]> 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 autogenerated-by\: DAG-Edit version 1.417\nsaved-by\: eilbeck\ndate\: Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $ kareneilbeck sequence 18:12:2008 14:17 biosapiens protein feature ontology has_genome_location sequence non_functional_homolog_of A relationship between a pseudogenic feature and its functional ancestor. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence paralogous_to sequence regulated_by sequence adjacent_to adjacent_to A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence associated_with This relationship is vague and up for discussion. sequence complete_evidence_for_feature If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence evidence_for_feature This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. B is evidence_for_feature A, if an instance of B supports the existence of A. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence genome_of sequence has_origin sequence has_quality The relationship between a feature and an attribute. sequence homologous_to sequence member_of A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. sequence Super property for all Sequence Ontology object properties. orthologous_to sequence partial_evidence_for_feature B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence position_of sequence sequence_of sequence similar_to sequence Super class of all Sequnce Ontology classes. Sequence_Ontology sequence region sequence 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_secondary_structure sequence secondary structure A folded sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence G_quartet G tetrad G_quadruplex G-quadruplex guanine tetrad G quartet G-quartet G-tetrad 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 sequence interior_coding_exon interior coding exon sequence satellite_DNA 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 sequence PCR_product This term is mapped to MGED. Do not obsolete without consulting MGED ontology. PCR product A region amplified by a PCR reaction. SO:ke http://purl.org/obo/owl/SO#SO_ke amplicon sequence read_pair read-pair 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 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 small cytoplasmic RNA transcript scRNA primary transcript scRNA 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 small cytoplasmic RNA small_cytoplasmic_RNA sequence scRNA small cytoplasmic RNA 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 sequence INR_motif INR motif initiator motif initiator 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 DMp2 sequence DPE_motif downstream core promoter element DPE motif 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 CRWMGCGWKCGCTTS sequence BRE_motif transcription factor B-recognition element BRE motif B-recognition element 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 TFIIB recognition element sequence PSE_motif proximal sequence element 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 sequence linkage_group 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 sequence RNA_internal_loop 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 sequence asymmetric_RNA_internal_loop 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 sequence A_minor_RNA_motif 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 sequence K_turn_RNA_motif K turn RNA motif K-turn kink turn kink-turn 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 sequence sarcin_like_RNA_motif sarcin like RNA motif sarcin/ricin domain sarcin/ricin loop sarcin/ricin RNA domain A loop in ribosomal RNA containing the sites of attack for ricin and sarcin. URL:http://proton.chem.yale.edu/pdf/7897662.pdf http://proton.chem.yale.edu/pdf/7897662.pdf sequence symmetric_RNA_internal_loop A-minor RNA motif 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 sequence RNA_junction_loop RNA junction loop sequence RNA_hook_turn hook-turn motif RNA hook turn hook turn sequence base_pair base pair sequence WC_base_pair Watson Crick base pair Watson-Crick pair WC base pair canonical 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 Watson-Crick base pair sequence sugar_edge_base_pair sugar edge base pair A type of non-canonical base-pairing. PMID:12177293 http://purl.org/obo/owl/PMID#PMID_12177293 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 DNA_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 sequence RNA_aptamer 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 sequence morpholino_oligo 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/ sequence riboswitch riboswitch RNA 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 sequence matrix_attachment_site scaffold attachment site matrix attachment site S/MAR MAR nuclear matrix attachment site scaffold matrix attachment region matrix association region SMAR nuclear matrix association region matrix attachment region 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 S/MAR element sequence locus_control_region LCR 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 locus control element sequence match_set A collection of match parts. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence match_part 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 sequence genomic_clone genomic clone A clone of a DNA region of a genome. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence sequence_operation 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 pseudogene_attribute pseudogene attribute An attribute of a pseudogene (SO:0000336). SO:ma http://purl.org/obo/owl/SO#SO_ma sequence processed_pseudogene Please not the synonym R psi M uses the spelled out form of the greek letter. processed pseudogene retropseudogene A pseudogene that is processed. SO:xp http://purl.org/obo/owl/SO#SO_xp R psi G pseudogene by reverse transcription sequence pseudogene_by_unequal_crossing_over pseudogene by unequal crossing over A pseudogene caused by unequal crossing over at recombination. SO:ke http://purl.org/obo/owl/SO#SO_ke 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 assortment_derived_deficiency assortment-derived_deficiency sequence mutation_affecting_regulatory_region mutation affecting regulatory region A kind of mutation that affects a regulatory region of a gene. SO:ke http://purl.org/obo/owl/SO#SO_ke 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 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 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 operator operator segment 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 sequence assortment_derived_aneuploid assortment-derived_aneuploid sequence nuclease_binding_site nuclease binding site A region of a molecule that binds to a nuclease. SO:cb http://purl.org/obo/owl/SO#SO_cb sequence compound_chromosome_arm compound chromosome arm sequence restriction_enzyme_binding_site restriction endonuclease binding site restriction enzyme binding site A region of a molecule that binds to a restriction enzyme. SO:cb http://purl.org/obo/owl/SO#SO_cb restriction endonuclease recognition site restriction enzyme recognition site sequence deficient_intrachromosomal_transposition deficient intrachromosomal transposition sequence deficient_interchromosomal_transposition 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 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 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 sequence inside_intron_antiparallel 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 sequence inside_intron_parallel 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 sequence end_overlapping_gene sequence five_prime_three_prime_overlap 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 sequence five_prime_five_prime_overlap 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 sequence three_prime_three_prime_overlap 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 sequence three_prime_five_prime_overlap 5' 3' overlap 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 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 polycistronic_transcript polycistronic transcript A transcript that is polycistronic. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence dicistronic_transcript dicistronic transcript A transcript that is dicistronic. SO:ke http://purl.org/obo/owl/SO#SO_ke 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 nuclear gene A gene from nuclear sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence mt_gene mitochondrial gene mt gene A gene located in mitochondrial sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence kinetoplast_gene kinetoplast gene A gene located in kinetoplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence plastid_gene plastid gene A gene from plastid sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence apicoplast_gene apicoplast gene A gene from apicoplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence ct_gene chloroplast gene ct gene A gene from chloroplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence chromoplast_gene chromoplast gene A gene from chromoplast_sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence cyanelle_gene cyanelle gene A gene from cyanelle sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence leucoplast_gene leucoplast gene A plastid gene from leucoplast sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence proplastid_gene proplastid gene A gene from proplastid sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence nucleomorph_gene nucleomorph gene A gene from nucleomorph sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence plasmid_gene plasmid gene A gene from plasmid sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence proviral_gene proviral gene A gene from proviral sequence. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence endogenous_retroviral_gene endogenous retroviral gene A proviral gene with origin endogenous retrovirus. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence transposable_element transposable element transposon 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 sequence expressed_sequence_match expressed sequence match A match to an EST or cDNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence clone_insert_end clone insert end The end of the clone insert. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence polypeptide This term is mapped to MGED. Do not obsolete without consulting MGED ontology.nThe term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequenece_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. SO:0000358 protein 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 sequence chromosome_arm 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 sequence non_capped_primary_transcript sequence sequencing_primer sequencing primer sequence mRNA_with_frameshift frameshifted mRNA mRNA with frameshift An mRNA with a frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp 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 located_sequence_feature sequence feature An extent of biological sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke located sequence feature sequence transposable_element_gene 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 sequence primer primer polynucleotide primer oligonucleotide DNA primer primer sequence A short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase. URL:http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/glossary.html http://www.ornl.gov/TechResources/Human_Genome/publicat/primer2001/glossary.html sequence proviral_region proviral region A viral sequence which has integrated into a host genome. SO:ke http://purl.org/obo/owl/SO#SO_ke proviral sequence sequence methylated_C methylated cytosine residue methylated cytosine base methylated cytosine methylated C A methylated deoxy-cytosine. SO:ke http://purl.org/obo/owl/SO#SO_ke 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 transcript with translational frameshift A transcript with a translational frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp 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. protein coding primary transcript 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 sequence forward_primer This term is mapped to MGED. Do not obsolete without consulting MGED ontology. DNA forward primer forward DNA primer forward primer polynucleotide forward primer oligonucleotide forward primer forward primer sequence forward primer oligo A single stranded oligo used for polymerase chain reaction. URL:http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php sequence RNA_sequence_secondary_structure RNA sequence secondary structure A folded RNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence transcriptionally_regulated By:<protein_id>. transcriptionally regulated An attribute describing a gene that is regulated at transcription. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence transcriptionally_constitutive 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 sequence transcriptionally_induced transcriptionally induced An inducer molecule is required for transcription to occur. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence transcriptionally_repressed transcriptionally repressed A repressor molecule is required for transcription to stop. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence silenced_gene silenced gene A gene that is silenced. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence gene_silenced_by_DNA_modification gene silenced by DNA modification A gene that is silenced by DNA modification. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence gene_silenced_by_DNA_methylation gene silenced by DNA methylation methylation-silenced gene A gene that is silenced by DNA methylation. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence post_translationally_regulated post translationally regulated 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 sequence translationally_regulated translationally regulated An attribute describing a gene that is regulated as it is translated. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence reverse_primer This term is mapped to MGED. Do not obsolete without consulting MGED ontology. reverse primer oligonucleotide reverse DNA primer reverse primer oligo reverse primer sequence reverse primer DNA reverse primer A single stranded oligo used for polymerase chain reaction. URL:http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php sequence epigenetically_modified 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 sequence 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 sequence maternally_imprinted maternally imprinted The maternal copy of the gene is modified, rendering it transcriptionally silent. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence paternally_imprinted paternally imprinted The paternal copy of the gene is modified, rendering it transcriptionally silent. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence allelically_excluded Exapmles are x-innactivation and immunoglobulin formation. allelically excluded Allelic exclusion is a process occuring in diploid organisms, where a gene is inactivated and not expressed in that cell. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence gene_rearranged_at_DNA_level gene rearranged at DNA level An epigenetically modified gene, rearranged at the DNA level. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence ribosome_entry_site Gene:<gene_id>. ribosome entry site Region in mRNA where ribosome assembles. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence attenuator attenuator sequence 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 sequence terminator terminator sequence 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 sequence DNA_sequence_secondary_structure DNA sequence secondary structure A folded DNA sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence assembly_component 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 sequence primary_transcript_attribute sequence recoded_codon 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 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 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 unvailable bases. SO:ls http://purl.org/obo/owl/SO#SO_ls sequence 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 YAC This term is mapped to MGED. Do not obsolete without consulting MGED ontology. yeast artificial chromosome 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 sequence BAC This term is mapped to MGED. Do not obsolete without consulting MGED ontology. bacterial artificial chromosome 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 sequence PAC This term is mapped to MGED. Do not obsolete without consulting MGED ontology.nDrosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome. P1 P1 artificial chromosome A single-copy cloning vector that is derived from the F-factor of Escherichia coli. PACs can contain large genomic fragments. URL:http://www.nature.com/nrg/journal/v6/n3/glossary/nrg1553_glossary.html http://www.nature.com/nrg/journal/v6/n3/glossary/nrg1553_glossary.html sequence plasmid This term is mapped to MGED. Do not obsolete without consulting MGED ontology. plasmid sequence 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 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. cosmid vector 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 sequence 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 fosmid Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996. A cloning vector that utilises the E. coli F factor. SO:ma http://purl.org/obo/owl/SO#SO_ma fosmid vector sequence deletion deleted_sequence The point at which a deletion occured. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence 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 methylated adenine residue methylated adenine base methylated A methylated adenine A modified RNA base in which adenine has been methylated. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence splice_site With spliceosomal introns, the splice sites bind the spliceosomal machinary. splice site Consensus region of primary transcript bordering junction of splicing. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence five_prime_cis_splice_site splice donor site 5' splice site donor splice site five prime splice site The junction between the 3 prime end of an exon and the following intron. URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html donor sequence three_prime_cis_splice_site splice acceptor site three prime splice site acceptor splice site The junction between the 3 prime end of an intron and the following exon. URL:http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html acceptor 3' splice site sequence enhancer An enhancer may participate in an enhanceosome GO:0034206.nA 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.nThis comment is a placeholder 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 enhancer_bound_by_factor enhancer bound by factor An enhancer bound by a factor. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence promoter This term is mapped to MGED. Do not obsolete without consulting MGED ontology.nThe region on a DNA molecule involved in RNA polymerase binding to initiate transcription. promoter sequence 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 sequence 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 pol I promoter polymerase I promoter RNA polymerase A promoter 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 sequence RNApol_II_promoter RNApol II promoter RNA polymerase B promoter polymerase 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 sequence RNApol_III_promoter RNApol III promoter polymerase III promoter RNA polymerase C promoter pol 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 sequence CAAT_signal CAAT box CAAT signal CAAT-box 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 sequence GC_rich_promoter_region GC rich promoter region GC-rich 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 sequence TATA_box Goldstein-Hogness box TATA box 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 sequence minus_10_signal minus 10 signal Pribnow box -10 signal Pribnow-Schaller box Pribnow Schaller box 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. 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 minus_35_signal -35 signal minus 35 signal A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. 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 cross_genome_match cross genome match A nucleotide match against a sequence from another organism. SO:ma http://purl.org/obo/owl/SO#SO_ma 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 clone_insert_start clone insert start The start of the clone insert. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence retrotransposon class I transposon retrotransposon element 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 sequence translated_nucleotide_match translated nucleotide match A match against a translated sequence. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence DNA_transposon class II transposon 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 sequence non_transcribed_region non-transcribed sequence non transcribed region nontranscribed region nontranscribed sequence A region of the gene which is not transcribed. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence U2_intron May have either GT-AG or AT-AG 5' and 3' boundaries. U2 intron 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 sequence primary_transcript precursor RNA primary transcript A transcript that in its initial state requires modification to be functional. SO:ma http://purl.org/obo/owl/SO#SO_ma sequence LTR_retrotransposon long terminal repeat retrotransposon LTR retrotransposon A retrotransposon flanked by long terminal repeat sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke 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 segment of DNA 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 non_LTR_retrotransposon non LTR retrotransposon A retrotransposon without long terminal repeat sequences. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence five_prime_intron 5' intron 5' intron sequence five prime intron sequence interior_intron interior intron sequence three_prime_intron 3' intron three prime intron 3' intron sequence sequence RFLP_fragment restriction fragment length polymorphism RFLP 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 sequence LINE_element LINE LINE element Long interspersed element Long interspersed nuclear 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 sequence coding_exon coding exon An exon whereby at least one base is part of a codon (here, 'codon'nis inclusive of the stop_codon). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence five_prime_coding_exon_coding_region five prime 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 sequence three_prime_coding exon_coding_region three prime 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 sequence noncoding_exon noncoding exon An exon that does not contain any codons. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence translocation translocated sequence A region of nucleotide sequence that has translocated to a new position. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence five_prime_coding_exon 5' coding exon five prime coding exon The 5' most coding exon. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence interior_exon interior exon An exon that is bounded by 5' and 3' splice sites. PMID:10373547 http://purl.org/obo/owl/PMID#PMID_10373547 sequence three_prime_coding_exon 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 sequence UTR untranslated region 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 sequence five_prime_UTR 5' UTR five prime UTR five_prime_untranslated_region 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 sequence three_prime_UTR three prime untranslated region 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 sequence SINE_element Short interspersed element Short interspersed nuclear element 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 sequence simple_sequence_length_variation simple sequence length variation simple sequence length polymorphism sequence terminal_inverted_repeat_element terminal inverted repeat element TIR 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 sequence rRNA_primary_transcript ribosomal RNA primary transcript rRNA primary transcript A primary transcript encoding a ribosomal RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence tRNA_primary_transcript tRNA primary transcript A primary transcript encoding a transfer RNA (SO:0000253). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence alanine_tRNA_primary_transcript alanine tRNA primary transcript A primary transcript encoding alanyl tRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence arginine_tRNA_primary_transcript arginine tRNA primary transcript A primary transcript encoding arginyl tRNA (SO:0000255). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence asparagine_tRNA_primary_transcript asparagine tRNA primary transcript A primary transcript encoding asparaginyl tRNA (SO:0000256). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence aspartic_acid_tRNA_primary_transcript aspartic acid tRNA primary transcript A primary transcript encoding aspartyl tRNA (SO:0000257). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence cysteine_tRNA_primary_transcript cysteine tRNA primary transcript A primary transcript encoding cysteinyl tRNA (SO:0000258). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence glutamic_acid_tRNA_primary_transcript glutamic acid tRNA primary transcript A primary transcript encoding glutaminyl tRNA (SO:0000260). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence glutamine_tRNA_primary_transcript glutamine tRNA primary transcript A primary transcript encoding glutamyl tRNA (SO:0000260). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence glycine_tRNA_primary_transcript glycine tRNA primary transcript A primary transcript encoding glycyl tRNA (SO:0000263). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence histidine_tRNA_primary_transcript histidine tRNA primary transcript A primary transcript encoding histidyl tRNA (SO:0000262). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence isoleucine_tRNA_primary_transcript isoleucine tRNA primary transcript A primary transcript encoding isoleucyl tRNA (SO:0000263). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence leucine_tRNA_primary_transcript leucine tRNA primary transcript A primary transcript encoding leucyl tRNA (SO:0000264). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence lysine_tRNA_primary_transcript lysine tRNA primary transcript A primary transcript encoding lysyl tRNA (SO:0000265). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence methionine_tRNA_primary_transcript methionine tRNA primary transcript A primary transcript encoding methionyl tRNA (SO:0000266). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence phenylalanine_tRNA_primary_transcript phenylalanine tRNA primary transcript A primary transcript encoding phenylalanyl tRNA (SO:0000267). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence proline_tRNA_primary_transcript proline tRNA primary transcript A primary transcript encoding prolyl tRNA (SO:0000268). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence serine_tRNA_primary_transcript serine tRNA primary transcript A primary transcript encoding seryl tRNA (SO:000269). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence threonine_tRNA_primary_transcript threonine tRNA primary transcript A primary transcript encoding threonyl tRNA (SO:000270). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence tryptophan_tRNA_primary_transcript tryptophan tRNA primary transcript A primary transcript encoding tryptophanyl tRNA (SO:000271). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence tyrosine_tRNA_primary_transcript tyrosine tRNA primary transcript A primary transcript encoding tyrosyl tRNA (SO:000272). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence valine_tRNA_primary_transcript valine tRNA primary transcript A primary transcript encoding valyl tRNA (SO:000273). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence snRNA_primary_transcript snRNA primary transcript A primary transcript encoding a small nuclear RNA (SO:0000274). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence snoRNA_primary_transcript snoRNA primary transcript A primary transcript encoding a small nucleolar mRNA (SO:0000275). SO:ke http://purl.org/obo/owl/SO#SO_ke sequence mature_transcript A processed transcript cannot contain introns. mature transcript 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 sequence 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 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 sequence TF_binding_site TF binding site transcription factor binding site A region of a molecule that binds a TF complex [GO:0005667]. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence ORF The definition was modified by Rama. This term is now basically the same as a CDS. This must be revised. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. open reading frame The inframe 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. SO:ma http://purl.org/obo/owl/SO#SO_ma SO:rb http://purl.org/obo/owl/SO#SO_rb sequence transcript_attribute transcript attribute sequence foldback_element foldback element A transposable element with extensive secondary structure, characterised 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 long inverted repeat element LVR element sequence flanking_region flanking region The sequences extending on either side of a specific region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence chromosome_variation chromosome variation sequence internal_UTR 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 sequence untranslated_region_polycistronic_mRNA untranslated region polycistronic mRNA The untranslated sequence separating the 'cistrons' of multicistronic mRNA. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence internal_ribosome_entry_site IRES internal ribosomal entry site internal ribosome entry site internal ribosomal entry sequence Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation. SO:ke http://purl.org/obo/owl/SO#SO_ke internal ribosome entry sequence sequence 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 modified RNA base feature A post_transcriptionally modified base. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence eight_cutter_restriction_site 8-cutter_restriction_site eight-cutter_restriction_site sequence rRNA ribosomal ribonucleic acid ribosomal RNA 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 sequence 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 alanyl_tRNA alanyl tRNA alanyl-transfer ribonucleic acid alanyl-transfer RNA A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence rRNA_small_subunit_primary_transcript rRNA small subunit primary transcript A primary transcript encoding a small ribosomal subunit RNA. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence asparaginyl_tRNA asparaginyl tRNA asparaginyl-transfer ribonucleic acid asparaginyl-transfer RNA A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence aspartyl_tRNA aspartyl tRNA aspartyl-transfer ribonucleic acid aspartyl-transfer RNA 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 sequence cysteinyl_tRNA cysteinyl tRNA cysteinyl-transfer ribonucleic acid cysteinyl-transfer RNA A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence glutaminyl_tRNA glutaminyl tRNA glutaminyl-transfer ribonucleic acid glutaminyl-transfer RNA A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence glutamyl_tRNA glutamyl tRNA glutamyl-transfer ribonucleic acid 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-transfer RNA sequence glycyl_tRNA 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-transfer ribonucleic acid glycyl-transfer RNA sequence histidyl_tRNA histidyl tRNA histidyl-transfer ribonucleic acid histidyl-transfer RNA A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence isoleucyl_tRNA isoleucyl tRNA isoleucyl-transfer ribonucleic acid isoleucyl-transfer RNA A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence leucyl_tRNA leucyl tRNA leucyl-transfer ribonucleic acid leucyl-transfer RNA A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence lysyl_tRNA lysyl tRNA lysyl-transfer ribonucleic acid lysyl-transfer RNA A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence methionyl_tRNA methionyl tRNA methionyl-transfer ribonucleic acid methionyl-transfer RNA A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence phenylalanyl_tRNA phenylalanyl tRNA phenylalanyl-transfer ribonucleic acid phenylalanyl-transfer RNA A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence prolyl_tRNA prolyl tRNA prolyl-transfer ribonucleic acid prolyl-transfer RNA A tRNA sequence that has a proline anticodon, and a 3' proline binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence seryl_tRNA seryl tRNA seryl-transfer RNA 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-transfer ribonucleic acid sequence threonyl_tRNA threonyl tRNA threonyl-transfer ribonucleic acid 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-transfer RNA sequence tryptophanyl_tRNA tryptophanyl tRNA tryptophanyl-transfer ribonucleic acid tryptophanyl-transfer RNA A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence tyrosyl_tRNA tyrosyl tRNA tyrosyl-transfer ribonucleic acid 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-transfer RNA sequence valyl_tRNA valyl tRNA valyl-transfer ribonucleic acid 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-transfer RNA sequence snRNA This term is mapped to MGED. Do not obsolete without consulting MGED ontology. small nuclear RNA 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 sequence snoRNA small nucleolar RNA 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 sequence miRNA micro RNA microRNA 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 sequence bound_by_factor Formerly called transcript_by_bound_factor. bound by factor An attribute describing a sequence that is bound by another molecule. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence transcript_bound_by_nucleic_acid Formerly called transcript_by_bound_nucleic_acid. transcript bound by nucleic acid A transcript that is bound by a nucleic acid. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence transcript_bound_by_protein Formerly called transcript_by_bound_protein. transcript bound by protein A transcript that is bound by a protein. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence engineered_gene engineered gene A gene that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence engineered_foreign_gene engineered foreign gene A gene that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence mRNA_with_minus_1_frameshift mRNA with minus 1 frameshift An mRNA with a minus 1 frameshift. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence engineered_foreign_transposable_element_gene engineered foreign transposable element gene A transposible_element that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp 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 foreign gene A gene that is foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence long_terminal_repeat long terminal repeat LTR 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 sequence fusion_gene fusion gene A gene that is a fusion. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence engineered_fusion_gene engineered fusion gene A fusion gene that is engineered. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence microsatellite microsatellite locus microsatellite marker VNTR 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 sequence dinucleotide_repeat_microsatellite_feature dinucleotide repeat microsatellite dinucleotide repeat microsatellite feature dinucleotide repeat microsatellite locus dinucleotide repeat microsatellite marker sequence trinucleotide_repeat_microsatellite_feature rinucleotide repeat microsatellite trinucleotide repeat microsatellite feature trinucleotide repeat microsatellite locus dinucleotide repeat microsatellite marker sequence repetitive_element sequence engineered_foreign_repetitive_element engineered foreign repetitive element A repetitive element that is engineered and foreign. SO:xp http://purl.org/obo/owl/SO#SO_xp sequence inverted_repeat inverted repeat inverted repeat sequence 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 sequence U12_intron May have either GT-AC or AT-AC 5' and 3' boundaries. U12 intron U12-dependent intron 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 sequence origin_of_replication ori 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 sequence D_loop 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 displacement loop sequence 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 J gene recombination feature J-RS Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence. URL:http://imgt.cines.fr/cgi-bin/IMGTlect.jv?query=7# http://imgt.cines.fr/cgi-bin/IMGTlect.jv?query=7# 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_site Modified base:<modified_base>. modified base site A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U. 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 methylated_base_feature methylated base feature A nucleotide modified by methylation. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence CpG_island CG island 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 sequence 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 experimentally determined Attribute to describe a feature that has been experiemntally verified. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence stem_loop SO:0000019 RNA_hairpin_loop stem loop 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 sequence direct_repeat 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 sequence TSS transcription start site The first base where RNA polymerase begins to synthesize the RNA transcript. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence CDS coding sequence 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 sequence cDNA_clone This term is mapped to MGED. Do not obsolete without consulting MGED ontology. cDNA clone 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 sequence start_codon initiation codon start codon First codon to be translated by a ribosome. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence stop_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 sequence intronic_splice_enhancer 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 sequence mRNA_with_plus_1_frameshift mRNA with plus 1 frameshift An mRNA with a plus 1 frameshift. SO:ke http://purl.org/obo/owl/SO#SO_ke sequence nuclease_hypersensitive_site nuclease hypersensitive site sequence coding_start coding start translation initiation site The first base to be translated into protein. SO:ke