http://dna.kdna.ucla.edu/rna/index.aspx http://dna.kdna.ucla.edu/rna/index.aspx editing block sequence intergenic_region This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome. SO:cjm http://purl.org/obo/owl/SO#SO_cjm intergenic region sequence URL:http://en.wikipedia.org/wiki/Intergenic_region http://en.wikipedia.org/wiki/Intergenic_region editing_domain Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602). URL:http://dna.kdna.ucla.edu/rna/index.aspx http://dna.kdna.ucla.edu/rna/index.aspx editing domain sequence unedited_region The region of an edited transcript that will not be edited. URL:http://dna.kdna.ucla.edu/rna/index.aspx http://dna.kdna.ucla.edu/rna/index.aspx unedited region sequence H_ACA_box_snoRNA_encoding H ACA box snoRNA encoding sequence oligo_U_tail The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602). URL:http://www.rna.ucla.edu/ http://www.rna.ucla.edu/ oligo U tail sequence polyA_sequence Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. SO:ke http://purl.org/obo/owl/SO#SO_ke polyA sequence sequence branch_site A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat. SO:ke http://purl.org/obo/owl/SO#SO_ke branch point branch site branch_point sequence polypyrimidine_tract The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. URL:http://nar.oupjournals.org/cgi/content/full/25/4/888 http://nar.oupjournals.org/cgi/content/full/25/4/888 polypyrimidine tract sequence URL:http://en.wikipedia.org/wiki/Polypyrimidine_tract http://en.wikipedia.org/wiki/Polypyrimidine_tract bacterial_RNApol_promoter A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke bacterial RNApol promoter sequence bacterial_terminator A terminator signal for bacterial transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke bacterial terminator sequence terminator_of_type_2_RNApol_III_promoter A terminator signal for RNA polymerase III transcription. SO:ke http://purl.org/obo/owl/SO#SO_ke terminator of type 2 RNApol III promoter sequence transcription_end_site The base where transcription ends. SO:ke http://purl.org/obo/owl/SO#SO_ke transcription end site sequence RNApol_III_promoter_type_1 RNApol III promoter type 1 sequence RNApol_III_promoter_type_2 RNApol III promoter type 2 tRNA promoter sequence A_box Binds TFIIIC. A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG. SO:ke http://purl.org/obo/owl/SO#SO_ke A-box sequence URL:http://en.wikipedia.org/wiki/A-box http://en.wikipedia.org/wiki/A-box B_box Binds TFIIIC. A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC. SO:ke http://purl.org/obo/owl/SO#SO_ke B-box sequence RNApol_III_promoter_type_3 RNApol III promoter type 3 sequence C_box An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn. SO:ke http://purl.org/obo/owl/SO#SO_ke C-box sequence snRNA_encoding snRNA encoding sequence telomere A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. SO:ma http://purl.org/obo/owl/SO#SO_ma telomeric DNA telomeric sequence sequence URL:http://en.wikipedia.org/wiki/Telomere http://en.wikipedia.org/wiki/Telomere silencer A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Silencer_(DNA) http://en.wikipedia.org/wiki/Silencer_(DNA) chromosomal_regulatory_element chromosomal regulatory element sequence insulator A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression. SO:regcreative http://purl.org/obo/owl/SO#SO_regcreative insulator element sequence URL:http://en.wikipedia.org/wiki/Insulator_(genetics) http://en.wikipedia.org/wiki/Insulator_(genetics) chromosomal_structural_element chromosomal structural element sequence five_prime_open_reading_frame five prime open reading frame sequence upstream_AUG_codon A start codon upstream of the ORF. SO:ke http://purl.org/obo/owl/SO#SO_ke upstream AUG codon sequence polycistronic_primary_transcript A primary transcript encoding for more than one gene product. SO:ke http://purl.org/obo/owl/SO#SO_ke polycistronic primary transcript sequence monocistronic_primary_transcript A primary transcript encoding for one gene product. SO:ke http://purl.org/obo/owl/SO#SO_ke monocistronic primary transcript sequence monocistronic_mRNA An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap. SO:rd http://purl.org/obo/owl/SO#SO_rd monocistronic mRNA monocistronic processed transcript sequence URL:http://en.wikipedia.org/wiki/Monocistronic_mRNA http://en.wikipedia.org/wiki/Monocistronic_mRNA polycistronic_mRNA An mRNA that encodes multiple proteins from at least two non-overlapping regions. SO:rd http://purl.org/obo/owl/SO#SO_rd polycistronic mRNA polycistronic processed transcript sequence URL:http://en.wikipedia.org/wiki/Polycistronic_mRNA http://en.wikipedia.org/wiki/Polycistronic_mRNA mini_exon_donor_RNA A primary transcript that donates the spliced leader to other mRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke mini exon donor RNA mini-exon donor RNA sequence spliced_leader_RNA mini-exon spliced leader RNA sequence engineered_plasmid A plasmid that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered plasmid engineered plasmid gene sequence transcribed_spacer_region Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA. URL:http://oregonstate.edu/instruction/bb492/general/glossary.html http://oregonstate.edu/instruction/bb492/general/glossary.html transcribed spacer region sequence internal_transcribed_spacer_region Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs. SO:ke http://purl.org/obo/owl/SO#SO_ke internal transcribed spacer region sequence external_transcribed_spacer_region Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke external transcribed spacer region sequence tetranucleotide_repeat_microsatellite_feature tetranucleotide repeat microsatellite feature sequence SRP_RNA_encoding SRP RNA encoding sequence minisatellite A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. URL:http://www.informatics.jax.org/silver/glossary.shtml http://www.informatics.jax.org/silver/glossary.shtml sequence URL:http://en.wikipedia.org/wiki/Minisatellite http://en.wikipedia.org/wiki/Minisatellite antisense_RNA Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke antisense RNA sequence URL:http://en.wikipedia.org/wiki/Antisense_RNA http://en.wikipedia.org/wiki/Antisense_RNA antisense_primary_transcript The reverse complement of the primary transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke antisense primary transcript sequence siRNA A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules. PMID:12592000 http://purl.org/obo/owl/PMID#PMID_12592000 small interfering RNA sequence URL:http://en.wikipedia.org/wiki/SiRNA http://en.wikipedia.org/wiki/SiRNA miRNA_primary_transcript A primary transcript encoding a micro RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke micro RNA primary transcript miRNA primary transcript sequence stRNA_primary_transcript A primary transcript encoding a small temporal mRNA (SO:0000649). SO:ke http://purl.org/obo/owl/SO#SO_ke small temporal RNA primary transcript stRNA primary transcript sequence stRNA Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. PMID:11081512 http://purl.org/obo/owl/PMID#PMID_11081512 small temporal RNA sequence URL:http://en.wikipedia.org/wiki/StRNA http://en.wikipedia.org/wiki/StRNA small_subunit_rRNA Ribosomal RNA transcript that structures the small subunit of the ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke small subunit rRNA SSU RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb SSU rRNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence large_subunit_rRNA Ribosomal RNA transcript that structures the large subunit of the ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke large subunit rRNA LSU RNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb LSU rRNA RSC:cb http://purl.org/obo/owl/RSC#RSC_cb sequence rRNA_5S 5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription. URL:http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001 http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001 5S LSU rRNA 5S ribosomal RNA 5S rRNA rRNA 5S sequence URL:http://en.wikipedia.org/wiki/5S_ribosomal_RNA http://en.wikipedia.org/wiki/5S_ribosomal_RNA rRNA_28S A component of the large ribosomal subunit. SO:ke http://purl.org/obo/owl/SO#SO_ke 28S LSU rRNA 28S ribosomal RNA 28S rRNA rRNA 28S sequence URL:http://en.wikipedia.org/wiki/28S_ribosomal_RNA http://en.wikipedia.org/wiki/28S_ribosomal_RNA maxicircle_gene A mitochondrial gene located in a maxicircle. SO:xp http://purl.org/obo/owl/SO#SO_xp maxi-circle gene maxicircle gene sequence ncRNA A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. SO:ke http://purl.org/obo/owl/SO#SO_ke noncoding RNA sequence URL:http://en.wikipedia.org/wiki/NcRNA http://en.wikipedia.org/wiki/NcRNA stRNA_encoding stRNA encoding sequence repeat_region A region of sequence containing one or more repeat units. SO:ke http://purl.org/obo/owl/SO#SO_ke repeat region sequence dispersed_repeat A repeat that is located at dispersed sites in the genome. SO:ke http://purl.org/obo/owl/SO#SO_ke dispersed repeat interspersed repeat sequence URL:http://en.wikipedia.org/wiki/Interspersed_repeat http://en.wikipedia.org/wiki/Interspersed_repeat tmRNA_encoding tmRNA encoding sequence DNA_invertase_target_sequence sequence intron_attribute sequence spliceosomal_intron GO:0000398. An intron which is spliced by the spliceosome. SO:ke http://purl.org/obo/owl/SO#SO_ke spliceosomal intron sequence tRNA_encoding tRNA encoding sequence introgressed_chromosome_region introgressed chromosome region sequence monocistronic_transcript A transcript that is monocistronic. SO:xp http://purl.org/obo/owl/SO#SO_xp monocistronic transcript sequence mobile_intron An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility. SO:ke http://purl.org/obo/owl/SO#SO_ke mobile intron sequence insertion The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke insertion URL:http://www.ncbi.nlm.nih.gov/dbvar/ http://www.ncbi.nlm.nih.gov/dbvar/ nucleotide insertion nucleotide_insertion sequence SO:1000034 loinc:LA6687-3 http://purl.org/obo/owl/loinc#loinc_LA6687-3 EST_match A match against an EST sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke EST match sequence sequence_rearrangement_feature sequence rearrangement feature sequence chromosome_breakage_sequence A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation. SO:ma http://purl.org/obo/owl/SO#SO_ma chromosome breakage sequence sequence internal_eliminated_sequence A sequence eliminated from the genome of ciliates during nuclear differentiation. SO:ma http://purl.org/obo/owl/SO#SO_ma internal eliminated sequence sequence macronucleus_destined_segment A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome. SO:ma http://purl.org/obo/owl/SO#SO_ma macronucleus destined segment sequence transcript An RNA synthesized on a DNA or RNA template by an RNA polymerase. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence URL:http://en.wikipedia.org/wiki/RNA http://en.wikipedia.org/wiki/RNA non_canonical_splice_site A splice site where the donor and acceptor sites differ from the canonical form. SO:ke http://purl.org/obo/owl/SO#SO_ke non canonical splice site non-canonical splice site sequence canonical_splice_site The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively. SO:ke http://purl.org/obo/owl/SO#SO_ke canonical splice site sequence canonical_three_prime_splice_site The canonical 3' splice site has the sequence "AG". SO:ke http://purl.org/obo/owl/SO#SO_ke canonical 3' splice site canonical three prime splice site sequence canonical_five_prime_splice_site The canonical 5' splice site has the sequence "GT". SO:ke http://purl.org/obo/owl/SO#SO_ke canonical 5' splice site canonical five prime splice site sequence non_canonical_three_prime_splice_site A 3' splice site that does not have the sequence "AG". SO:ke http://purl.org/obo/owl/SO#SO_ke non canonical 3' splice site non canonical three prime splice site non-canonical three prime splice site sequence non_canonical_five_prime_splice_site A 5' splice site which does not have the sequence "GT". SO:ke http://purl.org/obo/owl/SO#SO_ke non canonical 5' splice site non canonical five prime splice site non-canonical five prime splice site sequence non_canonical_start_codon A start codon that is not the usual AUG sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke non ATG start codon non canonical start codon non-canonical start codon sequence aberrant_processed_transcript A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons. SO:ke http://purl.org/obo/owl/SO#SO_ke aberrant processed transcript sequence splicing_feature sequence exonic_splice_enhancer Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron. URL:http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=12403462&amp;dopt=Abstract http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=12403462&amp;dopt=Abstract exonic splice enhancer sequence nuclease_sensitive_site A region of nucleotide sequence targeted by a nuclease enzyme. SO:ma http://purl.org/obo/owl/SO#SO_ma nuclease sensitive site sequence DNAseI_hypersensitive_site DHS DNAseI hypersensitive site sequence translocation_element A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations. SO:ma http://purl.org/obo/owl/SO#SO_ma translocation element sequence deletion_junction The space between two bases in a sequence which marks the position where a deletion has occurred. SO:ke http://purl.org/obo/owl/SO#SO_ke deletion junction sequence golden_path A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. SO:ls http://purl.org/obo/owl/SO#SO_ls golden path sequence cDNA_match A match against cDNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke cDNA match sequence gene_with_polycistronic_transcript A gene that encodes a polycistronic transcript. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with polycistronic transcript sequence cleaved_initiator_methionine The initiator methionine that has been cleaved from a mature polypeptide sequence. EBIBS:GAR http://purl.org/obo/owl/EBIBS#EBIBS_GAR cleaved initiator methionine init_met uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type initiator methionine sequence BS:00067 gene_with_dicistronic_transcript A gene that encodes a dicistronic transcript. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with dicistronic transcript sequence gene_with_recoded_mRNA A gene that encodes an mRNA that is recoded. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with recoded mRNA sequence SNP SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. SO:cb http://purl.org/obo/owl/SO#SO_cb single nucleotide polymorphism sequence reagent Requested by Lynn Crosby, jan 2006. A sequence used in experiment. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence oligo A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. SO:ma http://purl.org/obo/owl/SO#SO_ma oligonucleotide sequence URL:http://en.wikipedia.org/wiki/Oligonucleotide http://en.wikipedia.org/wiki/Oligonucleotide gene_with_stop_codon_read_through A gene that encodes a transcript with stop codon readthrough. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with stop codon read through sequence gene_with_stop_codon_redefined_as_pyrrolysine A gene encoding an mRNA that has the stop codon redefined as pyrrolysine. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with stop codon redefined as pyrrolysine sequence junction A junction is a boundary between regions. A boundary has an extent of zero. A sequence_feature with an extent of zero. SO:ke http://purl.org/obo/owl/SO#SO_ke boundary breakpoint sequence remark A comment about the sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence possible_base_call_error A region of sequence where the validity of the base calling is questionable. SO:ke http://purl.org/obo/owl/SO#SO_ke possible base call error sequence possible_assembly_error A region of sequence where there may have been an error in the assembly. SO:ke http://purl.org/obo/owl/SO#SO_ke possible assembly error sequence experimental_result_region A region of sequence implicated in an experimental result. SO:ke http://purl.org/obo/owl/SO#SO_ke experimental result region sequence gene This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. SO:immuno_workshop http://purl.org/obo/owl/SO#SO_immuno_workshop sequence URL:http://en.wikipedia.org/wiki/Gene http://en.wikipedia.org/wiki/Gene tandem_repeat Two or more adjcent copies of a region (of length greater than 1). SO:ke http://purl.org/obo/owl/SO#SO_ke tandem repeat sequence URL:http://en.wikipedia.org/wiki/Tandem_repeat http://en.wikipedia.org/wiki/Tandem_repeat URL:http://www.sci.sdsu.edu/~smaloy/Glossary/T.html http://www.sci.sdsu.edu/~smaloy/Glossary/T.html trans_splice_acceptor_site This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans. The 3' splice site of the acceptor primary transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke 3' trans splice site trans splice acceptor site sequence trans_splice_donor_site SL RNA contains a donor site. The 5' five prime splice site region of the donor RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke 5 prime trans splice site trans splice donor site trans-splice donor site sequence SL1_acceptor_site A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs. SO:nlw http://purl.org/obo/owl/SO#SO_nlw SL1 acceptor site sequence SL2_acceptor_site A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:nlw http://purl.org/obo/owl/SO#SO_nlw SL2 acceptor site sequence gene_with_stop_codon_redefined_as_selenocysteine A gene encoding an mRNA that has the stop codon redefined as selenocysteine. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with stop codon redefined as selenocysteine sequence gene_with_mRNA_recoded_by_translational_bypass A gene with mRNA recoded by translational bypass. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with mRNA recoded by translational bypass sequence gene_with_transcript_with_translational_frameshift A gene encoding a transcript that has a translational frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with transcript with translational frameshift sequence DNA_motif A motif that is active in the DNA form of the sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke DNA motif sequence URL:http://en.wikipedia.org/wiki/DNA_motif http://en.wikipedia.org/wiki/DNA_motif nucleotide_motif A region of nucleotide sequence corresponding to a known motif. SO:ke http://purl.org/obo/owl/SO#SO_ke nucleotide motif sequence RNA_motif A motif that is active in RNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke RNA motif sequence dicistronic_mRNA An mRNA that has the quality dicistronic. SO:ke http://purl.org/obo/owl/SO#SO_ke dicistronic mRNA dicistronic processed transcript sequence reading_frame This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop. A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. SGD:rb http://purl.org/obo/owl/SGD#SGD_rb reading frame sequence URL:http://en.wikipedia.org/wiki/Reading_frame http://en.wikipedia.org/wiki/Reading_frame blocked_reading_frame Term requested by Rama from SGD. A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons. SGD:rb http://purl.org/obo/owl/SGD#SGD_rb blocked reading frame sequence ultracontig An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers. FB:WG http://purl.org/obo/owl/FB#FB_WG superscaffold sequence foreign_transposable_element requested by Michael on 19 Nov 2004. A transposable element that is foreign. SO:ke http://purl.org/obo/owl/SO#SO_ke foreign transposable element sequence gene_with_dicistronic_primary_transcript Requested by Michael, 19 nov 2004. A gene that encodes a dicistronic primary transcript. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with dicistronic primary transcript sequence gene_with_dicistronic_mRNA Requested by MA nov 19 2004. A gene that encodes a polycistronic mRNA. SO:xp http://purl.org/obo/owl/SO#SO_xp gene with dicistronic mRNA gene with dicistronic processed transcript sequence iDNA Genomic sequence removed from the genome, as a normal event, by a process of recombination. SO:ma http://purl.org/obo/owl/SO#SO_ma intervening DNA sequence URL:http://en.wikipedia.org/wiki/IDNA http://en.wikipedia.org/wiki/IDNA oriT A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html origin of transfer sequence URL:http://en.wikipedia.org/wiki/Origin_of_transfer http://en.wikipedia.org/wiki/Origin_of_transfer transit_peptide Added to bring SO inline with the embl ddbj genbank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle. The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle). URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html signal transit uniprot:feature_type http://purl.org/obo/owl/uniprot#uniprot_feature_type transit peptide sequence BS:00055 repeat_unit Added to comply with the feature table. A single repeat. The simplest repeated component of a repeat region. A single repeat. SO:ke http://purl.org/obo/owl/SO#SO_ke repeat unit sequence URL:http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html CRM Requested by Stepen Grossmann Dec 2004. A regulatory_region where more than 1 TF_binding_site together are regulatorily active. SO:SG http://purl.org/obo/owl/SO#SO_SG cis regulatory module TF module sequence intein Intein-mediated protein splicing occurs after mRNA has been translated into a protein. A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond. SO:ke http://purl.org/obo/owl/SO#SO_ke protein intron sequence URL:http://en.wikipedia.org/wiki/Intein http://en.wikipedia.org/wiki/Intein intein_containing An attribute of protein-coding genes where the initial protein product contains an intein. SO:ke http://purl.org/obo/owl/SO#SO_ke intein containing sequence gap A gap in the sequence of known length. The unknown bases are filled in with N's. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence fragmentary Term added because of request by MO people. An attribute to describe a feature that is incomplete. SO:ke http://purl.org/obo/owl/SO#SO_ke fragment sequence predicted An attribute describing an unverified region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence URL:http://en.wikipedia.org/wiki/Predicted http://en.wikipedia.org/wiki/Predicted feature_attribute An attribute describing a located_sequence_feature. SO:ke http://purl.org/obo/owl/SO#SO_ke feature attribute sequence exemplar_mRNA Added for the MO people. An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group. URL:http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php exemplar mRNA sequence sequence_location sequence location sequence organelle_sequence organelle sequence sequence mitochondrial_sequence This term is mapped to MGED. Do not obsolete without consulting MGED ontology. mitochondrial sequence sequence nuclear_sequence nuclear sequence sequence nucleomorphic_sequence nucleomorphic sequence sequence plastid_sequence plastid sequence sequence kinetoplast A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species. PMID:8395055 http://purl.org/obo/owl/PMID#PMID_8395055 kinetoplast_chromosome sequence SO:0000826 URL:http://en.wikipedia.org/wiki/Kinetoplast http://en.wikipedia.org/wiki/Kinetoplast maxicircle A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method. PMID:8395055 http://purl.org/obo/owl/PMID#PMID_8395055 maxicircle_chromosome sequence SO:0000827 apicoplast_sequence apicoplast sequence sequence chromoplast_sequence chromoplast sequence sequence chloroplast_sequence chloroplast sequence sequence cyanelle_sequence cyanelle sequence sequence leucoplast_sequence leucoplast sequence sequence proplastid_sequence proplastid sequence sequence plasmid_location plasmid location sequence amplification_origin An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence. SO:ma http://purl.org/obo/owl/SO#SO_ma amplification origin sequence proviral_location proviral location sequence gene_group_regulatory_region gene group regulatory region sequence clone_insert The region of sequence that has been inserted and is being propagated by the clone. SO:ke http://purl.org/obo/owl/SO#SO_ke clone insert sequence lambda_vector The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. ISBN:0-1767-2380-8 http://purl.org/obo/owl/ISBN#ISBN_0-1767-2380-8 lambda vector sequence plasmid_vector plasmid vector sequence URL:http://en.wikipedia.org/wiki/Plasmid_vector#Vectors http://en.wikipedia.org/wiki/Plasmid_vector#Vectors cDNA DNA synthesized by reverse transcriptase using RNA as a template. SO:ma http://purl.org/obo/owl/SO#SO_ma complementary DNA sequence URL:http://en.wikipedia.org/wiki/CDNA http://en.wikipedia.org/wiki/CDNA single_stranded_cDNA single strand cDNA single stranded cDNA single-strand cDNA sequence double_stranded_cDNA double strand cDNA double stranded cDNA double-strand cDNA sequence plasmid_clone sequence YAC_clone sequence phagemid_clone sequence PAC_clone P1_clone sequence fosmid_clone sequence BAC_clone sequence cosmid_clone sequence pyrrolysyl_tRNA A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke pyrrolysyl tRNA pyrrolysyl-transfer ribonucleic acid pyrrolysyl-transfer RNA sequence clone_insert_start sequence episome A plasmid that may integrate with a chromosome. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence tmRNA_coding_piece Added in response to comment from Kelly Williams from Indiana. Nov 2005. The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. doi:10.1093/nar/gkh795 http://purl.org/obo/owl/doi#doi_10.1093/nar/gkh795 Indiana:kw http://purl.org/obo/owl/Indiana#Indiana_kw issn:1362-4962 http://purl.org/obo/owl/issn#issn_1362-4962 tmRNA coding piece sequence tmRNA_acceptor_piece Added in response to Kelly Williams from Indiana. Date: Nov 2005. The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. doi:10.1093/nar/gkh795 http://purl.org/obo/owl/doi#doi_10.1093/nar/gkh795 Indiana:kw http://purl.org/obo/owl/Indiana#Indiana_kw tmRNA acceptor piece sequence QTL Added in respose to request by Simon Twigger November 14th 2005. A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. URL:http://rgd.mcw.edu/tu/qtls/ http://rgd.mcw.edu/tu/qtls/ quantitative trait locus sequence genomic_island Genomic islands are transmissible elements characterized by large size (>10kb). A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility. Phigo:at http://purl.org/obo/owl/Phigo#Phigo_at SO:ke http://purl.org/obo/owl/SO#SO_ke genomic island sequence URL:http://en.wikipedia.org/wiki/Genomic_island http://en.wikipedia.org/wiki/Genomic_island pathogenic_island Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species. SO:ke http://purl.org/obo/owl/SO#SO_ke pathogenic island sequence metabolic_island Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands. A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria. SO:ke http://purl.org/obo/owl/SO#SO_ke metabolic island sequence adaptive_island The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. An adaptive island is a genomic island that provides an adaptive advantage to the host. SO:ke http://purl.org/obo/owl/SO#SO_ke adaptive island sequence symbiosis_island Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149. A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria. SO:ke http://purl.org/obo/owl/SO#SO_ke symbiosis island sequence pseudogenic_rRNA Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. A non functional descendent of an rRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogenic rRNA sequence pseudogenic_tRNA Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. A non functional descendent of a tRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke pseudogenic tRNA sequence engineered_episome Requested by Lynn Crosby Jan 2006. An episome that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered episome sequence transposable_element_attribute Added by KE Jan 2006 to capture the kinds of attributes of TEs sequence transgenic Attribute describing sequence that has been integrated with foreign sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence natural An attribute describing a feature that occurs in nature. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence engineered An attribute to describe a region that was modified in vitro. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence foreign An attribute to describe a region from another species. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence cloned_region Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions. cloned region cloned segment sequence reagent_attribute Added jan 2006 by KE. reagent attribute sequence clone_attribute sequence cloned sequence validated An attribute to describe a feature that has been proven. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence invalidated An attribute describing a feature that is invalidated. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence cloned_genomic sequence cloned_cDNA sequence engineered_DNA sequence engineered_rescue_region A rescue region that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered rescue fragment engineered rescue region engineered rescue segment sequence rescue_mini_gene A mini_gene that rescues. SO:xp http://purl.org/obo/owl/SO#SO_xp rescue mini gene rescue mini-gene sequence transgenic_transposable_element Modified as requested by Lynn - FB. May 2007. TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE. FB:mc http://purl.org/obo/owl/FB#FB_mc transgenic transposable element sequence natural_transposable_element TE that exists (or existed) in nature. FB:mc http://purl.org/obo/owl/FB#FB_mc natural transposable element sequence engineered_transposable_element TE that has been modified by manipulations in vitro. FB:mc http://purl.org/obo/owl/FB#FB_mc engineered transposable element sequence engineered_foreign_transposable_element A transposable_element that is engineered and foreign. FB:mc http://purl.org/obo/owl/FB#FB_mc engineered foreign transposable element sequence assortment_derived_duplication A multi-chromosome duplication aberration generated by reassortment of other aberration components. FB:gm http://purl.org/obo/owl/FB#FB_gm assortment derived duplication sequence assortment_derived_deficiency_plus_duplication A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication. FB:gm http://purl.org/obo/owl/FB#FB_gm assortment derived deficiency plus duplication sequence assortment_derived_deficiency A multi-chromosome deficiency aberration generated by reassortment of other aberration components. FB:gm http://purl.org/obo/owl/FB#FB_gm assortment-derived deficiency sequence assortment_derived_aneuploid A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication. FB:gm http://purl.org/obo/owl/FB#FB_gm assortment derived aneuploid sequence engineered_region A region that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp construct engineered region engineered sequence sequence engineered_foreign_region A region that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered foreign region sequence fusion sequence engineered_tag A tag that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp engineered tag sequence validated_cDNA_clone A cDNA clone that has been validated. SO:xp http://purl.org/obo/owl/SO#SO_xp validated cDNA clone sequence invalidated_cDNA_clone A cDNA clone that is invalid. SO:xp http://purl.org/obo/owl/SO#SO_xp invalidated cDNA clone sequence chimeric_cDNA_clone A cDNA clone invalidated because it is chimeric. SO:xp http://purl.org/obo/owl/SO#SO_xp chimeric cDNA clone sequence genomically_contaminated_cDNA_clone A cDNA clone invalidated by genomic contamination. SO:xp http://purl.org/obo/owl/SO#SO_xp genomically contaminated cDNA clone sequence polyA_primed_cDNA_clone A cDNA clone invalidated by polyA priming. SO:xp http://purl.org/obo/owl/SO#SO_xp polyA primed cDNA clone sequence partially_processed_cDNA_clone A cDNA invalidated clone by partial processing. SO:xp http://purl.org/obo/owl/SO#SO_xp partially processed cDNA clone sequence rescue An attribute describing a region's ability, whe