2024-09-29 08:11:55, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
LOCUS NM_112299 2758 bp mRNA linear PLN 20-OCT-2022 DEFINITION Arabidopsis thaliana ubiquitin-specific protease 25 (UBP25), mRNA. ACCESSION NM_112299 VERSION NM_112299.4 DBLINK BioProject: PRJNA116 BioSample: SAMN03081427 KEYWORDS RefSeq. SOURCE Arabidopsis thaliana (thale cress) ORGANISM Arabidopsis thaliana Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis. REFERENCE 1 (bases 1 to 2758) AUTHORS Salanoubat,M., Lemcke,K., Rieger,M., Ansorge,W., Unseld,M., Fartmann,B., Valle,G., Blocker,H., Perez-Alonso,M., Obermaier,B., Delseny,M., Boutry,M., Grivell,L.A., Mache,R., Puigdomenech,P., De Simone,V., Choisne,N., Artiguenave,F., Robert,C., Brottier,P., Wincker,P., Cattolico,L., Weissenbach,J., Saurin,W., Quetier,F., Schafer,M., Muller-Auer,S., Gabel,C., Fuchs,M., Benes,V., Wurmbach,E., Drzonek,H., Erfle,H., Jordan,N., Bangert,S., Wiedelmann,R., Kranz,H., Voss,H., Holland,R., Brandt,P., Nyakatura,G., Vezzi,A., D'Angelo,M., Pallavicini,A., Toppo,S., Simionati,B., Conrad,A., Hornischer,K., Kauer,G., Lohnert,T.H., Nordsiek,G., Reichelt,J., Scharfe,M., Schon,O., Bargues,M., Terol,J., Climent,J., Navarro,P., Collado,C., Perez-Perez,A., Ottenwalder,B., Duchemin,D., Cooke,R., Laudie,M., Berger-Llauro,C., Purnelle,B., Masuy,D., de Haan,M., Maarse,A.C., Alcaraz,J.P., Cottet,A., Casacuberta,E., Monfort,A., Argiriou,A., flores,M., Liguori,R., Vitale,D., Mannhaupt,G., Haase,D., Schoof,H., Rudd,S., Zaccaria,P., Mewes,H.W., Mayer,K.F., Kaul,S., Town,C.D., Koo,H.L., Tallon,L.J., Jenkins,J., Rooney,T., Rizzo,M., Walts,A., Utterback,T., Fujii,C.Y., Shea,T.P., Creasy,T.H., Haas,B., Maiti,R., Wu,D., Peterson,J., Van Aken,S., Pai,G., Militscher,J., Sellers,P., Gill,J.E., Feldblyum,T.V., Preuss,D., Lin,X., Nierman,W.C., Salzberg,S.L., White,O., Venter,J.C., Fraser,C.M., Kaneko,T., Nakamura,Y., Sato,S., Kato,T., Asamizu,E., Sasamoto,S., Kimura,T., Idesawa,K., Kawashima,K., Kishida,Y., Kiyokawa,C., Kohara,M., Matsumoto,M., Matsuno,A., Muraki,A., Nakayama,S., Nakazaki,N., Shinpo,S., Takeuchi,C., Wada,T., Watanabe,A., Yamada,M., Yasuda,M. and Tabata,S. CONSRTM European Union Chromosome 3 Arabidopsis Sequencing Consortium; Institute for Genomic Research; Kazusa DNA Research Institute TITLE Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana JOURNAL Nature 408 (6814), 820-822 (2000) PUBMED 11130713 REFERENCE 2 (bases 1 to 2758) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (19-OCT-2022) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA REFERENCE 3 (bases 1 to 2758) AUTHORS Krishnakumar,V., Cheng,C.-Y., Chan,A.P., Schobel,S., Kim,M., Ferlanti,E.S., Belyaeva,I., Rosen,B.D., Micklem,G., Miller,J.R., Vaughn,M. and Town,C.D. TITLE Direct Submission JOURNAL Submitted (17-MAY-2016) Plant Genomics, J. Craig Venter Institute, 9704 Medical Center Dr, Rockville, MD 20850, USA REMARK Protein update by submitter REFERENCE 4 (bases 1 to 2758) AUTHORS Swarbreck,D., Lamesch,P., Wilks,C. and Huala,E. CONSRTM TAIR TITLE Direct Submission JOURNAL Submitted (18-FEB-2011) Department of Plant Biology, Carnegie Institution, 260 Panama Street, Stanford, CA, USA COMMENT REVIEWED REFSEQ: This record has been curated by TAIR and Araport. This record is derived from an annotated genomic sequence (NC_003074). On Sep 12, 2016 this sequence version replaced NM_112299.3. FEATURES Location/Qualifiers source 1..2758 /organism="Arabidopsis thaliana" /mol_type="mRNA" /db_xref="taxon:3702" /chromosome="3" /ecotype="Columbia" gene 1..2758 /gene="UBP25" /locus_tag="AT3G14400" /gene_synonym="ubiquitin-specific protease 25; UBIQUITIN-SPECIFIC PROTEASE 25" /note="Encodes a ubiquitin-specific protease." /db_xref="Araport:AT3G14400" /db_xref="GeneID:820662" /db_xref="TAIR:AT3G14400" CDS 306..2291 /gene="UBP25" /locus_tag="AT3G14400" /gene_synonym="ubiquitin-specific protease 25; UBIQUITIN-SPECIFIC PROTEASE 25" /inference="Similar to RNA sequence, EST:INSD:BP576063.1,INSD:BP840905.1,INSD:EH978125.1, INSD:ES116215.1,INSD:EG454292.1,INSD:AV532395.1, INSD:ES056882.1,INSD:BP790098.1,INSD:AV442700.1, INSD:DR195616.1,INSD:ES056379.1,INSD:BP794578.1, INSD:AV551221.1,INSD:DR261226.1,INSD:BP665142.1, INSD:DR195618.1,INSD:ES023180.1,INSD:AV548104.1, INSD:EL195166.1,INSD:AV440649.1,INSD:DR195617.1, INSD:EH862534.1,INSD:BP658364.1,INSD:BP655743.1, INSD:ES026277.1,INSD:CB255814.1,INSD:BU636576.1, INSD:DR261227.1,INSD:CD529336.1,INSD:EG455443.1, INSD:EG455442.1,INSD:EL094744.1,INSD:ES206180.1, INSD:BP653384.1,INSD:EL168009.1,INSD:ES173114.1, INSD:EL165145.1,INSD:ES012955.1,INSD:CD534291.1, INSD:BP830243.1,INSD:AV828809.1,INSD:EL996918.1, INSD:BP816929.1,INSD:DR375829.1,INSD:AV535624.1, INSD:CD529545.1,INSD:EG454291.1,INSD:ES195971.1, INSD:EH869858.1,INSD:ES034817.1,INSD:BP781013.1, INSD:BX839605.1,INSD:ES214307.1,INSD:AV565675.1, INSD:EH944178.1,INSD:EG455436.1,INSD:EG483290.1, INSD:EH800353.1,INSD:EG455437.1,INSD:AV802906.1, INSD:AA404755.1,INSD:BP794729.1" /inference="Similar to RNA sequence, mRNA:INSD:BT021128.1,INSD:AF302673.1,INSD:AY064992.1" /note="ubiquitin-specific protease 25 (UBP25); FUNCTIONS IN: ubiquitin-specific protease activity, ubiquitin thiolesterase activity; INVOLVED IN: ubiquitin-dependent protein catabolic process; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (InterPro:IPR018200), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (InterPro:IPR001394); BEST Arabidopsis thaliana protein match is: ubiquitin-specific protease 23 (TAIR:AT5G57990.1); Has 8659 Blast hits to 7314 proteins in 254 species: Archae - 0; Bacteria - 9; Metazoa - 4447; Fungi - 1449; Plants - 1041; Viruses - 9; Other Eukaryotes - 1704 (source: NCBI BLink)." /codon_start=1 /product="ubiquitin-specific protease 25" /protein_id="NP_566486.1" /db_xref="GeneID:820662" /db_xref="TAIR:AT3G14400" /db_xref="Araport:AT3G14400" /translation="
MGFKLQMSWMPSLLSQKRRNGPPLGLRNLGNTCYLNSVLQCLTFTPPLANFCLTHKHSSHCDTYVDGERKRDCPFCIVEKRIARSLSVDLTTDAPNKISSCLKIFAEHFKLGRQEDAHEFLRYVIDACHNTSLRLKKLRYNGNEPFNGNSVVKEIFGGALQSQVKCLSCGAESNKADEIMDISLEILQSSSVKESLQKFFQSEILDGNNKYRCESCEKLVTARKQMSILQAPNILVIQLKRFGGIFGGKIDKAISFGEILVLSNFMSKASKDPQPEYKLFGIIVHSGFSPESGHYYAYVKDSLGRWYCCNDSFVSLSTLQEVLSEKAYILFFSRSNQRPASAKTLVTSNGTTSHEVNGCETSNPQKFIGPLNGFNMKPQAEQSFQKGNLASSKPHKFIRPKPRAEQAPLEDNLLSSKVEKAPLRPHAKVSISVNLGAKRVSPVNGRLSFHQDENIAPKANKENSVSVLPTKVNSGTERKFGTENGGNGVKENGSAPGSSNHKVALHPHERSNGSSNGGDHHKDNLHPCGSNGSQNGTAHPETERNGVSTTQSKGLCSSTKEDPCILLRKDESSRNELEAIKESLKKDALSHLRSCGWYDKVLISMHAKKRLRTEQSGGEDGSDLKRRLIEDVKSSLKSQIPEELKADLVNRIWEISKKKYS"
misc_feature 372..1304 /gene="UBP25" /locus_tag="AT3G14400" /gene_synonym="ubiquitin-specific protease 25; UBIQUITIN-SPECIFIC PROTEASE 25" /note="A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl...; Region: Peptidase_C19E; cd02661" /db_xref="CDD:239126" misc_feature order(387..389,402..404,1185..1187,1236..1238) /gene="UBP25" /locus_tag="AT3G14400" /gene_synonym="ubiquitin-specific protease 25; UBIQUITIN-SPECIFIC PROTEASE 25" /note="active site" /db_xref="CDD:239126" misc_feature 2031..2261 /gene="UBP25" /locus_tag="AT3G14400" /gene_synonym="ubiquitin-specific protease 25; UBIQUITIN-SPECIFIC PROTEASE 25" /note="Transcription factor e(y)2; Region: EnY2; pfam10163" /db_xref="CDD:462972" ORIGIN
atcgcgaagggattgtggggtttgttgctgggcgggtctcttccctcggcagttaccttcatcgaattcgatcttcatcttcttccttccccaactctttcaaattcgtgaaaatcttcctttaatttcgactacaaattgattggaggaagcccccaaaacgtgaattagaagagaaagagaaaagcgaggaaaacgcgtggtgacaaaagatgcgatcgcagctgttggcttggccgcggcggcgagtcagcgatgagcggttgcttggttggttttctccggcggagaataaccgattttgaatgggatttaaactgcagatgagctggatgccgagtctactgagtcaaaagcgtaggaatggtcctcccttagggttacggaatctcggcaacacctgttacctcaatagtgtccttcagtgtctcactttcactcctcctctcgctaatttctgccttactcacaaacactcctctcactgcgacacatatgtggatggagagaggaaaagggattgtccattttgcatagttgagaaaagaatagcaaggtctcttagtgtggatctaactaccgatgcgcctaacaagatttcaagctgtctcaaaatttttgctgagcattttaagcttggtcgtcaagaggatgctcatgagttcttgcgctatgtcattgatgcatgccacaatacgtctctcagactcaagaagttgcgatacaacggtaacgagccctttaatggcaatagtgtcgtgaaggagatttttggtggtgctttgcagagccaggtcaagtgtttgtcttgtggtgcggagtctaataaagccgatgagattatggatatcagtcttgagattttgcagagtagctctgtgaaggagtcattgcaaaagttctttcaatcagagattttagatggcaacaataagtatagatgcgagtcctgtgaaaaactggtgacggcgaggaagcagatgtctatactgcaagcgcctaatatccttgttatccaattgaaaaggtttgggggcatttttggtgggaagattgataaagccatttcatttggtgagattctggttctctcgaacttcatgagtaaagcaagcaaggaccctcaaccggaatacaagctctttgggataattgtgcactcaggattttctcctgaatctgggcactattatgcatacgttaaggattccttgggtcgatggtattgctgcaatgattcgtttgtctcgctctccaccttgcaggaggttttatcagagaaagcttatatcctgtttttcagccgttcaaaccagaggccagcgtctgctaaaactctggtaacatccaatgggactacatctcatgaagttaatggctgtgagacatcaaatccccagaagtttattgggccccttaatggtttcaacatgaaacctcaagccgagcagtccttccagaagggtaacctggcttcttcaaagccccataaatttattaggcccaaaccacgagccgagcaggccccactagaggataacctgctttcttccaaagttgaaaaggcgcctttaaggccacatgcgaaagtcagtatatctgtcaaccttggtgccaaaagggtctctcctgtcaatggtagactttctttccaccaagatgagaacatagctccaaaggcaaacaaagagaatagtgtatcagttttgccgactaaagttaactctggtacggagagaaagtttggtactgaaaatggtggcaatggagttaaagaaaacggcagtgcaccaggtagtagtaatcataaagtggcattgcatcctcatgagcggagtaatggctccagcaatgggggtgatcaccacaaggataacttacatccatgtggaagtaatggctcacaaaatggaactgctcaccccgaaactgagaggaacggtgttagtaccacccaatccaaaggcttgtgttcttcaacaaaggaagacccctgcattttgctgagaaaagacgaatcatctcggaatgaacttgaagcaataaaagagagcctgaaaaaagacgcgctgtcacatctacgttcatgcggatggtatgacaaggttctcatctccatgcatgccaagaagagattgcgtacagagcaatcaggtggagaagatggtagcgacttgaaaaggaggttgattgaagatgtgaaatcaagtttgaaatcacagattccagaggagttgaaagcagatctggtaaatcgtatctgggagattagcaagaagaagtactcgtgaaccattgttttttgcttcaacaaaaatgactcgaatctctggaagcatgaagcctctacttggtcccttcacacacacactcctcattcctcatttcatcattgcttaacccatccggctagtctgattatacagagtgagcggatcgagattttttcctgcgactgtgatgatggtgaagtgagtttttttcttttctattattattacatttttggaagagagtaaaagtaattaccggaaaaaaaaagaaaaaaaaaacagatctcattctgtataatataacgccttcttgttttttgcctcttatcgatgaagctttacacaaatatacaagtcctgtggaaatttttagtataagaacgttcttgaatttgtgtattgtatttgtggtttttcgttaaacatattaacatcggacatggtttcgtgctttcgttccagtaaaatatatggatggttcgttg
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If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596.
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