2024-09-28 09:26:08, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
LOCUS NM_124072 4547 bp mRNA linear PLN 20-OCT-2022 DEFINITION Arabidopsis thaliana RNA helicase (LBA1), mRNA. ACCESSION NM_124072 VERSION NM_124072.3 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 4547) AUTHORS Tabata,S., Kaneko,T., Nakamura,Y., Kotani,H., Kato,T., Asamizu,E., Miyajima,N., Sasamoto,S., Kimura,T., Hosouchi,T., Kawashima,K., Kohara,M., Matsumoto,M., Matsuno,A., Muraki,A., Nakayama,S., Nakazaki,N., Naruo,K., Okumura,S., Shinpo,S., Takeuchi,C., Wada,T., Watanabe,A., Yamada,M., Yasuda,M., Sato,S., de la Bastide,M., Huang,E., Spiegel,L., Gnoj,L., O'Shaughnessy,A., Preston,R., Habermann,K., Murray,J., Johnson,D., Rohlfing,T., Nelson,J., Stoneking,T., Pepin,K., Spieth,J., Sekhon,M., Armstrong,J., Becker,M., Belter,E., Cordum,H., Cordes,M., Courtney,L., Courtney,W., Dante,M., Du,H., Edwards,J., Fryman,J., Haakensen,B., Lamar,E., Latreille,P., Leonard,S., Meyer,R., Mulvaney,E., Ozersky,P., Riley,A., Strowmatt,C., Wagner-McPherson,C., Wollam,A., Yoakum,M., Bell,M., Dedhia,N., Parnell,L., Shah,R., Rodriguez,M., See,L.H., Vil,D., Baker,J., Kirchoff,K., Toth,K., King,L., Bahret,A., Miller,B., Marra,M., Martienssen,R., McCombie,W.R., Wilson,R.K., Murphy,G., Bancroft,I., Volckaert,G., Wambutt,R., Dusterhoft,A., Stiekema,W., Pohl,T., Entian,K.D., Terryn,N., Hartley,N., Bent,E., Johnson,S., Langham,S.A., McCullagh,B., Robben,J., Grymonprez,B., Zimmermann,W., Ramsperger,U., Wedler,H., Balke,K., Wedler,E., Peters,S., van Staveren,M., Dirkse,W., Mooijman,P., Lankhorst,R.K., Weitzenegger,T., Bothe,G., Rose,M., Hauf,J., Berneiser,S., Hempel,S., Feldpausch,M., Lamberth,S., Villarroel,R., Gielen,J., Ardiles,W., Bents,O., Lemcke,K., Kolesov,G., Mayer,K., Rudd,S., Schoof,H., Schueller,C., Zaccaria,P., Mewes,H.W., Bevan,M. and Fransz,P. CONSRTM Kazusa DNA Research Institute; Cold Spring Harbor and Washington University in St Louis Sequencing Consortium; European Union Arabidopsis Genome Sequencing Consortium TITLE Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana JOURNAL Nature 408 (6814), 823-826 (2000) PUBMED 11130714 REFERENCE 2 (bases 1 to 4547) 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 4547) 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 4547) 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_003076). On Sep 12, 2016 this sequence version replaced NM_124072.2. FEATURES Location/Qualifiers source 1..4547 /organism="Arabidopsis thaliana" /mol_type="mRNA" /db_xref="taxon:3702" /chromosome="5" /ecotype="Columbia" gene 1..4547 /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /note="Required for nonsense-mediated mRNA decay. Involved in RNA interference. lba1 mutants has reduced sugar-induced expression of Atb- amylase, is hypersensitive to glucose and abscisic acid and resistant to mannose, and shows early flowering, short day-sensitive growth, and seed germination phenotypes." /db_xref="Araport:AT5G47010" /db_xref="GeneID:834747" /db_xref="TAIR:AT5G47010" CDS 186..3950 /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /inference="Similar to RNA sequence, EST:INSD:ES203269.1,INSD:EL138262.1,INSD:EL311317.1, INSD:EG499455.1,INSD:EG525461.1,INSD:AV546416.1, INSD:ES177958.1,INSD:AV546188.1,INSD:AV545909.1, INSD:BP635121.1,INSD:AV546182.1,INSD:AI994922.1, INSD:EL106236.1,INSD:ES206740.1,INSD:ES015996.1, INSD:AV551650.1,INSD:AV545805.1,INSD:BP611793.1, INSD:BP797241.1,INSD:W43593.1,INSD:AV545830.1, INSD:AV551523.1,INSD:ES088887.1,INSD:EH898100.1, INSD:BP643776.1,INSD:ES124254.1,INSD:EL193706.1, INSD:DR351267.1,INSD:T44378.1,INSD:AV545800.1, INSD:ES007894.1,INSD:EH970935.1,INSD:ES042198.1, INSD:EH851103.1,INSD:EH883336.1,INSD:EG499456.1, INSD:AV546008.1,INSD:AV530410.1,INSD:EL256323.1, INSD:AV539244.1,INSD:EH798981.1,INSD:BP806608.1, INSD:AV554786.1,INSD:AV545820.1,INSD:AU228948.1, INSD:ES009612.1,INSD:ES080981.1,INSD:AA395276.1" /inference="similar to RNA sequence, mRNA:INSD:AF484122.1" /note="LOW-LEVEL BETA-AMYLASE 1 (LBA1); FUNCTIONS IN: in 6 functions; INVOLVED IN: sugar mediated signaling pathway, RNA interference, nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, response to sucrose stimulus; LOCATED IN: plasma membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Restriction endonuclease, type I, R subunit/Type III, Res subunit (InterPro:IPR006935), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), RNA helicase UPF1, UPF2-interacting domain (InterPro:IPR018999); BEST Arabidopsis thaliana protein match is: DNA-binding protein, putative (TAIR:AT2G03270.1); Has 9640 Blast hits to 8330 proteins in 1330 species: Archae - 182; Bacteria - 2840; Metazoa - 3001; Fungi - 1369; Plants - 807; Viruses - 148; Other Eukaryotes - 1293 (source: NCBI BLink)." /codon_start=1 /product="RNA helicase" /protein_id="NP_199512.2" /db_xref="GeneID:834747" /db_xref="TAIR:AT5G47010" /db_xref="Araport:AT5G47010" /translation="
MDSQQSDLFDTASQPDTVADEYTFLEFNTQGDSEFDYQDFGSPTAWPTPSDSISIADVADRGEGGAAADHHSEASSPSSLSAGAGNGAKVGRGGVGGSGGVSSSSQVDALAAGVGNLNFEETGDDDGFDYGKNDFTEHACKYCGISNPACVVRCNVASCRKWFCNSRGNTSGSHIVNHLVRAKHKEVCLHRDSPLGETILECYNCGCRNVFLLGFISAKTDSVVVLLCRDPCLNVNALKDMNWDLSQWCPLIDDRCFLPWLVKVPSEQEQLRARQISAQQINKIEELWKTNPDATLEDLEKPGVDDEPQPVQPKYEDAYQYQNVFAPLIKLEADYDKMMKESQSKENLTVRWDIGLNKKRVAYFVFPKEENELRLVPGDELRLRYSGDAVHPSWQSVGHVIKLTAQEEVALELRANQGVPIDVNHGFSVDFVWKSTSFDRMQGAMKNFAVDETSVSGYIYHQLLGHEVEAQMVRNTLPRRFGVPGLPELNASQVNAVKSVLQKPISLIQGPPGTGKTVTSAAIVYHMAKQGQGQVLVCAPSNVAVDQLAEKISATGLKVVRLCAKSREAVSSPVEYLTLHYQVRHLDTSEKSELHKLQQLKDEQGELSSSDEKKYKNLKRATEREITQSADVICCTCVGAADLRLSNFRFRQVLIDESTQATEPECLIPLVLGVKQVVLVGDHCQLGPVIMCKKAARAGLAQSLFERLVTLGIKPIRLQVQYRMHPALSEFPSNSFYEGTLQNGVTIIERQTTGIDFPWPVPNRPMFFYVQLGQEEISASGTSYLNRTEAANVEKLVTAFLKSGVVPSQIGVITPYEGQRAYIVNYMARNGSLRQQLYKEIEVASVDSFQGREKDYIILSCVRSNEHQGIGFLNDPRRLNVALTRARYGIVILGNPKVLSKQPLWNGLLTHYKEHECLVEGPLNNLKQSMVQFQKPRKIYNDRRLFYGGGAGMIGNDNFGSGNPNADRRGSRGRAGGSYLPSGPPNGARPGLHPAGYPIPRVPLSPFPGGPPSQPYAIPTRGPVGAVPHAPQPGNHGFGAGRGTSVGGHLPHQQATQHNVGTIGPSLNFPLDSPNSQPSPGGPLSQPGYGSQAFRDGFSMGGISQDFLADDIKSQGSHDPYNMADFATQASPGGFAVDYATQGAHGAFPGNFMNQNSQGGYSRFSGINDFMSQEYMAHGGQGLFTQAGFIDSSQDDGQQNPYGVNNPNLQSQGLPNSLYSQPFAHYNTQPLNLSGPQQSQPNQSSQNPKHPYNG"
misc_feature 597..1058 /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /note="RNA helicase (UPF2 interacting domain); Region: UPF1_Zn_bind; pfam09416" /db_xref="CDD:401391" misc_feature 1215..1478 /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /note="1B domain of eukaryotic UPF1 RNA helicase and related proteins; Region: 1B_UPF1-like; cd21407" /db_xref="CDD:394815" misc_feature order(1317..1325,1380..1382) /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /note="nucleic acid substrate binding site [nucleotide binding]; other site" /db_xref="CDD:394815" misc_feature 1494..2945 /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /note="DNA helicase, putative; Region: TIGR00376" /db_xref="CDD:273041" misc_feature 1647..2354 /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /note="DEXXQ-box helicase domain of UPF1; Region: DEXXQc_UPF1; cd18039" /db_xref="CDD:350797" misc_feature order(1647..1655,1662..1664,1719..1739,2238..2240, 2349..2354) /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /note="ATP binding site [chemical binding]; other site" /db_xref="CDD:350797" misc_feature order(1803..1811,1875..1886,2043..2045,2091..2093, 2097..2099,2250..2252,2256..2258) /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /note="RNA binding site [nucleotide binding]; other site" /db_xref="CDD:350797" ORIGIN
ctcacgcgcccctcttttcttcttcattgacacggacattcgtttccaattctctctaatgtttcactaaagcgcatacataaccctaaccctaactctctcgtactgcacaaaaaaaaaaaaaaaattgaagaagagcgatacgatcgtaaccagggagcttgatttctcccctgatttttctaatggattctcaacagagcgatctctttgacaccgcatcgcagccggacacggtggccgacgagtatacctttttggaattcaatactcaaggcgattcagagttcgattaccaggattttggatcgccgacggcatggccgacaccgtctgattctatttccatcgctgacgttgccgatcgtggtgaaggaggagctgccgcggatcatcattctgaggcttcgtcaccttcgtccctctctgccggtgccgggaatggtgcgaaagtgggacgcggtggagttggtggaagtggtggtgttagtagtagtagtcaggttgatgcattggccgctggtgtgggaaatttgaactttgaagagactggtgatgatgatggttttgattatggtaaaaatgatttcacggagcacgcttgtaagtattgtggtatctcgaacccagcttgcgtcgttaggtgtaatgtggcttcttgtagaaagtggttctgcaattcaaggggaaacacctcaggctctcatattgtgaatcacctggtgcgagcaaaacacaaggaagtttgtctccatagagacagtccactaggggaaacaattctcgaatgctacaactgtgggtgtcggaatgtctttcttctcggtttcatctcagcaaagacagatagtgttgtcgtccttctctgtagagatccttgtctaaatgtaaatgccctgaaggatatgaactgggacctaagtcagtggtgtcccttgattgacgacagatgtttcctcccctggcttgttaaggtcccatcagagcaagaacagctaagggcacgccaaattagcgcacagcaaataaacaagatagaggaattatggaagacaaatccggatgctactcttgaagaccttgaaaaacctggtgtagatgatgaacctcagcctgttcaacctaagtatgaagatgcgtaccagtatcaaaatgtgtttgcacctctaatcaaactcgaagcagactatgacaagatgatgaaagagtctcaaagcaaggaaaacctcactgttcggtgggatattggtcttaacaagaagcgtgttgcatacttcgtcttcccaaaggaggaaaatgaattgcgattggtaccgggtgatgaactacgtctgcggtactcgggagatgctgttcatccatcctggcagtcagttggacatgtgatcaagctaacggcgcaagaggaggttgctcttgaactccgagctaatcagggagttccgattgacgtaaatcatggattcagtgttgattttgtttggaaaagtacaagctttgatcgaatgcagggagcaatgaagaattttgctgtagatgaaacaagtgtgagtggttatatctaccatcagttattgggacatgaagttgaggcccagatggttcgtaacacactacctcgacgttttggggtacctggtcttccagaactgaatgcatctcaggttaatgcggtgaaaagtgtccttcagaagcccatcagcttgatccaaggtccacctggcacaggcaaaactgtgacttctgcagcaattgtgtatcacatggcaaaacagggccagggacaggttctcgtttgtgccccaagtaatgttgctgtggaccaactagctgaaaaaattagtgctactgggttaaaggttgttcgcctttgcgcaaaatcaagggaagctgtaagttctcctgtagagtatttgacccttcactaccaggtaagacatcttgacacatctgaaaagagcgaactgcataagttgcagcagttgaaagatgaacaaggtgagctgtcaagcagtgatgaaaagaaatacaaaaatttgaaaagagcgacagaacgcgagataacccagagtgctgatgtcatatgctgcacatgtgttggtgctgctgatcttcggttgtcaaactttagatttagacaggtacttattgatgagtctactcaagcaacagaacctgagtgccttatccctttggtccttggagtaaaacaggttgttcttgttggtgatcattgtcagcttggccccgtcattatgtgcaaaaaagcagctcgtgctggcttggcacagtctctctttgaacgacttgtgactcttggtattaaaccaatcagattgcaggttcaatatcgtatgcatccagctttgtccgagtttccatccaacagcttctatgaaggaactctacagaatggagtcacaattattgaaaggcaaacaacagggattgatttcccgtggcctgttcctaaccggcccatgtttttctatgttcagctgggacaagaggagatcagtgctagtggaacatcatatcttaatagaactgaggctgctaatgtggagaaacttgtgactgctttcttaaagagtggagttgtccccagtcagattggagttataactccatatgagggacagagggcatacattgttaattacatggcaagaaatggttctctccgacagcaactgtacaaggaaattgaggttgccagtgttgattcttttcaaggaagggaaaaagattacatcatattgtcctgtgtgagaagtaatgagcatcagggcattggattccttaatgatccacggaggcttaatgttgcacttacgcgagctcgttatggaattgttattcttggaaacccaaaagttcttagtaaacagcctctgtggaatggattgttgacacattacaaggaacatgagtgcttggtcgagggacctcttaataatctaaagcagagcatggtacagtttcagaaaccaagaaagatttacaatgatcggagactattttatggtggtggagctggcatgattggaaatgataattttggttcgggtaaccctaatgctgacagaagaggcagtcgaggaagggctggtggttcctatcttccttctggcccacctaatggtgctagacctggactacacccggcagggtacccgatacctagggttccactttcaccctttcctggtggtcctccttctcagccatacgctattccaactcgtggacctgttggtgctgttcctcatgctcctcaacctggaaaccatggttttggagctggtcgtggaacttcagttggggggcaccttccgcaccaacaagccacccaacataatgttggaactattggccctagtttaaactttccccttgatagtccgaatagccagccttcacctggtggtccgctatcccaacctggatatggtagccaagcgttcagggatggattttctatgggtggaatatctcaggatttcttggctgatgatatcaagagccagggatctcatgatccttacaacatggccgactttgctacacaggcctcaccgggtggatttgctgttgattatgccacacaaggagcacatggggcgtttcctggaaactttatgaatcagaattctcaaggcggttattctcgtttcagcggaattaatgatttcatgtctcaggagtatatggcacatggaggtcaaggtcttttcacccaagctggctttatcgactcatcccaggatgatggacagcagaatccttatggtgtgaacaatccaaatcttcagtctcagggtctcccaaattcgctctactcgcagccattcgcacactacaacacacagccactaaacctttcaggcccacagcaatctcaacctaaccagagctcacaaaacccaaaacatccttacaatggctgagggtgagaaagacaaaacttggatgcaacgggtttataaactcttttgcaaattcaccggcttggttccatgctgttcacggctccaaacaaacatctggtgacttccgggtgcttgaaagatacacgcctttctggctcgcttaacgcagcaaacaggtaaatggttatgcaaagaaacgggtacctaagtagcctggggaaaaaagtcttcggtccgtaaatccttttggcttatatgttttgtttttgccttgtattattaatatacgctcatatgctctatattattatagtcagatatctgaagcctacccatatttaaaattggtggtggtgtttaatggtgatattgatatgatttacaagttcttttgctttatttggtttttatttttttcacggtctgaattcatgatttgtgtgcaagttttggtatcattggcttatgggcttgtccaatctgaaatttgttttggatttctaagtttcgttaaaactgattcgacttgaattttatgttctcaaaatatctctgagttgaagaatttcataaagattatatttcctaggtttagccgacatgattttgttgtcc
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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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