definition definition_source database_cross_reference has_exact_synonym has_related_synonym has_structure has_region results_in For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) RO:part_of part_of mirnao:DNA_Sequence The sequence of nucleotide residues along a DNA chain. NCI Thesaurus:DNA_Sequence NCIThesaurus:DNA_Sequence DNA Sequence mirnao:RNA_Sequence The sequence of nucleotide residues along an RNA chain. NCI Thesaurus:RNA_Sequence NCIThesaurus:DNA_Sequence RNA Sequence mirnao:Reptilia Cold-blooded, air-breathing VERTEBRATES belonging to the class Reptilia, usually covered with external scales or bony plates. MSH:D012104 Reptilia mirnao:Transcription_Factor A role palyed by a protein that binds to specific DNA sequences, thereby controlling the transcription of genetic information from DNA to mRNA. modified definition from WIkipedia, http://en.wikipedia.org/wiki/Transcription_factor GRO:TranscriptionFactor Transcription Factor mirnao:Xenacoelomorpha A phylum of kingdom Animalia. Xenacoelomorpha Thesaurus:Plant Any living organism that typically synthesizes its food from inorganic substances, possesses cellulose cell walls, responds slowly and often permanently to a stimulus, lacks specialized sense organs and nervous system, and has no powers of locomotion. (EPA Terminology Reference System). NCIThesaurus:Plant Plants BFO:0000030 Object BFO:0000141 BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth). BFO:0000141 Immaterial Entity CHEBI:16991 High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. CHEBI:16991 DNA CHEBI:33696 A macromolecule made up of nucleotide units and hydrolyzable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. CHEBI:33696 Nucleic Acid CHEBI:33697 High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. CHEBI:33697 RNAO_0000000 RNA CHEBI:36080 A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. CHEBI:36080 Protein GO:0005575 The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. GO:0005575 Cellular Component GO:0005694 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information. GO:0005694 Chromosome NCBITaxon:10029 A species of genus Cricetulus. Chinese hamster Cricetulus aureus Cricetulus barabensis griseus Cricetus griseus Cricetulus griseus NCBITaxon:10090 A species of genus Mus. House mouse Mouse Mus muscaris mice C57BL/6xCBA/CaJ hybrid Mus musculus NCBITaxon:10116 A species of genus Rattus. Brown rat Norway rat Rat Rattus sp. strain Wistar Gunn rats Rattus norvegicus8 Rattus norwegicus Rattus rattiscus Rattus norvegicus NCBITaxon:10219 A phylum of kingdom Animalia. Hemichordata NCBITaxon:10220 A class of phylum Hemichordata. Enteropneusta NCBITaxon:10224 A species of genus Saccoglossus. Saccoglossus kowalesvskii Saccoglossus kowalevskyi Saccoglossus kowalevskii NCBITaxon:10239 An infectious agent which consists of two parts, genetic material and a protein coat. These organisms lack independent metabolism, and they must infect the cells of other types of organisms to reproduce. Most viruses are capable of passing through fine filters that retain bacteria, and are not visible through a light microscope. NCIThesaurus:Virus Virus NCBITaxon:10298 A dsDNA virus of family Herpesviridae. Herpes simplex virus type 1 Herpes simplex virus 1 Human Herpesvirus-1 Human herpesvirus type 1 herpes simplex virus 1 HSV-1 herpes simplex virus HSV-1 herpes simplex virus type 1 HSV-1 herpes simplex virus type 1 HSV1 herpes simplex virus type-1 HSV-1 Human herpesvirus 1 NCBITaxon:10310 A dsDNA virus of family Herpesviridae. Herpes simplex virus (type 2) Herpes simplex virus 2 Herpes simplex virus type 2 herpes simplex virus type 2 HSV-2 Human herpesvirus 2 NCBITaxon:10320 A dsDNA virus of family Herpesviridae. Bovine herpesvirus type 1 Bovine herpesvirus-1 Bovine rhinotracheitis virus Infectious bovine rhinotracheitis virus bovine herpesvirus 1 BHV 1 bovine herpesvirus 1 BHV-1 bovine herpesvirus 1 BHV1 bovine herpesvirus BHV-1 bovine herpesvirus type 1 BHV-1 bovine herpesvirus type-1 BHV-1 infectious bovine rhinotracheitis virus BHV-1 Bovine herpesvirus 1 NCBITaxon:10325 A dsDNA virus of family Herpesviridae. Monkey B virus B virus Cercopithecid herpesvirus 1 Cercopithecine herpesvirus 1 Herpes B virus Herpes virus B Herpesvirus simiae Simian herpes B virus Simian herpes B virus SHBV Simian herpesvirus B Macacine herpesvirus 1 NCBITaxon:10345 A dsDNA virus of family Herpesviridae. Pseudorabies virus Alphaherpesvirus pseudorabies virus PRV Aujeszky's disease virus Pseudorabies Virus PRV Suid herpesvirus type 1 Suid herpesvirus 1 NCBITaxon:10359 A dsDNA virus of family Herpesviridae. Human cytomegalovirus Human cytomegalovirus HCMV human cytomegalovirus CMV human herpesvirus type 5 Human herpesvirus 5 NCBITaxon:10366 A dsDNA virus of family Herpesviridae Murine cytomegalovirus Mouse cytomegalovirus 1 murine cytomegalovirus (MCMV) murine cytomegalovirus MCMV murine herpesvirus 1 Murid herpesvirus 1 NCBITaxon:10376 A dsDNA virus of family Herpesviridae. Epstein-Barr virus Epstein-Barr virus EBV Epstein-Barr-virus EBV Human herpesvirus type 4 Human herpesvirus 4 NCBITaxon:10383 A dsDNA virus of family Herpesviridae. Herpesvirus saimiri (strain 11) NCBITaxon:10386 A dsDNA virus of family Herpesviridae. Avian infectious laryngotracheitis virus Gallid herpesvirus type 1 Infectious laryngotracheitis virus Laryngotracheitis virus infectious laryngotracheitis virus ILTV Gallid herpesvirus 1 NCBITaxon:10390 A dsDNA virus of family Herpesviridae. Marek disease virus type 1 Gallid herpesvirus 1 (serotype 1) Gallid herpesvirus type 2 Marek disease virus Marek's disease herpesvirus Marek's disease herpesvirus 1 Marek's disease virus Marek's disease virus (MDV) Marek's disease virus MDV Marek's disease virus MDV1 Marek's disease virus serotype 1 MDV-1 Marek's disease virus type 1 Marek's disease virus type 1 MDV1 Gallid herpesvirus 2 NCBITaxon:104388 A dsDNA virus of family Herpesviridae. Anatid Herpes virus-1 Duck enteritis virus Duck plague virus Anatid herpesvirus 1 NCBITaxon:10629 A dsDNA virus of family Polyomaviridae. BK virus BK virus BKV Human polyomavirus (type BK) Human polyomavirus BK Human polyomavirus BKV Papovavirus BKV Polyomavirus hominis 1 human polyomavirus type BK BKV polyomavirus BK polyomavirus homonis 1 BK polyomavirus NCBITaxon:10632 A dsDNA virus of family Polyomaviridae Human polyomavirus (type JC) JC polyomavirus JCV JC virus Polyomavirus hominis 2 human polyomavirus JCV polyoma virus JC JCV polyomavirus JC JC polyomavirus NCBITaxon:10633 A dsDNA virus of family Polyomaviridae. Polyomavirus maccacae Polyomavirus maccacae 1 Rhesus macaque polyomavirus rhesus polyomavirus Simian virus 40 NCBITaxon:106616 A species of genus Bruguiera. Bruguiera cylindrica (L.) Blume Bruguiera cylindrica NCBITaxon:11053 Dengue virus type 1 Type 1 dengue virus dengue type 1 D1 virus dengue virus type 1 DEN1 dengue virus type I dengue virus-1 DEN-1 type 1 dengue virus DEN-1 Dengue virus 1 NCBITaxon:11060 Dengue virus type 2 Dengue virus type II dengue 2 virus DEN-2 dengue-2 virus dengue-2 virus DEN-2 Dengue virus 2 NCBITaxon:11069 Dengue virus type 3 dengue 3 virus Dengue Virus 3 NCBITaxon:11070 Dengue virus type 4 dengue type 4 virus DEN4 Dengue Virus 4 NCBITaxon:11082 A ssRNA virus of family Flaviviridae. West Nile Virus NCBITaxon:11676 A retro-transcribing virus of family Retroviridae. AIDS virus Human immundeficiency virus type 1 Human immunodeficiencey virus type 1 Human immunodeficiency virus type 1 human immunodeficiency virus 1 HIV-1 human immunodeficiency virus HIV-1 human immunodeficiency virus type 1 ,HIV-1 human immunodeficiency virus type 1 HIV 1 human immunodeficiency virus type 1 HIV-1 human immunodeficiency virus type 1 HIV1 human immunodeficiency virus type 1, HIV-1 human immunodeficiency virus type I HIV-1 human immunodeficiency virus type-1 HIV-1 human immunodeficiency virus-1 HIV-1 Human immunodeficiency virus 1 NCBITaxon:11709 A retro-transcribing virus of family Retroviridae. AIDS virus HIV type 2 Human immunodeficiency virus type 2 Human immunodeficiency virus-2 human immunodeficiency virus type 2 HIV-2 human immunodeficiency virus type 2, HIV-2 Human immunodeficiency virus 2 NCBITaxon:11901 A retro-transcribing virus of family Retroviridae. bovine leukemia virus BLV bovine leukemia virus, BLV Bovine leukemia virus NCBITaxon:12637 A ssRNA virus of family Flaviviridae. Dengue virus NCBITaxon:126957 A species of genus Strigamia. Strigamia maritima NCBITaxon:131567 Cellular Organism NCBITaxon:135651 A species of genus Caenorhabditis. Caenorhabditis CB5161 Caenorhabditis n. sp. CB5161 Caenorhabditis sp. 1 CB5161 Caenorhabditis sp. CB5161 Caenorhabditis sp. PB2801 Caenorhabditis brenneri NCBITaxon:13616 A species of genus Monodelphis. Gray short-tailed opossum Monodelphis domesticus Monodelphis domestica NCBITaxon:15368 A species of genus Brachypodium. Brachypodium distachyon NCBITaxon:166384 A class of phylum Platyhelminthes. Turbellaria NCBITaxon:190402 A species of genus Pinus. Pinus densata NCBITaxon:205027 A species of genus Acacia. Acacia auriculiformis A.Cunn. ex Benth. Acacia auriculiformis NCBITaxon:218851 A species of genus Aquilegia. Aquilegia caerulea Aquilegia coerulea NCBITaxon:224085 A species of genus Acacia. Acacia mangium Willd Acacia mangium NCBITaxon:225164 A species of genus Lottia. Lottia gigantea NCBITaxon:242395 A species of genus Xenoturbella. Xenoturbella bocki NCBITaxon:2711 A species of genus Citrus. Apfelsine Naranja Navel orange Sweet orange Valencia orange Citrus sinensis (L.) Osbeck Citrus x sinensis Citrus sinensis NCBITaxon:27405 A species of genus Marsupenaeus. Penaeus (Marsupenaeus) japonicus Penaeus (Melicertus) japonicus Penaeus japonicus Marsupenaeus japonicus NCBITaxon:27929 A class of phylum Porifera. Calcarea NCBITaxon:27933 A species of genus Sycon. Scypha ciliata Sycon ciliatum NCBITaxon:28377 A species of genus Anolis. Green anole Anolis carolinensis NCBITaxon:283909 A species of genus Capitella. Capitella sp. I Capitella sp. I AF-2005 Capitella sp. I ECS-2004 Capitella sp. I ES-2005 Capitella sp. I Grassle & Grassle, 1976 Capitella telata Capitella teleta NCBITaxon:2850 A species of genus Phaeodactylum. Phaeodactylum tricornutum NCBITaxon:2880 A species of genus Ectocarpus. Ectocarpus siliculosus NCBITaxon:28977 A species of genus Cunninghamia. China fir Cunninghamia lanceolata (Lamb.) Hook. Cunninghamia lanceolata NCBITaxon:29729 A species of genus Gossypium. Tree cotton Gossypium arboreum L. Gossypium arboreum NCBITaxon:29730 A species of genus Gossypium. Gossypium raimondii Ulbr. Gossypium raimondii NCBITaxon:29760 A species of genus Vitis. Wine grape Vitis vinifera subsp. vinifera Vitis vinifera NCBITaxon:30302 A class of phylum Chordata. Appendicularia NCBITaxon:3041 A phylum of Eukaryota. Chlorophyta NCBITaxon:3055 A species of genus Chlamydomonas. Chlamydomonas reihhardtii Chlamydomonas reinhardtii P.A.Dangeard Chlamydomonas smithii Chlamydomonas smithii R.W.Howshaw & H.Ettl Chlamydomonas reinhardtii NCBITaxon:31033 A species of genus Takifugu. Tiger puffer Torafugu Fugu rubripes Sphaeroides rubripes Takifugu rubripes (Temminck & Schlegel, 1850) Tetraodon rubripes Takifugu rubripes NCBITaxon:31234 A species of genus Caenorhabditis. Caenorhabditis vulgarensis Caenorhabditis vulgariensis Caenorhabditis vulgaris Caenorhabditis vulgaris Baird, Fitch & Emmons, 1994 Caenorhabditis remanei NCBITaxon:3208 A phylum of Eukaryota. Bryophyta NCBITaxon:3218 A species of genus Physcomitrella. Physcomitrella patens NCBITaxon:32264 A species of genus Tetranychus. Red spider mite Two-spotted spider mite Twospotted mite Tetranychus urticae Koch, 1836 Tetranychus urticae NCBITaxon:3242 A division of Eukaryota. Lycopodiophyta NCBITaxon:32604 A dsDNA virus of family Herpesviridae. Human herpesvirus 6 type B Human herpesvirus 6B NCBITaxon:33208 Animalia Animals Metazoa NCBITaxon:3329 A species of genus Picea. Norway spruce Picea abies L., Karst Picea excelsa Pinus abies Picea abies NCBITaxon:3352 A species of genus Pinus. Loblolly pine Pinus taeda NCBITaxon:33634 Heterokonts Chromophyta Stramenopiles NCBITaxon:33708 A dsDNA virus of family Herpesviridae. Murine herpesvirus 68 mouse herpesvirus 68 mouse herpesvirus strain 68 murine gammaherpesvirus 68 murine herpesvirus type 68 Murid herpesvirus 4 NCBITaxon:34274 A species of genus Gossypium. Arabian cotton Gossypium herbaceum L. Gossypium herbaceum NCBITaxon:34305 A species of genus Lotus. Lotus corniculatus var. japonicus Lotus japonicus NCBITaxon:34515 A species of genus Glottidia. Glottidea pyramidata Glottidia pyramidata NCBITaxon:34740 A species of genus Heliconius. Heliconius melpomene NCBITaxon:34765 A species of genus Oikopleura. Oikopleura dioica NCBITaxon:35237 A virus having a dsDNA molecule as genetic material. No RNA intermediate molecules are involved during its replication. dsDNA virus, no RNA stage NCBITaxon:35268 A virus that replicates by the reverse transcription of a RNA or DNA intermediate. Retro-transcribing virus NCBITaxon:3635 A species of genus Gossypium. American cotton Cotton Upland cotton Gossypium hirsutum subsp. mexicanum Gossypium lanceolatum Gossypium purpurascens Gossypium hirsutum NCBITaxon:3641 A species of genus Theobroma. Cacao Cocoa Theobroma cacao NCBITaxon:3649 A species of genus Carica. Mamon Papaya Carica papaya L. Carica payaya Carica papaya NCBITaxon:3656 A species of genus Cucumis. Muskmelon Oriental melon Cucumis melo var. markuwa Markino Cucurbita melo L. Cucumis melo NCBITaxon:3694 A species of genus Populus. Black cottonwood Western balsam poplar Populus balsamifera subsp. trichocarpa Populus balsamifera subsp. trichocarpa (Torr. et A.Gray) Brayshaw Populus trichocarpa Torr. & A.Gray Populus trichocarpa Torr. et A.Gray Populus trichocarpa NCBITaxon:3702 A species of genus Arabidopsis. Mouse-ear cress Thale cress Thale-cress Arabidopsis thaliana (thale cress) Arbisopsis thaliana Arabidopsis thaliana NCBITaxon:3708 A species of genus Brassica. Oilseed rape Rape Rapeseeds Brassica napus NCBITaxon:37108 A dsDNA virus of family Herpesviridae. Turkey herpesvirus Meleagrid herpesvirus type 1 herpesvirus of turkey herpesvirus of turkeys turkey herpesvirus HVT Meleagrid herpesvirus 1 NCBITaxon:3711 A species of genus Brassica. Field mustard Brassica rapa L. Brassica rapa NCBITaxon:3712 A species of genus Brassica. Brassica oleracea L. Brassica oleracea NCBITaxon:37296 A dsDNA virus of family Herpesviridae. Human herpesvirus 8 type P Kaposi's sarcoma-associated herpes-like virus Kaposi's sarcoma-associated herpesvirus Kaposi's sarcoma-associated herpesvirus - Human herpesvirus 8 Kaposi's sarcoma-associated herpesvirus KSHV Kaposi's sarcoma-associated human herpes virus Karposi's sarcoma-associated herpes-like virus Human herpesvirus 8 NCBITaxon:3750 A species of genus Malus. Apple Apple tree Cultivated apple Malus domestica Malus pumila auct. Malus pumila var. domestica Malus sylvestris var. domestica Pyrus malus Malus x domestica NCBITaxon:3760 A species of genus Prunus. peach Amygdalus persica Persica vulgaris Prunus persica var densa Prunus persica NCBITaxon:37682 A species of genus Aegilops. Aegilops squarrosa Aegilops squarrosa auct. Aegilops squarrosa subsp. squarrosa Aegilops tauschii Coss. Aegilops tauschii Cosson Patropyrum tauschii Patropyrum tauschii subsp. tauschii Triticum tauschii Aegilops tauschii NCBITaxon:37690 A species of genus Citrus. Hardy orange Trifoliate orange Citrus trifoliatus Poncirus trifoliata Poncirus trifoliate Poncirus trifoliatus Citrus trifoliata NCBITaxon:3818 A species of genus Arachis. Goober Ground-nut Peanut Arachis hypogea Arachis hypogaea NCBITaxon:3847 A species of genus Glycine. Soybean Glycine max; cv. Wye Glycine max NCBITaxon:3848 A species of genus Glycine. Wild soybean Glycine soja NCBITaxon:3880 A species of genus Medicago. Barrel medic Medicago truncatula NCBITaxon:3885 A species of genus Phaseolus. French bean Kidney bean String bean Phaseolus vulgaris NCBITaxon:38869 A species of genus Salvia. Clary Salvia sclarea L. Salvia sclarea NCBITaxon:3917 A species of genus Vigna. Cowpea Phaseolus unguiculatus Vigna unguiculata NCBITaxon:3981 A species of genus Hevea. Jebe Para rubber tree Rubbertree Siringa Hevea brasiliensis (Willd. ex A.Juss.) Muell. Arg. Hevea brasiliensis NCBITaxon:3983 A species of genus Manihot. Cassava Manioc Tapioca Yuca Manihot esculenta Crantz Manihot esculenta0 Manihot utilissima Manihot esculenta NCBITaxon:3988 A species of genus Ricinus. Castor bean Ricimus communis Ricinis communis Ricinus communis L. Ricinus comunis Ricinus sanguineus Ricinus sanguineus hort. ex Groenl. Ricinus communis NCBITaxon:39984 A species of genus Bruguiera. Burma mangrove Bruguiera gymnorhiza (L.) Savigny Bruguiera gymnorrhiza Bruguiera gymnorrhizza Bruguiera gymnorhiza NCBITaxon:400408 A species of genus Helianthus. Helianthus exilis A.Gray Helianthus exilis NCBITaxon:4006 A species of genus Linum. Linum usitatissimum L. Linum usitatissimum NCBITaxon:400682 A species of genus Amphimedon. Reniera sp. JGI-2005 Amphimedon queenslandica NCBITaxon:4054 A species of genus Panax. Chinese ginseng Korean ginseng ginseng hong shen insam ninjin ren seng Panax ginseng NCBITaxon:40674 A class of phylum Chordata. Mammalia NCBITaxon:4081 A species of genus Solanum. Tomato Lycopersicon esculentum Lycopersicon esculentum Mill. Lycopersicon esculentum var. esculentum Lycopersicon lycopersicum Lycopersicum esculentum Solanum esculentum Solanum esculentum Dunal Solanum lycopersicon Solanum lycopersicum L. Solanum lycopersicum NCBITaxon:4097 A species of genus Nicotiana. American tobacco Common tobacco Tobacco Nicotania tabacum Nicotiana tabacum var. Samsun Nicotiana tabacum NCBITaxon:4113 A species of genus Solanum. Potato Solanum tuberosum subsp. tuberosum Solanum tuberosum NCBITaxon:4164 A species of genus Digitalis. Common foxglove Digitalis purpurea L. Digitalis purpurea NCBITaxon:4232 A species of genus Helianthus. Common sunflower Helianthus annus Helianthus annuus8 Helianthus annuus NCBITaxon:4233 A species of genus Helianthus. Jerusalem artichoke Helianthus tuberosus L. Helianthus tuberosus NCBITaxon:4234 A species of genus Helianthus. Helianthus petiolaris Nutt. Helianthus petiolaris NCBITaxon:4265 A species of genus Cynara. Cardoon Wild artichoke Cynara cardunculus L. Cynara cardunculus NCBITaxon:433461 A species of genus Leucosolenia. Leucosolenia complicata NCBITaxon:439488 ssRNA virus NCBITaxon:44689 A species of genus Dictyostelium. Dictyostelium discoideum NCBITaxon:4513 A species of genus Hordeum. Barley Hordeum vulgare L. Horedum vulgare Hordeum vulgare NCBITaxon:4530 A species of genus Oryza. Red rice Rice Oryza sativa NCBITaxon:45351 A species of genus Nematostella. Starlet sea anemone Nematostella vectensis Stephenson, 1935 Nematostella vectensis NCBITaxon:45455 A dsDNA virus of family Herpesviridae. monkey B virus B virus Cercopithecid herpesvirus 1 Cercopithecine herpesvirus 1 Herpesvirus simiae Simian herpes B virus Simian herpesvirus B herpes B virus herpes virus B simian herpes B virus SHBV Macacine herpesvirus 4 NCBITaxon:4547 A species of genus Saccharum. Noble cane Sugarcane Saccharum officinarum NCBITaxon:4558 A species of genus Sorghum. Broomcorn Milo Sorghum Sorghum bicolor milo Sorghum saccharatum Sorghum vulgare Sorghum bicolor NCBITaxon:4565 A species of genus Triticum. Bread wheat Canadian hard winter wheat Common wheat Wheat Tricum aestivum Triticum aestivam Triticum aestivum subsp. aestivum Triticum aestivum8 Triticum vulgare Triticum aestivum NCBITaxon:4571 A species of genus Triticum. Cone wheat English wheat Poulard wheat Rivet wheat Triticum aethiopicum Triticum aethiopicum Jakubz. Triticum turgidum L. Triticum turgidum8 Triticum turgidum NCBITaxon:4577 A species of genus Zea. Maize Zea mays mays Zea mays var. japonica Zea mays NCBITaxon:4606 A species of genus Festuca. Tall fescue Festuca elatior Lolium arundinaceum Schedonorus arundinaceus Schedonorus phoenix Festuca arundinacea NCBITaxon:479058 A dsDNA virus of family Papillomaviridae. Bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1) Bandicoot papillomatosis carcinomatosis virus type 1 NCBITaxon:493803 A dsDNA virus of family Polyomaviridae. Merkel cell polyomavirus NCBITaxon:500654 A dsDNA virus of family Papillomaviridae. Bandicoot papillomatosis carcinomatosis virus type 2 NCBITaxon:50557 A class of phylum Arthropoda. Insecta NCBITaxon:51511 A species of genus Ciona. Ciona savignyi NCBITaxon:51953 A species of genus Elaeis. African oil palm Elaeis guineensis Jacq. Elaeis guineensis var. tenera Elaeis guineensis var. tenera (Oil palm) Elaeis guinensi Elaeis gunieensis Elaeis guineensis NCBITaxon:54126 A species of genus Pristionchus. Pristionchus pacificus NCBITaxon:554915 Amoebozoa NCBITaxon:58024 A subset of Embryophytes. Spermatophyta NCBITaxon:59689 A species of genus Arabidopsis. Lyrate rockcress Arabidopsis lyrata (L.) O'Kane & Al-Shehbaz Arabidopsis lyrata NCBITaxon:59729 A species of genus Taeniopygia. Zebra finch Poephila guttata Taenopygia guttata Taeniopygia guttata NCBITaxon:6040 A phylum of kingdom Animalia. Porifera NCBITaxon:6042 A class of phylum Porifera. Demospongiae NCBITaxon:6073 A phylum of kingdom Animalia. Cnidaria NCBITaxon:6074 A class of phylum Cnidaria. Hydrozoa NCBITaxon:6085 A species of genus Hydra. Hydra magnipapillata NCBITaxon:6101 A class of phylum Cnidaria. Anthozoa NCBITaxon:6157 A phylum of kingdom Animalia. Platyhelminthes NCBITaxon:61621 A species of genus Pygathrix. Black snub-nosed monkey Pygathrix bieti Rhinopithecus bieti NCBITaxon:6179 A subclass of phylum Platyhelminthes. Digenea NCBITaxon:6182 A species of genus Schistosoma. Schistosoma japonicum NCBITaxon:6183 A species of genus Schistosoma. Schistosoma mansoni NCBITaxon:6199 A class of phylum Platyhelminthes. Cestoda NCBITaxon:6210 A species of genus Echinococcus. Echinococcus granulosus (Batsch, 1786) Echinococcus granulosus G1 strain Echinococcus granulosus G2 strain Echinococcus granulosus G3 strain Echinococcus granulosus Tasmanian sheep strain Echinococcus granulosus buffalo strain Echinococcus granulosus s. s. Echinococcus granulosus sensu stricto Echinococcus granulosus sheep strain Echinococcus granulosus NCBITaxon:6211 A species of genus Echinococcus. Echinococcus multilocularis NCBITaxon:6217 A phylum of kingdom Animalia. Nemertea NCBITaxon:6221 A species of genus Cerebratulus. Milky ribbon worm Milky ribbon-worm Cerebratulus lacteus NCBITaxon:6231 A phylum of kingdom Animalia. Nematoda NCBITaxon:6233 A species of genus Panagrellus. Panagrellus redivivus NCBITaxon:6238 A species of genus Caenorhabditis. Caenorhabditis briggsae NCBITaxon:6239 A species of genus Caenorhabditis. Nematode Rhabditis elegans Caenorhabditis elegans NCBITaxon:6253 A species of genus Ascaris. Pig roundworm Ascaris suum NCBITaxon:6279 A species of genus Brugia. Agent of lymphatic filariasis Brugia malayi NCBITaxon:6289 A species of genus Haemonchus. Barber pole worm Red stomach worm Haemonchus contortus NCBITaxon:6340 A phylum of kingdom Animalia. Annelida NCBITaxon:6447 A phylum of kingdom Animalia. Mollusca NCBITaxon:6448 A class of phylum Mollusca. Gastropoda NCBITaxon:6454 A species of genus Haliotis. California red abalone Red abalone Haliotis rufescens NCBITaxon:6656 A phylum of kingdom Animalia. Arthropoda NCBITaxon:6658 A class of phylum Arthropoda. Branchiopoda NCBITaxon:6669 A species of genus Daphnia. Common water flea Daphnia pulex NCBITaxon:6681 A class of phylum Arthropoda. Malacostraca NCBITaxon:6854 A class of phylum Arthropoda. Arachnida NCBITaxon:69256 A dsDNA virus of family Herpesviridae. Macaca mulatta rhadinovirus 26-95 Rhesus monkey rhadinovirus H26-95 NCBITaxon:69293 A species of genus Gasterosteus. Three spined stickleback Three-spined stickleback Gasterosteus aculeatus Linnaeus, 1758 Gasterosteus aculeatus NCBITaxon:6941 A species of genus Rhipicephalus. Cattle tick Southern cattle tick Boophilus microplus Rhipicephalus (Boophilus) microplus Rhipicephalus microplus NCBITaxon:6945 A species of genus Ixodes. Black-legged tick Blacklegged tick Deer tick Shoulder tick Ixodes dammini Ixodes scapularis NCBITaxon:7004 A species of genus Locusta. Migratory locust Locusta migratoria NCBITaxon:7029 A species of genus Acyrthosiphon. Pea aphid Acyrthosiphum pisum Acyrthosiphon pisum NCBITaxon:7070 A species of genus Tribolium. Red flour beetle Rust-red flour beetle Tribolium castaneum NCBITaxon:707683 A species of genus Saccharum. Saccharum sp. NCBITaxon:7091 A species of genus Bombyx. Domestic silkworm Silk moth Silkworm Bombyx mori Linnaeus, 1758 Bombyx mori NCBITaxon:7130 A species of genus Manduca. Carolina sphinx Hornblower Tobacco hornworm Tomato hornworm Tobacco hawkmoth Manduca sexta NCBITaxon:7159 A species of genus Aedes. Yellow fever mosquito Stegomyia aegypti Aedes aegypti NCBITaxon:7165 A species of genus Anopheles. African malaria mosquito Anopheles gambiae sensu stricto Anopheles gambia Anopheles gambiae Giles, 1902 Anopheles gambiae NCBITaxon:7176 A species of genus Culex. Southern house mosquito Culex pipiens quinquefasciatus Culex pipiens quiquefasciatus Culex quinquifasciatus Culex quinquifasiatus Culex quiquefasciatus Culex quinquefasciatus NCBITaxon:7217 A species of genus Drosophila. Drosophila annanassae Drosophila ananassae NCBITaxon:7220 A species of genus Drosophila. Drosophila erecta NCBITaxon:7222 A species of genus Drosophila. Idiomyia grimshawi Drosophila grimshawi NCBITaxon:7227 A species of genus Drosophila. Fruit fly Drosophila melangaster Drosophila melanogaster NCBITaxon:7230 A species of genus Drosophila. Drosophila mohavensis Drosophila mojavensis NCBITaxon:7234 A species of genus Drosophila. Drosophila persimilis NCBITaxon:7237 A species of genus Drosophila. Drosophila pseudoobscura NCBITaxon:7238 A species of genus Drosophila. Drosophila sechellia Tsacas and Bachli, 1981 Drosophila sechellia NCBITaxon:7240 A species of genus Drosophila. Drosophila simulans NCBITaxon:7244 A species of genus Drosophila. Drosophila irilis Drosophila virilis Sturtevant, 1916 Drosophila virilis NCBITaxon:7245 A species of genus Drosophila. Drosophila yakuba NCBITaxon:7260 A species of genus Drosophila. Drosophila willistoni NCBITaxon:73275 A species of genus Helianthus. Helianthus argophyllus Torr. & A.Gray Helianthus argophyllus NCBITaxon:73280 A species of genus Helianthus. Helianthus cilaris Helianthus ciliaris DC. Helianthus ciliaris NCBITaxon:73304 A species of genus Helianthus. Helianthus paradoxus Heiser Helianthus paradoxus NCBITaxon:73382 A species of genus Capitella. Capitella sp. 1 NCBITaxon:7425 A species of genus Nasonia. Jewel wasp Nasonia vitripennis (Walker, 1836) Nasonia vitripennis NCBITaxon:7426 A species of genus Nasonia. Nasonia giraulti NCBITaxon:7427 A species of genus Nasonia. Nasonia lonigicornis Nasonia longicornis NCBITaxon:7460 A species of genus Apis. Bee Honey bee Honeybee Apis mellifica Apis mellifera NCBITaxon:7540 A class of phylum Arthropoda. Chilopoda NCBITaxon:7568 A phylum of kingdom Animalia. Brachiopoda NCBITaxon:75702 A species of genus Populus. Popolus euphratica Populus diversifolia Populus euphratica NCBITaxon:7580 A species of genus Terebratulina. Terebratulina retusa NCBITaxon:7586 A phylum of kingdom Animalia. Echinodermata NCBITaxon:7625 A class of phylum Echinodermata. Echinoidea NCBITaxon:7668 A species of genus Strongylocentrotus. Purple sea urchin Purple urchin Strongylocentrotus purpuratus (Stimpson, 1857) Strongylocentrotus purpuratus NCBITaxon:7711 A phylum of kingdom Animalia. Chordata NCBITaxon:7713 A class of phylum Chordata. Ascidiacea NCBITaxon:7719 A species of genus Ciona. Ciona intestinalis NCBITaxon:7736 A class of phylum Chordata. Leptocardii Branchiostomidae NCBITaxon:7739 A species of genus Branchiostoma. Florida lancelet Amphioxus floridae Branchiostoma floridea Branchiostoma floridae NCBITaxon:7741 A species of genus Branchiostoma. Belcher's lancelet Branchiostoma belcheri NCBITaxon:7746 A class of phylum Chordata. Petromyzontidae NCBITaxon:7757 A species of genus Petromyzon. Marine lamprey Sea lamprey Petromyzon marinus NCBITaxon:78454 A species of genus Saguinus. Red-chested mustached tamarin Saguinus labiatus NCBITaxon:7898 A class of phylum Chordata. Actinopterygii NCBITaxon:79327 A species of genus Schmidtea. Freshwater planarian Dugesia (Schmidtea) mediterranea Dugesia mediterranea Schmidtea mediterranea NCBITaxon:7955 A species of genus Danio. Leopard danio Zebra danio Zebra fish Zebrafish Brachidanio rerio Brachydanio rerio Brachydanio rerio frankei Cyprinus rerio Cyprinus rerio Hamilton, 1822 Danio frankei Danio rerio (Hamilton, 1822) Danio rerio frankei Danio rerio NCBITaxon:7962 A species of genus Cyprinus. Carp Common carp Cyprinus cyprio Cyrpinus carpio Cyprinus carpio NCBITaxon:7998 A species of genus Ictalurus. Channel catfish Ictalurus punctatus (Rafinesque, 1818) Silurus punctatus Ictalurus punctatus NCBITaxon:8090 A species of genus Oryzias. Japanese medaka Japanese rice fish Medaka Oryzias latipes NCBITaxon:8255 A species of genus Paralichthys. Bastard halibut False halibut Japanese flounder Olive flounder Paralichthyidae sp. KYJ-2011 Hippoglossus olivaceus Paralichthys olivaceous Paralichthys olivaceus (Temminck & Schlegel, 1846) Paralichtys olivaceus Paralichthys olivaceus NCBITaxon:8267 A species of genus Hippoglossus. Atlantic halibut Hippoglossus hippoglossus (Linnaeus, 1758) Hippoglossus hippoglossus NCBITaxon:8292 A class of phylum Chordata. Amphibia NCBITaxon:82927 A species of genus Avicennia. Avicennia marina NCBITaxon:8355 A species of genus Xenopus. African clawed frog Clawed frog Common platanna Platanna Bufo laevis Xenopus laevis (Daudin, 1802) Xenopus leavis Xenopus laevis NCBITaxon:8364 A species of genus Xenopus. Western clawed frog Silurana tropicalis Xenopus laevis tropicalis Xenopus tropicalis Xenopus (Silurana) tropicalis NCBITaxon:85571 A species of genus Citrus. Mandarin orange Tangerine Citrus poonensis Citrus reticulata NCBITaxon:85681 A species of genus Citrus. Citrus clementina hort. ex Tanaka Citrus clementina NCBITaxon:8782 A class of phylum Chordata. Aves NCBITaxon:88036 A species of genus Selaginella. Selaginella moellendorffii Hieron Selaginella moellendorfii Selaginella moellendorffii NCBITaxon:9031 A species of genus Gallus. Bantam Chicken Chickens Gallus domesticus Gallus gallus domesticus Gallus gallus NCBITaxon:9258 A species of genus Ornithorhynchus. Duck-billed platypus Duckbill platypus Platypus Ornythorhynchus anatinus Ornithorhynchus anatinus NCBITaxon:9305 A species of genus Sarcophilus. Tasmanian devil Sarcophilus laniarius Sarcophilus harrisii NCBITaxon:9315 A species of genus Macropus. Tammar wallaby Macropus eugenii NCBITaxon:9417 A species of genus Artibeus. GC_ID:1 Jamaican fruit-eating bat Artibeus jamaicensis NCBITaxon:9447 A species of genus Lemur. Ring-tailed lemur Lemur catta NCBITaxon:9509 A species of genus Ateles. Black-handed spider monkey Central American spider monkey Ateles geoffreyi Ateles jeoffroyi Ateles geoffroyi NCBITaxon:9519 A species of genus Lagothrix. Brown woolly monkey Common woolly monkey Humboldt's woolly monkey Lagothrix lagothricha Lagothrix lagotricha lagotricha Lagothrix lagotricha NCBITaxon:9544 A species of genus Macaca. Rhesus macaque Rhesus monkey Macaca mulatta NCBITaxon:9545 A species of genus Macaca. Pig-tailed macaque Pigtail macaque Pigtail monkey Macaca nemestrina NCBITaxon:9590 A species of genus Symphalangus. Siamang Hylobates syndactylus Symphalangus syndactylus NCBITaxon:9593 A species of genus Gorilla. Gorilla Western gorilla Gorilla gorilla NCBITaxon:9597 A species of genus Pan. Bonobo Pygmy chimpanzee Pan paniscus NCBITaxon:9598 A species of genus Pan. Chimpanzee Chimpansee troglodytes Pan troglodytes NCBITaxon:9600 A species of genus Pongo. Bornean orangutan Orang utan Orang-utan Orangutan Pongo pygmaeus NCBITaxon:9606 A species of genus Homo. Human Man Homo sapiens NCBITaxon:9615 A species of genus Canis. Dog Canis canis Canis domesticus Canis familiaris Canis lupus familiaris NCBITaxon:9796 A species of genus Equus. Domestic horse Equine Horse Equus ferus caballus Equus przewalskii f. caballus Equus przewalskii forma caballus Equus caballus NCBITaxon:9823 A species of genus Sus. Pig Swine Wild boar Sus scrofus Sus scrofa NCBITaxon:9913 A species of genus Bos. Bovine Cattle Cow Domestic cattle Domestic cow Bos bovis Bos primigenius taurus Bos tauurus Bos taurus NCBITaxon:99300 A species of genus Rehmannia. Chinese foxglove Rehmannia glutinosa NCBITaxon:9940 A species of genus Ovis. Domestic sheep Lambs Sheep Wild sheep Ovis ammon aries Ovis orientalis aries Ovis ovis Ovis aries NCBITaxon:99883 A species of genus Tetraodon. Spotted green pufferfish Tetraodon nigroviridis Marion de Proce, 1822 Tetraodon nigroviridis OBI:0100026 A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. OBI:0100026 Organism OGMS:0000031 A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. IDO:Disease Disease RNAO:0000095 A collection of one or more adjacent nucleotide residues in which at least one residue is part of a base pair. RNAO:0000095 Paired Region RNAO:0000096 A collection of one or more nucleotides that are not involved in base pairing. RNAO:0000096 Unpaired Region RNAO:0000097 A paired region made up of two contiguous collections of nucleotides, in which each nucleotide forms a base pair. [RNAO:0000097] RNAO:0000097 Unbroken Stem RNAO:0000098 A contiguous sequence of nucleotide residues that directly links the two halves of an unbroken stem (but does not participate in the stem); this structure is also known as a "hairpin loop". Because a terminal loop may also participate in other inter-base interactions, (a) it is defined relative to a particular unbroken_stem, and (b) it is not implicitly defined as unpaired (or paired). [RNAO:0000098] RNAO:0000098 Terminal Loop RNAO:0000099 A collection of nucleotide residues that link two given unbroken_stems. RNAO:0000099 Internal Loop RNAO:0000106 A collection of nucleotide residues consisting of all and only the nucleotide regions that link more than two unbroken stems such that each region links exactly two unbroken stems. This term is defined relative to the particular unbroken_stems involved and, again, does not imply anything about the pairedness/unpairedness of the bases in this region. The degree of a junction is a property (e.g. 3-junction, 4-junction), so the different degrees do not get separate entries in the ontology. RNAO:0000106 Stem Junction RNAO:0000107 A sequence_region bounded at one end by the 5' or 3' end of the molecule, and at the other by an unbroken_stem. [RNAO:0000107] RNAO:0000107 Strand End RNAO:0000108 A collection of nucleotide residues is a part of a nucleic acid consisting of one or more nucleotides. RNAO:0000108 Collection of Nucleotides Residues RNAO:0000110 Collection of Material Entities SO:0000001 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:0000001 Region SO:0000004 Interior Coding Exon SO:0000012 The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote. SO:0000012 scRNA Primary Transcript SO:0000013 Any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote. SO:0000013 scRNA SO:0000035 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. SO:0000035 Riboswitch SO:0000078 A transcript that is polycistronic. SO:0000078 Polycistronic Transcript SO:0000108 An mRNA with a frameshift. SO:0000108 mRNA with Frameshift SO:0000118 A transcript with a translational frameshift. SO:0000118 Transcript with Translational Frameshift SO:0000120 A primary transcript that, at least in part, encodes one or more proteins. SO:0000120 Protein Coding Primary Transcript SO:0000122 A folded RNA sequence. SO:0000122 RNA Sequence Secondary Structure SO:0000139 Region in mRNA where ribosome assembles. SO:0000139 Ribosome Entry Site SO:0000142 A folded DNA sequence. SO:0000142 DNA Sequence Secondary Structure SO:0000145 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:0000145 Recoded Codon SO:0000147 A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. SO:0000147 Exon SO:0000162 Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. SO:0000162 Splice Site SO:0000163 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. SO:0000163 5' cis Splice Site SO:0000164 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. SO:0000164 3' cis Splice Site SO:0000184 A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs. SO:0000184 U2 Intron SO:0000185 A transcript that in its initial state requires modification to be functional. SO:0000185 Primary Transcript SO:0000188 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. SO:0000188 Intron SO:0000190 5' Intron SO:0000191 Interior Intron SO:0000192 3' Intron SO:0000195 An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon). SO:0000195 Coding Exon SO:0000196 The sequence of the five_prime_coding_exon that codes for protein. SO:0000196 Five Prime Coding Exon Coding Region SO:0000197 The sequence of the three_prime_coding_exon that codes for protein. SO:0000197 Three Prime Coding Exon Coding Region SO:0000198 An exon that does not contain any codons. SO:0000198 Noncoding Exon SO:0000200 The 5' most coding exon. SO:0000200 Five Prime Coding Exon SO:0000201 An exon that is bounded by 5' and 3' splice sites. SO:0000201 Interior Exon SO:0000202 The coding exon that is most 3-prime on a given transcript. SO:0000202 Three Prime Coding Exon SO:0000203 Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. SO:0000203 UTR SO:0000204 A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein. SO:0000204 Five Prime UTR SO:0000205 A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein. SO:0000205 Three Prime UTR SO:0000209 A primary transcript encoding a ribosomal RNA. SO:0000209 rRNA Primary Transcript SO:0000210 A primary transcript encoding a transfer RNA. SO:0000210 tRNA Primary Transcript SO:0000211 A primary transcript encoding alanyl tRNA. SO:0000211 Alanine tRNA Primary Transcript SO:0000212 A primary transcript encoding arginyl tRNA. SO:0000212 Arginine tRNA Primary Transcript SO:0000213 A primary transcript encoding asparaginyl tRNA. SO:0000213 Asparagine tRNA Primary Transcript SO:0000214 A primary transcript encoding aspartyl tRNA. SO:0000214 Aspartic acid tRNA Primary Transcript SO:0000215 A primary transcript encoding cysteinyl tRNA. SO:0000215 Cysteine tRNA Primary Transcript SO:0000216 A primary transcript encoding glutaminyl tRNA. SO:0000216 Glutamic acid tRNA Primary Transcript SO:0000217 A primary transcript encoding glutamyl tRNA. SO:0000217 Glutamine tRNA Primary Transcript SO:0000218 A primary transcript encoding glycyl tRNA. SO:0000218 Glycine tRNA Primary Transcript SO:0000219 A primary transcript encoding histidyl tRNA. SO:0000219 Histidine tRNA Primary Transcript SO:0000220 A primary transcript encoding isoleucyl tRNA. SO:0000220 Isoleucine tRNA Primary Transcript SO:0000221 A primary transcript encoding leucyl tRNA. SO:0000221 Leucine tRNA Primary Transcript SO:0000222 A primary transcript encoding lysyl tRNA. SO:0000222 Lysine tRNA Primary Transcript SO:0000223 A primary transcript encoding methionyl tRNA. SO:0000223 Methionine tRNA Primary Transcript SO:0000224 A primary transcript encoding phenylalanyl tRNA. SO:0000224 Phenylalanine tRNA Primary Transcript SO:0000225 A primary transcript encoding prolyl tRNA. SO:0000225 Proline tRNA Primary Transcript SO:0000226 A primary transcript encoding seryl tRNA. SO:0000226 Serine tRNA Primary Transcript SO:0000227 A primary transcript encoding threonyl tRNA. SO:0000227 Threonine tRNA Primary Transcript SO:0000228 A primary transcript encoding tryptophanyl tRNA. SO:0000228 Tryptophan tRNA Primary Transcript SO:0000229 A primary transcript encoding tyrosyl tRNA. SO:0000229 Tyrosine tRNA Primary Transcript SO:0000230 A primary transcript encoding valyl tRNA. SO:0000230 Valine tRNA Primary Transcript SO:0000231 A primary transcript encoding a small nuclear RNA. SO:0000231 snRNA Primary Transcript SO:0000232 A primary transcript encoding a small nucleolar mRNA. SO:0000232 snoRNA Primary Transcript SO:0000233 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:0000233 Mature Transcript SO:0000234 Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. SO:0000234 mRNA SO:0000235 A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex. SO:0000235 Transcription Factor Binding Site SO:0000241 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:0000241 Internal UTR SO:0000242 The untranslated sequence separating the 'cistrons' of multicistronic mRNA. SO:0000242 Untranslated Region Polycistronic mRNA SO:0000243 Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation. SO:0000243 Internal Ribosome Entry Site SO:0000252 RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. SO:0000252 rRNA SO:0000253 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. SO:0000253 tRNA SO:0000254 A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region. SO:0000254 Alanyl tRNA SO:0000255 A primary transcript encoding a small ribosomal subunit RNA. SO:0000255 rRNA Small Subunit Primary Transcript SO:0000256 A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region. SO:0000256 Asparaginyl tRNA SO:0000257 A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region. SO:0000257 Aspartyl tRNA SO:0000258 A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region. SO:0000258 Cysteinyl tRNA SO:0000259 A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region. SO:0000259 Glutaminyl tRNA SO:0000260 A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region. SO:0000260 Glutamyl tRNA SO:0000261 A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region. SO:0000261 Glycyl tRNA SO:0000262 A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region. SO:0000262 Histidyl tRNA SO:0000263 A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region. SO:0000263 Isoleucyl tRNA SO:0000264 A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region. SO:0000264 Leucyl tRNA SO:0000265 A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region. SO:0000265 Lysyl tRNA SO:0000266 A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region. SO:0000266 Methionyl tRNA SO:0000267 A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region. SO:0000267 Phenylalanyl tRNA SO:0000268 A tRNA sequence that has a proline anticodon, and a 3' proline binding region. SO:0000268 Prolyl tRNA SO:0000269 A tRNA sequence that has a serine anticodon, and a 3' serine binding region. SO:0000269 Seryl tRNA SO:0000270 A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region. SO:0000270 Threonyl tRNA SO:0000271 A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region. SO:0000271 Tryptophanyl tRNA SO:0000272 A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region. SO:0000272 Tyrosyl tRNA SO:0000273 A tRNA sequence that has a valine anticodon, and a 3' valine binding region. SO:0000273 Valyl tRNA SO:0000274 A small nuclear RNA molecule involved in pre-mRNA splicing and processing. SO:0000274 snRNA SO:0000275 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. SO:0000275 snoRNA SO:0000276 Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules 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. SO:0000276 miRNA SO:0000278 A transcript that is bound by a nucleic acid. SO:0000278 Transcript Bound by Nucleic Acid SO:0000279 A transcript that is bound by a protein. SO:0000279 Transcript Bound by Protein SO:0000282 An mRNA with a minus 1 frameshift. SO:0000282 mRNA with Minus 1 Frameshift SO:0000295 A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs. SO:0000295 U12 Intron SO:0000303 Part of the primary transcript that is clipped off during processing. SO:0000303 Clip SO:0000315 The first base where RNA polymerase begins to synthesize the RNA transcript. SO:0000315 TSS SO:0000316 A contiguous sequence which begins with, and includes, a start codon, and ends with, and includes, a stop codon. SO:0000316 CDS SO:0000318 First codon to be translated by a ribosome. SO:0000318 Start Codon SO:0000319 In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. SO:0000319 Stop Codon SO:0000320 Sequences within the intron that modulate splice site selection for some introns. SO:0000320 Intronic Splice Enhancer SO:0000321 An mRNA with a plus 1 frameshift. SO:0000321 mRNA with Plus 1 Frameshift SO:0000323 The first base to be translated into a protein. SO:0000323 Coding Start SO:0000325 A primary transcript encoding a large ribosomal subunit RNA. SO:0000325 rRNA Large Subunit Primary Transcript SO:0000327 The last base to be translated into protein. It does not include the stop codon. SO:0000327 Coding End SO:0000335 A mRNA with a minus 2 frameshift. SO:0000335 mRNA with Minus 2 Frameshift SO:0000360 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. SO:0000360 Codon SO:0000370 A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression. SO:0000370 Small Regulatory ncRNA SO:0000372 An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. SO:0000372 Enzymatic RNA SO:0000374 An RNA with catalytic activity. SO:0000374 Ribozyme SO:0000375 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. SO:0000375 rRNA 5_8S SO:0000376 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. SO:0000376 RNA 6S SO:0000377 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. SO:0000377 CsrB RsmB RNA SO:0000378 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. SO:0000378 DsrA RNA SO:0000379 A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. SO:0000379 GcvB RNA SO:0000381 Group IIA Intron SO:0000382 Group IIB Intron SO:0000383 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. SO:0000383 MicF RNA SO:0000384 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. SO:0000384 OxyS RNA SO:0000385 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. SO:0000385 RNase MRP RNA SO:0000386 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. SO:0000386 RNase P RNA SO:0000387 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. SO:0000387 RprA RNA SO:0000388 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. SO:0000388 RRE RNA SO:0000389 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. SO:0000389 Spot 42 RNA SO:0000390 The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. SO:0000390 Telomerase RNA SO:0000391 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. SO:0000391 U1 snRNA SO:0000392 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. SO:0000392 U2 snRNA SO:0000393 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. SO:0000393 U4 snRNA SO:0000394 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:0000394 U4atac snRNA SO:0000395 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. SO:0000395 U5 snRNA SO:0000396 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. SO:0000396 U6 snRNA SO:0000397 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:0000397 U6atac snRNA SO:0000398 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. SO:0000398 U11 snRNA SO:0000399 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. SO:0000399 U12 snRNA SO:0000403 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. SO:0000403 U14 snoRNA SO:0000404 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. SO:0000404 Vault RNA SO:0000405 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. SO:0000405 Y RNA SO:0000406 An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed. SO:0000406 Twintron SO:0000407 A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome. SO:0000407 rRNA 18S SO:0000409 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. SO:0000409 Binding Site SO:0000410 A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. SO:0000410 Protein Binding SIte SO:0000444 Non-coding exon in the 3' UTR. SO:0000444 Three Prime Noncoding Exon SO:0000445 Non-coding exon in the 5' UTR. SO:0000445 Five Prime Noncoding Exon SO:0000446 Intron located in the untranslated region. SO:0000446 UTR Intron SO:0000447 An intron located in the 5' UTR. SO:0000447 5' UTR Intron SO:0000448 An intron located in the 3' UTR. SO:0000448 3' UTR Intron SO:0000454 A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. SO:0000454 rasiRNA SO:0000479 A transcript that is trans-spliced. SO:0000479 Trans-spliced Transcript SO:0000483 A primary transcript that is never translated into a protein. SO:0000483 Noncoding Primary Transcript SO:0000484 The sequence of the 3' exon that is not coding. SO:0000484 Three Prime Coding Exon Noncoding Region SO:0000486 The sequence of the 5' exon preceding the start codon. SO:0000486 Five Prime Coding Exon Noncoding Region SO:0000552 A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex. SO:0000552 Shine Dalgarno Sequence SO:0000555 5' most region of a precursor transcript that is clipped off during processing. SO:0000555 5' Clip SO:0000557 3'-most region of a precursor transcript that is clipped off during processing. SO:0000557 3' Clip SO:0000579 A locatable feature on a transcript that is edited. SO:0000579 Edited Transcript Feature SO:0000580 A primary transcript encoding a methylation guide small nucleolar RNA. SO:0000580 Methylation Guide snoRNA Primary Transcript SO:0000582 A primary transcript encoding an rRNA cleavage snoRNA. SO:0000582 rRNA cleavage snoRNA Primary Transcript SO:0000583 The region of a transcript that will be edited. SO:0000583 Pre-edited Region SO:0000584 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. SO:0000584 tmRNA SO:0000586 A primary transcript encoding a tmRNA. SO:0000584 tmRNA Primary Transcript SO:0000587 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. SO:0000587 Group I Intron SO:0000588 A self spliced intron. SO:0000588 Autocatalutically Spliced Intron SO:0000589 A primary transcript encoding a signal recognition particle RNA. SO:0000589 SRP RNA Primary Transcript SO:0000590 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. SO:0000590 SRP RNA SO:0000593 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'. SO:0000593 C/D Box snoRNA SO:0000594 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. SO:0000594 H/ACA Box snoRNA SO:0000595 A primary transcript encoding a small nucleolar RNA of the box C/D family. SO:0000595 C/D Box snoRNA Primary Transcript SO:0000596 A primary transcript encoding a small nucleolar RNA of the box H/ACA family. SO:0000596 H/ACA Box snoRNA Primary Transcript SO:0000602 A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail) with a stretch of mature edited mRNA. SO:0000602 Guide RNA SO:0000603 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. SO:0000603 Group II Intron SO:0000604 Edited mRNA sequence mediated by a single guide RNA (SO:0000602). SO:0000604 Editing Block SO:0000606 Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602). SO:0000606 Editing Domain SO:0000607 The region of an edited transcript that will not be edited. SO:0000607 Unedited Region SO:0000611 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:0000611 Branch Site SO:0000612 The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. SO:0000612 Polypirimidine Tract SO:0000616 The base where transcription ends. SO:0000616 Transcription End Site SO:0000629 Five Prime Open Reading Frame SO:0000630 A start codon upstream of the ORF. SO:0000630 Upstream AUG Codon SO:0000631 A primary transcript encoding for more than one gene product. SO:0000631 Polycistronic Primary Transcript SO:0000632 A primary transcript encoding for one gene product. SO:0000632 Monocistronic Primary Transcript SO:0000633 An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap. SO:0000633 Monocistronic mRNA SO:0000634 An mRNA that encodes multiple proteins from at least two non-overlapping regions. SO:0000634 Polycistronic mRNA SO:0000635 A primary transcript that donates the spliced leader to other mRNA. SO:0000635 Mini Exon Donor RNA SO:0000636 Spliced Leader RNA SO:0000638 Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA. SO:0000638 Transcribed Spacer Region SO:0000639 Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs. SO:0000639 Internal Transcribed Spacer Region SO:0000640 Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA. SO:0000640 External Transcribed Spacer Region SO:0000644 Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. SO:0000644 Antisense RNA SO:0000645 The reverse complement of the primary transcript. SO:0000645 Antisense Primary Transcript SO:0000646 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. SO:0000646 siRNA SO:0000647 A primary transcript encoding a micro RNA. SO:0000647 pri-miRNA SO:0000648 A primary transcript encoding a small temporal mRNA. SO:0000648 stRNA Primary Transcript SO:0000649 Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans. [SO:0000649] SO:0000649 stRNA SO:0000650 Ribosomal RNA transcript that structures the small subunit of the ribosome. SO:0000650 Small Subunit rRNA SO:0000651 Ribosomal RNA transcript that structures the large subunit of the ribosome. SO:0000651 Large Subunit rRNA SO:0000652 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. SO:0000652 rRNA 5S SO:0000653 A component of the large ribosomal subunit. SO:0000653 rRNA 28S SO:0000655 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. SO:0000655 ncRNA SO:0000662 An intron which is spliced by the spliceosome. SO:0000662 Spliceosomal Intron SO:0000665 A transcript that is monocistronic. SO:0000665 Monocistronic Transcript SO:0000666 An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility. SO:0000666 Mobile Intron SO:0000673 An RNA synthesized on a DNA or RNA template by an RNA polymerase. SO:0000673 Transcript SO:0000676 The canonical 3' splice site has the sequence "AG". SO:0000676 Canonical 3' Splice Site SO:0000677 The canonical 5' splice site has the sequence "GT". SO:0000677 Canonical 5' Splice Site SO:0000678 A 3' splice site that does not have the sequence "AG". SO:0000678 Non-canonical 3' Splice Site SO:0000679 A 5' splice site which does not have the sequence "GT". SO:0000679 Non-canonical 5' Splice SIte SO:0000680 A start codon that is not the usual AUG sequence. SO:0000680 Non-canonical Start Codon SO:0000681 A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons. SO:0000681 Aberrant Processed Transcript SO:0000694 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:0000694 SNP SO:0000704 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:0000704 Gene SO:0000706 The 3' splice site of the acceptor primary transcript. SO:0000706 Trans Splice Acceptor Site SO:0000707 The 5' five prime splice site region of the donor RNA. SO:0000707 Trans Splice Donor Site SO:0000708 A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs. SO:0000708 SL1 Acceptor Site SO:0000709 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:0000709 SL2 Acceptor Site SO:0000716 An mRNA that has the quality dicistronic. SO:0000716 Dicistronic mRNA SO:0000734 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. SO:0000734 Exemplar mRNA SO:0000766 A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region. SO:0000766 Pyrrolysyl tRNA SO:0000769 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. SO:0000769 tmRNA Coding Piece SO:0000770 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. SO:0000770 tmRNA Acceptor Piece SO:0000833 A region of a transcript. SO:0000833 Transcript Region SO:0000834 A region of a mature transcript. SO:0000834 Mature Transcript Region SO:0000835 A part of a primary transcript. SO:0000835 Primary Transcript Region SO:0000836 A region of an mRNA. SO:0000836 mRNA Region SO:0000837 A region of UTR. SO:0000837 UTR Region SO:0000838 A region of an rRNA primary transcript. SO:0000838 rRNA Primary Transcript Region SO:0000841 A region within an intron. SO:0000841 Spliceosomal Intron Region SO:0000847 A region of a tmRNA. SO:0000847 tmRNA Region SO:0000851 A region of a CDS. SO:0000851 CDS Region SO:0000852 A region of an exon. SO:0000852 Exon Region SO:0000861 A primary transcript that is capped. SO:0000861 Capped Primary Transcript SO:0000862 An mRNA that is capped. SO:0000862 Capped mRNA SO:0000871 An mRNA that is polyadenylated. SO:0000871 Polyadenylated mRNA SO:0000872 An mRNA that is trans-spliced. SO:0000872 Trans Spliced mRNA SO:0000873 A transcript that is edited. SO:0000873 Edited Transcript SO:0000874 A transcript that has been edited by A to I substitution. SO:0000874 Edited Transcript by A to I Substitution SO:0000883 A stop codon redefined to be a new amino acid. SO:0000883 Stop Codon Read Through SO:0000884 A stop codon redefined to be the new amino acid, pyrrolysine. SO:0000884 Stop Codon Redefined as Pyrrolysine SO:0000885 A stop codon redefined to be the new amino acid, selenocysteine. SO:0000885 Stop Codon Redefined as Selenocysteine SO:0000929 An mRNA that is edited. SO:0000929 Edited mRNA SO:0000930 A region of guide RNA. SO:0000930 Guide RNA Region SO:0000931 A region of a guide_RNA that base-pairs to a target mRNA. SO:0000931 Anchor Region SO:0000932 pre-edited mRNA SO:0000934 A miRNA target site is a binding site where the molecule is a micro RNA. SO:0000934 miRNA Target Site SO:0000935 A CDS that is edited. SO:0000935 Edited CDS SO:0000977 Anchor Binding Site SO:0000978 A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA. SO:0000978 Template Region SO:0000989 Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. SO:0000989 Class II RNA SO:0000990 Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. SO:0000990 Class I RNA SO:0000995 Consensus mRNA SO:0000998 A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons. SO:0000998 Recursive Splice Site SO:0001000 A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome. SO:0001000 rRNA 16S SO:0001001 A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome. SO:0001001 rRNA 23S SO:0001002 A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes. SO:0001002 rRNA 25S SO:0001014 Intron Domain SO:0001016 A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity. SO:0001016 Internal Guide Sequence SO:0001034 A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage. SO:0001034 Mirtron SO:0001035 A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements. SO:0001035 piRNA SO:0001036 A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region. SO:0001036 Arginyl tRNA SO:0001171 A component of the large ribosomal subunit in mitochondrial rRNA. SO:0001171 rRNA 21S SO:0001172 A region of a tRNA. SO:0001172 tRNA Region SO:0001173 A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3. SO:0001173 Anticodon Loop SO:0001174 A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA. SO:0001174 Anticodon SO:0001175 Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid. SO:0001175 CCA Tail SO:0001176 Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues. SO:0001176 DHU Loop SO:0001177 Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C. SO:0001177 T Loop SO:0001178 A primary transcript encoding pyrrolysyl tRNA. SO:0001178 Pyrrolysine tRNA Primary Transcript SO:0001179 U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. SO:0001179 U3 snoRNA SO:0001180 A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable. SO:0001180 AU Rich Element SO:0001181 A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs. SO:0001181 Bruno Response Element SO:0001182 A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins. SO:0001182 Iron Responsive Element SO:0001187 A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue. SO:0001187 Pseudouridylation Guide snoRNA SO:0001210 The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. SO:0001210 Translational Frameshift SO:0001211 The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. SO:0001211 Plus 1 Translational Frameshift SO:0001212 The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. SO:0001212 Plus 2 Translational Frameshift SO:0001213 Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile. SO:0001213 Group III Intron SO:0001214 The maximal intersection of exon and UTR. SO:0001214 Noncoding Region of Exon SO:0001215 The region of an exon that encodes for protein sequence. SO:0001215 Coding Region of Exon SO:0001216 An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification. SO:0001216 Endonuclease Spliced Intron SO:0001238 Major TSS SO:0001239 Minor TSS SO:0001243 A part of an miRNA primary_transcript. SO:0001243 miRNA Primary Transcript Region SO:0001244 The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure. SO:0001244 pre-miRNA SO:0001245 The stem of the hairpin loop formed by folding of the pre-miRNA. SO:0001245 miRNA Stem SO:0001246 The loop of the hairpin loop formed by folding of the pre-miRNA. SO:0001246 miRNA Loop SO:0001384 CDS Fragment SO:0001411 A region defined by its disposition to be involved in a biological process. SO:0001411 Biological Region SO:0001419 Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. SO:0001419 cis Splice Site SO:0001420 Primary transcript region bordering trans-splice junction. SO:0001420 Trans Splice Site SO:0001429 A binding site that, in the molecule, interacts selectively and non-covalently with DNA. SO:0001429 DNA Binding SIte SO:0001463 A multiexonic non-coding RNA transcribed by RNA polymerase II. SO:0001463 Linc RNA SO:0001473 A region of the pri miRNA that basepairs with the guide to form the hairpin. SO:0001473 miRNA Antiguide SO:0001475 A region of a primary transcript, that is removed via trans splicing. SO:0001475 Outron SO:0001483 SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. SO:0001483 SNV SO:0001503 A transcript for which no open reading frame has been identified and for which no other function has been determined. SO:0001503 Processed Transcript SO:0001533 A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error. SO:0001533 Cryptic Splice SIte SO:0001647 A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence. SO:0001647 Kozak Sequence SO:0001654 A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. SO:0001654 Nucleotide to Protein Binding Site SO:0001655 A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues. SO:0001655 Nucleotide Binding Site SO:0001748 A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001748 SL3 Acceptor Site SO:0001749 A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001749 SL4 Acceptor Site SO:0001750 A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001750 SL5 Acceptor Site SO:0001751 A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001751 SL6 Acceptor Site SO:0001752 A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001752 SL7 Acceptor Site SO:0001753 A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001753 SL8 Acceptor Site SO:0001754 A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001754 SL9 Acceptor Site SO:0001755 A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001755 SL10 Acceptor Site SO:0001756 A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001756 SL11 Acceptor Site SO:0001757 A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts. SO:0001757 SL12 Acceptor Site SO:0001800 The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene. SO:0001800 tasiRNA SO:0001801 A primary transcript encoding a tasiRNA. SO:0001801 tasiRNA Primary Transcript SO:0001869 A CDS that is part of a transposable element. SO:0001869 Transposable Element CDS SO:0001870 A short ncRNA that is transcribed from an enhancer. May have a regulatory function. SO:0001870 Enhancer RNA SO:0001877 A non-coding RNA over 200nucleotides in length. SO:0001877 Lnc RNA SO:0001902 A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. SO:0001902 Splice Region SO:0001903 A lnc_RNA totally contained within an intron. SO:0001903 Intronic lncRNA SO:0001904 Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA. SO:0001904 Antisense lncRNA SO:0005837 The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. SO:0005837 U14 snoRNA Primary Transcript SO:0005841 A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue. SO:0005841 Methylation Guide snoRNA SO:0005843 An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules. SO:0005843 rRNA Cleavage RNA SO:0005845 An exon that is the only exon in a gene. SO:0005845 Exon of Single Exon Gene SO:0005856 A primary transcript encoding seryl tRNA. SO:0005856 Selenocysteine tRNA Primary Transcript SO:0005857 A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region. SO:0005857 Selenocysteinyl tRNA SO:1001187 A transcript that is alternatively spliced. SO:1001187 Alternatively Spliced Transcript SO:1001197 A primary transcript that has the quality dicistronic. SO:1001197 Dicistronic Primary Transcript SO:10012177 The recoding stimulatory signal located downstream of the recoding site. SO:1001277 3' Recoding Site SO:1001246 A CDS with the evidence status of being independently known. SO:1001246 CDS Independently Known SO:1001247 A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence. SO:1001247 Orphan CDS SO:1001249 A CDS that is supported by domain similarity. SO:1001249 CDS Supported by Domain Match Data SO:1001251 A CDS that is supported by sequence similarity data. SO:1001251 CDS Supported by Sequence SImilarity Data SO:1001254 A CDS that is predicted. SO:1001254 CDS Predicted SO:1001259 A CDS that is supported by similarity to EST or cDNA data. SO:1001259 CDS Supported by EST or cDNA Data SO:1001260 A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria. SO:1001260 Internal Shine Dalgarno Sequence SO:1001261 The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals. SO:1001261 Recoded mRNA SO:1001264 A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon. SO:1001264 mRNA Recoded by Translation Bypass SO:1001265 A recoded_mRNA that was modified by an alteration of codon meaning. SO:1001265 mRNA Recoded by Codon Redefinition SO:1001268 A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA. SO:1001268 Recoding Stimulatory Region SO:1001269 A non-canonical start codon with 4 base pairs. SO:1001269 4bp Start Codon SO:1001271 An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease. SO:1001271 Archaeal Intron SO:1001272 An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification. SO:1001272 tRNA Intron SO:1001273 A non-canonical start codon of sequence CTG. SO:1001273 CTG Start Codon SO:1001274 The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes. SO:1001274 SECIS Element SO:1001279 A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region. SO:1001279 3' Stem-loop Structure SO:1001280 The recoding stimulatory signal located upstream of the recoding site. SO:1001280 5' Recoding Site SO:1001281 Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons. SO:1001281 Flanking 3' Quadraplet Recoding Signal SO:1001282 A stop codon signal for a UAG stop codon redefinition. SO:1001282 UAG Stop Codon Signal SO:1001283 A stop codon signal for a UAA stop codon redefinition. SO:1001283 UAA Stop Codon Signal SO:1001285 A stop codon signal for a UGA stop codon redefinition. SO:1001285 UGA Stop Codon Signal SO:1001286 A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements. SO:1001286 3' Repeat Recoding Signal SO:1001287 A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon. SO:1001287 Distant 3' Recoding SIgnal SO:1001288 A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding. SO:1001288 Stop Codon Signal An mRNA with a plus 2 frameshift. SO:0000329 mRNA with Plus 2 Frameshift GO:GO_0003674 Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions. GO:0003674 Molecular Function GO:GO_0003676 Interacting selectively and non-covalently with any nucleic acid. GO:0003676 Nucleic Acid Binding GO:GO_0003677 Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid). GO:0003677 DNA Binding GO:GO_0003723 Interacting selectively and non-covalently with an RNA molecule or a portion thereof. GO:0003723 RNA Binding GO:GO_0005488 The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488] GO:0005488 Binding GO:GO_0006351 The cellular synthesis of RNA on a template of DNA. GO:0006351 Transcription, DNA-dependent GO:GO_0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:0006412 Translation GO:GO_0008150 Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0008150 Biological Process GO:GO_0008152 The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GO:0008152 Metabolic Process GO:GO_0010467 The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. GO:0010467 Gene Expression GO:GO_0010468 Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form. GO:0010468 Regulation of Gene Expression GO:GO_0010608 Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript. GO:0010608 Posttranscriptional Regulation of Gene Expression GO:GO_0016070 The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. GO:0016070 RNA Metabolic Process GO:GO_0016441 The inactivation of gene expression by a posttranscriptional mechanism. GO:0016441 Posttranscriptional Gene Silencing GO:GO_0019222 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0019222 Regulation of Metabolic Process GO:GO_0019538 The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. GO:0019538 Protein Metabolic Process GO:GO_0032774 The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. GO:0032774 RNA Biosynthetic Process GO:GO_0035194 Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation. GO:0035194 Posttranscriptional Gene Silencing by RNA GO:GO_0035195 Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression. GO:0035195 Gene Silencing by miRNA GO:GO_0035198 Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes. GO:0035198 miRNA Binding GO:GO_0050789 Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0050789 Regulation of Biological Process GO:GO_0065007 Any process that modulates the frequency, rate or extent of any biological process, quality or function. GO:0065007 Biological Regulation GO:GO_0070878 Interacting selectively and non-covalently with a primary microRNA (pri-miRNA) transcript, an RNA molecule that is processed into a short hairpin-shaped structure called a pre-miRNA and finally into a functional miRNA. Both double-stranded and single-stranded regions of a pri-miRNA are required for binding. GO:0070878 pri-miRNA Binding GO:GO_0070883 Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA. GO:0070883 pre-miRNA Binding GO:GO_0090304 Any cellular metabolic process involving nucleic acids. GO:0090304 Nucleic Acid Metabolic Process The cellular synthesis of RNA on a template of RNA. GO:0001172 Transcription, RNA-dependent GRO:InformationBiopolymer Naturally occurring macromolecules that harbor biological information in their structures, e.g. proteins, nucleic acids. GRO:InformationBiopolymer Information Biopolymer GRO:MolecularEntity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. http://en.wikipedia.org/wiki/Molecular_entity Molecular Entity snap:Continuant An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. snap:Continuant Continuant snap:DependentContinuant A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities. snap:DependentContinuant Dependent Continuant snap:Disposition A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C. snap:Disposition Disposition snap:FiatObjectPart A material entity that is part of an object but is not demarcated by any physical discontinuities. snap:FiatObjectPart Fiat Object Part snap:Function A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for. snap:Function Function snap:GenericallyDependentContinuant A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time. snap:GenericallyDependentContinuant Generically Dependent Continuant snap:IndependentContinuant A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything. snap:IndependentContinuant Independent Continuant snap:MaterialEntity An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. BFO:MaterialEntity Material Entity snap:Quality A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property). snap:Quality Quality snap:RealizableEntity A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. snap:RealizableEntity Realizable Entity snap:Role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. snap:Role Role snap:SpecificallyDependentContinuant A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. snap:SpecificallyDependentContinuant Specifically Dependent Continuant span:Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. span:Occurrent Occurent span:Process A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. span:Process Process guided_by regulates has_participant has_role C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity. RO:adjacent_to adjacent_to Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'. RO:derives_from derives_from As for has_participant, but with the additional condition that the component instance is causally active in the relevant process. RO:has_agent has_agent has_part P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. RO:preceded_by preceded_by