2024-09-28 11:15:59, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
LOCUS NM_001339114 4871 bp mRNA linear PLN 20-OCT-2022 DEFINITION Arabidopsis thaliana dicer-like 3 (DCL3), partial mRNA. ACCESSION NM_001339114 VERSION NM_001339114.1 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 4871) 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 4871) 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 4871) 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 4871) 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). COMPLETENESS: incomplete on the 3' end. FEATURES Location/Qualifiers source 1..4871 /organism="Arabidopsis thaliana" /mol_type="mRNA" /db_xref="taxon:3702" /chromosome="3" /ecotype="Columbia" gene 1..>4871 /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="Encodes a ribonuclease III family protein that is required for endogenous RDR2-dependent siRNA (but not miRNA) formation." /db_xref="Araport:AT3G43920" /db_xref="GeneID:823508" /db_xref="TAIR:AT3G43920" CDS 162..4871 /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /codon_start=1 /product="dicer-like 3" /protein_id="NP_001325812.1" /db_xref="GeneID:823508" /db_xref="Araport:AT3G43920" /db_xref="TAIR:AT3G43920" /translation="
MHSSLEPEKMEEGGGSNSLKRKFSEIDGDQNLDSVSSPMMTDSNGYELKVYEVAKNRNIIAVLGTGIDKSEITKRLIKAMGSSDTDKRLIIFLAPTVNLVKQQCCEIRALVNLKVEEYFGAKGVDKWTSQRWDEEFSKHDVLVMTPQILLDVLRSAFLKLEMVCLLIIDECHHTTGNHPYAKLMKEFYHESTSKPKIFGLTASAVIRKAQVSELERLMDSKIFNPEEREGVEKFATTVKEGPILYNPSPSCSLELKEKLETSHLKFDASLRRLQELGKDSFLNMDNKFETYQKRLSIDYREILHCLDNLGLICAHLAAEVCLEKISDTKEESETYKECSMVCKEFLEDILSTIGVYLPQDDKSLVDLQQNHLSAVISGHVSPKLKELFHLLDSFRGDKQKQCLILVERIITAKVIERFVKKEASLAYLNVLYLTENNPSTNVSAQKMQIEIPDLFQHGKVNLLFITDVVEEGFQVPDCSCMVCFDLPKTMCSYSQSQKHAKQSNSKSIMFLERGNPKQRDHLHDLMRREVLIQDPEAPNLKSCPPPVKNGHGVKEIGSMVIPDSNITVSEEAASTQTMSDPPSRNEQLPPCKKLRLDNNLLQSNGKEKVASSKSKSSSSAAGSKKRKELHGTTCANALSGTWGENIDGATFQAYKFDFCCNISGEVYSSFSLLLESTLAEDVGKVEMDLYLVRKLVKASVSPCGQIRLSQEELVKAKYFQQFFFNGMFGKLFVGSKSQGTKREFLLQTDTSSLWHPAFMFLLLPVETNDLASSATIDWSAINSCASIVEFLKKNSLLDLRDSDGNQCNTSSGQEVLLDDKMEETNLIHFANASSDKNSLEELVVIAIHTGRIYSIVEAVSDSSAMSPFEVDASSGYATYAEYFNKKYGIVLAHPNQPLMKLKQSHHAHNLLVDFNEEMVVKTEPKAGNVRKRKPNIHAHLPPELLARIDVPRAVLKSIYLLPSVMHRLESLMLASQLREEIDCSIDNFSISSTSILEAVTTLTCPESFSMERLELLGDSVLKYVASCHLFLKYPDKDEGQLSRQRQSIISNSNLHRLTTSRKLQGYIRNGAFEPRRWTAPGQFSLFPVPCKCGIDTREVPLDPKFFTENMTIKIGKSCDMGHRWVVSKSVSDCAEALIGAYYVSGGLSASLHMMKWLGIDVDFDPNLVVEAINRVSLRCYIPKEDELIELERKIQHEFSAKFLLKEAITHSSLRESYSYERLEFLGDSVLDFLITRHLFNTYEQTGPGEMTDLRSACVNNENFAQVAVKNNLHTHLQRCATVLETQINDYLMSFQKPDETGRSIPSIQGPKALGDVVESIAGALLIDTRLDLDQVWRVFEPLLSPLVTPDKLQLPPYRELNELCDSLGYFFRVKCSNDGVKAQATIQLQLDDVLLTGDGSEQTNKLALGKAASHLLTQLEKRNISRKTSLGDNQSSMDVNLACNHSDRETLTSETTEIQSIVIPFIGPINMKKGGPRGTLHEFCKKHLWPMPTFDTSEEKSRTPFEFIDGGEKRTSFSSFTSTITLRIPNREAVMYAGEARPDKKSSFDSAVVELLYELERRKIVIIQK"
misc_feature 294..839 /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="DEXH-box helicase domain of endoribonuclease Dicer; Region: DEXHc_dicer; cd18034" /db_xref="CDD:350792" misc_feature order(444..449,516..521,594..596,600..605,612..614, 687..695) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="nucleic acid binding site [nucleotide binding]; other site" /db_xref="CDD:350792" misc_feature 1299..1694 /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="C-terminal helicase domain of the endoribonuclease Dicer; Region: SF2_C_dicer; cd18802" /db_xref="CDD:350189" misc_feature order(1380..1388,1563..1565,1620..1622,1626..1628) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="DNA binding site [nucleotide binding]" /db_xref="CDD:350189" misc_feature order(1575..1577,1581..1583,1656..1658,1662..1664) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="ATP binding site [chemical binding]; other site" /db_xref="CDD:350189" misc_feature 2598..3014 /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA...; Region: PAZ_CAF_like; cd02844" /db_xref="CDD:239210" misc_feature order(2718..2720,2796..2798,2808..2810,2862..2864, 2973..2975,2979..2981) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="nucleic acid-binding interface [nucleotide binding]; other site" /db_xref="CDD:239210" misc_feature 3144..3653 /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional...; Region: RIBOc; cd00593" /db_xref="CDD:238333" misc_feature order(3192..3197,3204..3209,3216..3218,3225..3230, 3237..3242,3246..3254,3282..3284,3585..3587,3612..3614) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="dimerization interface [polypeptide binding]; other site" /db_xref="CDD:238333" misc_feature order(3192..3194,3201..3203,3213..3215,3555..3557, 3564..3566) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="active site" /db_xref="CDD:238333" misc_feature order(3201..3203,3555..3557,3564..3566) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="metal binding site [ion binding]; metal-binding site" /db_xref="CDD:238333" misc_feature 3768..4211 /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional...; Region: RIBOc; cd00593" /db_xref="CDD:238333" misc_feature order(3819..3824,3831..3836,3843..3845,3852..3857, 3864..3869,3873..3881,3909..3911,4134..4136,4167..4169) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="dimerization interface [polypeptide binding]; other site" /db_xref="CDD:238333" misc_feature order(3819..3821,3828..3830,3840..3842,4104..4106, 4113..4115) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="active site" /db_xref="CDD:238333" misc_feature order(3828..3830,4104..4106,4113..4115) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="metal binding site [ion binding]; metal-binding site" /db_xref="CDD:238333" misc_feature 4602..4844 /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="double-stranded RNA binding motif (DSRM) superfamily; Region: DSRM_SF; cl00054" /db_xref="CDD:444671" misc_feature order(4602..4607,4611..4613,4719..4721,4788..4796, 4803..4805) /gene="DCL3" /locus_tag="AT3G43920" /gene_synonym="ATDCL3; dicer-like 3; DICER-LIKE 3" /note="RNA binding site [nucleotide binding]; other site" /db_xref="CDD:380679" ORIGIN
attcaacattcgaaactcatgttctgacctcatttatacacttgcccagtggtcagtgcagaaaaagagaaaaagaatcacctttttgttttaatctcaaagtcgaaattcgaaattcctctactcttcccgttaagtgtgttcctttttatccgttcgtcatgcattcgtcgttggagccggagaaaatggaggaaggtgggggaagcaattcgcttaagagaaaattctctgaaatcgatggagatcaaaatcttgattctgtctcttctcctatgatgactgactctaatggttatgaattgaaagtgtacgaggttgctaagaacaggaacataattgctgttttggggacagggattgataagtcagagatcactaagaggcttatcaaagctatgggttcttctgatacagacaaaagattgataattttcttggccccaactgtgaatcttgttaaacagcaatgctgtgagatcagagcacttgtgaatttgaaagttgaagagtactttggagctaaaggagttgataaatggacatctcagcgctgggatgaggaatttagcaagcacgatgttttagttatgactcctcaaatattattggatgtccttagaagtgcattcctgaaactagagatggtatgtcttctaataatagatgaatgccaccataccactggcaatcatccctatgcgaagttaatgaaggaattctatcacgaatccactagcaaaccgaagatatttggattgactgcgtcagccgtcattagaaaagctcaagtatcagaacttgagagactcatggactcaaagatttttaatcctgaagagcgtgaaggagtggaaaagtttgctacaacggttaaagaaggtccaatattgtataacccatcaccatcctgtagtttggaattgaaagaaaagttagaaacttcacacctcaagtttgatgcttctcttagaaggcttcaagagttgggaaaagacagttttctgaatatggataataagtttgagacatatcaaaagagattgtctatcgactacagagagattttgcattgccttgataatcttggcctgatttgcgcacacttggcggctgaagtctgcttggagaaaatctcagatacgaaagaggaaagtgaaacttataaagaatgctcaatggtgtgcaaggaatttcttgaggatattttatccaccattggggtgtatttgccgcaagatgataagagtctggtagatttgcagcaaaaccatctgtcagcagtaatttctgggcatgtatctccaaagctaaaagaactcttccatctattggattcctttagaggtgacaagcaaaagcagtgccttattttagttgagagaattataactgcgaaagtgatcgaaagattcgttaagaaagaagcctctttggcttaccttaatgtcttgtatttaaccgaaaacaacccctccaccaatgtatcggcacagaaaatgcaaattgaaatccctgatttatttcaacatggcaaggtgaatcttttattcatcacagatgtggttgaagagggatttcaggttccagattgctcatgcatggtttgttttgacctgcccaaaacaatgtgtagttactcgcagtctcaaaaacatgccaaacagagtaattctaagtctatcatgtttcttgaaagagggaacccgaagcaaagagaccatctgcatgaccttatgcgaagagaagtcctaattcaagatccagaagctccaaacttgaaatcgtgtccacctccagtgaaaaatggacacggtgtgaaggagattggatccatggttatcccagattctaacataactgtatctgaggaagcagcttccacacaaactatgagtgatcctcctagcagaaatgagcagttaccaccgtgtaaaaagttacgcttggataacaatctcttacaatccaacggcaaagagaaggttgcctcttctaaaagtaaatcatcttcatcggctgcaggttcaaaaaaacgtaaggagttgcacggaacaacctgtgcaaacgcattgtcaggaacctggggagaaaatattgatggcgccacctttcaggcttataagtttgacttctgttgtaatatttctggcgaagtatactcgagtttctctcttttgcttgagtcaactctcgccgaggatgttggtaaagttgagatggacctttacttggtcaggaagcttgtcaaggcttctgtctcaccttgtggccagatacgtttgagtcaagaggagctggtcaaagcaaaatattttcagcagtttttctttaatggcatgtttggaaagttgtttgttggatctaagtcacagggaacaaagagagaatttttgcttcaaactgacactagttctctttggcaccctgcctttatgtttctactgctaccagttgaaacaaatgatctagcttcgagtgcgacaattgattggtcagctatcaactcctgtgcctcaatagttgagttcttgaagaaaaattctcttcttgatcttcgggatagtgatgggaatcagtgcaatacctcatccggtcaggaagtcttactagacgataaaatggaagaaacgaatctgattcattttgccaatgcttcgtctgataaaaatagtctcgaagaacttgtggtcattgcaattcatactggacggatatactctatagttgaagccgtaagcgattcttctgctatgagcccctttgaggtggatgcctcatcaggctatgctacttatgcagaatattttaacaaaaagtatgggattgttttagcgcacccgaaccagccgttgatgaagttgaagcagagtcaccatgcgcacaaccttttagtcgacttcaatgaagagatggttgtgaagacagaaccaaaagctggcaatgttaggaaaagaaaaccgaatatccatgcgcatttgcctccagagcttttggctagaattgatgtaccgcgtgctgtgctaaaatcaatctacttgctgccttcagtgatgcaccgcctagagtctctaatgttggccagccagcttagggaagagattgattgtagcatagataacttcagtatatcaagtacatcgattcttgaagcagttacaacacttacatgccccgaatcattttcaatggagcggttggaactgctcggggattcagtcttgaagtatgttgcgagctgtcatctattccttaagtatcctgacaaagatgaggggcaactatcacggcagagacaatcgattatatctaactcaaatcttcaccgcttgacaaccagtcgcaaactacagggatacataagaaatggcgcttttgaaccgcgtcgctggactgcacctggtcaattttctctttttcctgttccttgcaagtgtgggattgatactagagaagtaccattggacccaaaattcttcacagaaaacatgactatcaaaataggcaagtcttgcgacatgggtcatagatgggtagtttcaaaatctgtatcagattgcgctgaggccctgattggtgcctattatgtaagcggtggattgtctgcttctctccatatgatgaaatggctcggtattgacgtcgattttgacccaaacctagtcgttgaagccatcaatagagtttctctacggtgttacattcctaaagaagatgagctcatagagttggagagaaagatccaacatgaattctctgcaaagtttcttttaaaagaggctatcacacactcctctcttcgtgaatcctattcatacgagagattagagtttcttggcgattctgtactggattttctaataacccgtcatctttttaacacctacgaacaaactgggcctggagagatgaccgatcttcgttctgcatgtgtaaacaatgaaaattttgcgcaagttgcagtgaaaaataacctgcatacccaccttcaacgctgtgctacggttctcgagactcaaataaacgactatctgatgtcctttcaaaagccagatgagactggtagatcaatcccttcaatacagggccctaaggctcttggagatgttgtggagagtatcgctggagcattgctgatcgatacgaggttagatctcgatcaagtgtggagagtctttgagccgttgctttctccacttgtaactccagataaacttcagcttcctccataccgggagctcaatgagctatgcgactctcttgggtatttctttcgagtgaaatgttcaaatgatggtgtcaaagcacaagccacgatccagttgcagctggatgatgttcttttaactggagatggatctgaacagacaaataaactggccttgggaaaagcagcttcacatctgcttacacaacttgagaagagaaacatttcacgtaaaacctcgctcggggataatcaaagttccatggatgtcaatcttgcttgcaatcatagcgacagagaaactctgacttcagagactactgaaatccagagtatagtgattccatttattggacctataaacatgaagaaaggcgggcctcgtggaactctacatgagttttgcaagaagcatctgtggccaatgcctactttcgatacctcggaagagaaatccagaactccgtttgaattcatagatggcggtgagaagcggactagcttcagcagtttcacatcgaccataaccctaaggatacccaatcgtgaggctgtgatgtatgctggagaagcaaggcctgacaagaagagttccttcgactctgcagtcgtggaattgctttatgagctcgagcgccgcaagatcgtcataatacaaaagtag
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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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