2024-09-28 09:27:36, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
LOCUS NM_117687 814 bp mRNA linear PLN 20-OCT-2022 DEFINITION Arabidopsis thaliana RNA polymerase II, Rpb4, core protein (NRPD4), mRNA. ACCESSION NM_117687 VERSION NM_117687.2 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 814) AUTHORS Mayer,K., Schuller,C., Wambutt,R., Murphy,G., Volckaert,G., Pohl,T., Dusterhoft,A., Stiekema,W., Entian,K.D., Terryn,N., Harris,B., Ansorge,W., Brandt,P., Grivell,L., Rieger,M., Weichselgartner,M., de Simone,V., Obermaier,B., Mache,R., Muller,M., Kreis,M., Delseny,M., Puigdomenech,P., Watson,M., Schmidtheini,T., Reichert,B., Portatelle,D., Perez-Alonso,M., Boutry,M., Bancroft,I., Vos,P., Hoheisel,J., Zimmermann,W., Wedler,H., Ridley,P., Langham,S.A., McCullagh,B., Bilham,L., Robben,J., Van der Schueren,J., Grymonprez,B., Chuang,Y.J., Vandenbussche,F., Braeken,M., Weltjens,I., Voet,M., Bastiaens,I., Aert,R., Defoor,E., Weitzenegger,T., Bothe,G., Ramsperger,U., Hilbert,H., Braun,M., Holzer,E., Brandt,A., Peters,S., van Staveren,M., Dirske,W., Mooijman,P., Klein Lankhorst,R., Rose,M., Hauf,J., Kotter,P., Berneiser,S., Hempel,S., Feldpausch,M., Lamberth,S., Van den Daele,H., De Keyser,A., Buysshaert,C., Gielen,J., Villarroel,R., De Clercq,R., Van Montagu,M., Rogers,J., Cronin,A., Quail,M., Bray-Allen,S., Clark,L., Doggett,J., Hall,S., Kay,M., Lennard,N., McLay,K., Mayes,R., Pettett,A., Rajandream,M.A., Lyne,M., Benes,V., Rechmann,S., Borkova,D., Blocker,H., Scharfe,M., Grimm,M., Lohnert,T.H., Dose,S., de Haan,M., Maarse,A., Schafer,M., Muller-Auer,S., Gabel,C., Fuchs,M., Fartmann,B., Granderath,K., Dauner,D., Herzl,A., Neumann,S., Argiriou,A., Vitale,D., Liguori,R., Piravandi,E., Massenet,O., Quigley,F., Clabauld,G., Mundlein,A., Felber,R., Schnabl,S., Hiller,R., Schmidt,W., Lecharny,A., Aubourg,S., Chefdor,F., Cooke,R., Berger,C., Montfort,A., Casacuberta,E., Gibbons,T., Weber,N., Vandenbol,M., Bargues,M., Terol,J., Torres,A., Perez-Perez,A., Purnelle,B., Bent,E., Johnson,S., Tacon,D., Jesse,T., Heijnen,L., Schwarz,S., Scholler,P., Heber,S., Francs,P., Bielke,C., Frishman,D., Haase,D., Lemcke,K., Mewes,H.W., Stocker,S., Zaccaria,P., Bevan,M., Wilson,R.K., de la Bastide,M., Habermann,K., Parnell,L., Dedhia,N., Gnoj,L., Schutz,K., Huang,E., Spiegel,L., Sehkon,M., Murray,J., Sheet,P., Cordes,M., Abu-Threideh,J., Stoneking,T., Kalicki,J., Graves,T., Harmon,G., Edwards,J., Latreille,P., Courtney,L., Cloud,J., Abbott,A., Scott,K., Johnson,D., Minx,P., Bentley,D., Fulton,B., Miller,N., Greco,T., Kemp,K., Kramer,J., Fulton,L., Mardis,E., Dante,M., Pepin,K., Hillier,L., Nelson,J., Spieth,J., Ryan,E., Andrews,S., Geisel,C., Layman,D., Du,H., Ali,J., Berghoff,A., Jones,K., Drone,K., Cotton,M., Joshu,C., Antonoiu,B., Zidanic,M., Strong,C., Sun,H., Lamar,B., Yordan,C., Ma,P., Zhong,J., Preston,R., Vil,D., Shekher,M., Matero,A., Shah,R., Swaby,I.K., O'Shaughnessy,A., Rodriguez,M., Hoffmann,J., Till,S., Granat,S., Shohdy,N., Hasegawa,A., Hameed,A., Lodhi,M., Johnson,A., Chen,E., Marra,M., Martienssen,R. and McCombie,W.R. TITLE Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana JOURNAL Nature 402 (6763), 769-777 (1999) PUBMED 10617198 REFERENCE 2 (bases 1 to 814) 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 814) 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 814) 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_003075). On May 26, 2011 this sequence version replaced NM_117687.1. FEATURES Location/Qualifiers source 1..814 /organism="Arabidopsis thaliana" /mol_type="mRNA" /db_xref="taxon:3702" /chromosome="4" /ecotype="Columbia" gene 1..814 /gene="NRPD4" /locus_tag="AT4G15950" /gene_synonym="DL4012W; FCAALL.240; NRPE4; RDM2; RNA-DIRECTED DNA METHYLATION 2" /note="Non-catalytic subunit common to Nuclear DNA-dependent RNA polymerases IV and V; homologous to budding yeast RPB4. Role in gene silencing. Required for RNA-directed DNA methylation." /db_xref="Araport:AT4G15950" /db_xref="GeneID:827277" /db_xref="TAIR:AT4G15950" CDS 61..679 /gene="NRPD4" /locus_tag="AT4G15950" /gene_synonym="DL4012W; FCAALL.240; NRPE4; RDM2; RNA-DIRECTED DNA METHYLATION 2" /inference="similar to RNA sequence, EST:INSD:ES197708.1,INSD:EL316587.1,INSD:ES205252.1, INSD:ES196420.1" /exception="annotated by transcript or proteomic data" /note="NRPD4; FUNCTIONS IN: DNA-directed RNA polymerase activity, nucleotide binding, catalytic activity; INVOLVED IN: RNA interference, interphase, production of siRNA involved in RNA interference, DNA methylation on cytosine within a CHH sequence; LOCATED IN: DNA-directed RNA polymerase V complex, nucleus, DNA-directed RNA polymerase IV complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: HRDC-like (InterPro:IPR010997), RNA polymerase II, Rpb4 (InterPro:IPR005574), RNA polymerase II, Rpb4, core (InterPro:IPR006590); BEST Arabidopsis thaliana protein match is: RNA polymerase II, Rpb4, core protein (TAIR:AT5G09920.1); Has 23 Blast hits to 23 proteins in 3 species: Archae - 0; Bacteria - 0; Metazoa - 0; Fungi - 0; Plants - 23; Viruses - 0; Other Eukaryotes - 0 (source: NCBI BLink)." /codon_start=1 /product="RNA polymerase II, Rpb4, core protein" /protein_id="NP_193330.3" /db_xref="GeneID:827277" /db_xref="TAIR:AT4G15950" /db_xref="Araport:AT4G15950" /translation="
MSVIAHVDHGKSTLTDSLVAAAGIIAQETAGDVRMTDTRADEAERGITIKSTGISLYYEMTDASLKSFTGARDGNEYLINLIDSPGHVDFSSEVTAALRITDGALVVVDCIEGVCVQTETVLRQSLGERIRPVLTVNKMDRCFLELKVDGEEAYQNFQRVIENANVIMATHEDPLLGDVQVYPEKGTVAFSAGLHGWAFTLTNFAKMYASKFGVSESKMMERLWGENFFDSATRKWTTKTGSPTCKRGFVQFCYEPIKIMINTCMNDQKDKLWPMLEKLGIQMKPDEKELMGKPLMKRVMQAWLPASTALLEMMIFHLPSPYTAQRYRVENLYEGPLDDKYAAAIRNCDPDGPLMLYVSKMIPASDKGRFFAFGRVFSGTVSTGMKVRIMGPNYVPGEKKDLYVKSVQRTVIWMGKKQETVEDVPCGNTVAMVGLDQFITKNGTLTNEKEVDAHPLRAMKFSVSPVVRVAVKCKLASDLPKLVEGLKRLAKSDPMVLCTMEESGEHIVAGAGELHIEICVKDLQDFMGGADIIVSDPVVSLRETVFERSCRTVMSKSPNKHNRLYMEARPMEDGLAEAIDEGRIGPSDDPKIRSKILAEEFGWDKDLAKKIWAFGPDTTGPNMVVDMCKGVQYLNEIKDSVVAGFQWASKEGPLAEENMRGVCYEVCDVVLHADAIHRGCGQMISTARRAIYASQLTAKPRLLEPVYMVEIQAPEGALGGIYSVLNQKRGHVFEEMQRPGTPLYNIKAYLPVVESFGFSGQLRAATSGQAFPQCVFDHWDMMSSDPLETGSQAATLVADIRKRKGLKLQMTPLSDYEDKLGNLJCVIMRNAATGGNLJCVIATG"
misc_feature 61..679 /gene="NRPD4" /locus_tag="AT4G15950" /gene_synonym="DL4012W; FCAALL.240; NRPE4; RDM2; RNA-DIRECTED DNA METHYLATION 2" /note="translation elongation factor EF-2 subunit; Provisional; Region: PLN00116" /db_xref="CDD:177730" ORIGIN
atttttatctgttttgagtctttttgcttttttatctcaatcgtctctcgtagcagaaaaatgtcagagaaaggaggcaaggggctcaaatcctctctcaagtccaaagatggagggaaggatgggagctcaacaaagctcaagaagggtagaaaaatccactttgatcaacggactccacctgctaattacaagattctcaatgtttcttctgatcaacaaccatttcagagttctgctgctaaatgtgggaaaagtgacaaacctaccaagtctagcaaaaactctctgcattcgtttgagctcaaagatcttcctgagaatgctgaatgcatgatggactgtgaagcttttcagatattagatggaattaagggacaattggttggcttgtctgaagatccgtctaattaaaattcctgtatcttatgacagagcattggcttatgttgagagttgtgttcactacacaaaccctcaatctgtcagaaaagtccttgaacctctgaaaacgtatggtatctctgatggcgagatgtgtgttattgcaaatgcttcttcagagagcgtagatgaagttcttgcctttattccatcgctgaagactaaaaaagaggtgatcaatcaacctctacaagatgcattggaggagctatccaagctgaagaaatcggaatgatgagcagcagactgctgcagtgaatggttcaatgctaggagtagtttgcaggtagacatcataaaatgtaattgcgtctttgcctttctcaacattaaccaacctgtgcaatggcaatggcaacttttgtctagt
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Creative Commons Attribution 4.0 International License (CC BY 4.0).
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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