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Previous release (v1)
2024-04-17 05:06:54, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS NM_001084632 4125 bp mRNA linear PLN 20-OCT-2022
DEFINITION Arabidopsis thaliana dicer-like 2 (DCL2), partial mRNA.
ACCESSION NM_001084632
VERSION NM_001084632.1
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 4125)
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 4125)
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 4125)
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 4125)
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 both ends.
FEATURES Location/Qualifiers
source 1..4125
/organism="Arabidopsis thaliana"
/mol_type="mRNA"
/db_xref="taxon:3702"
/chromosome="3"
/ecotype="Columbia"
gene <1..>4125
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="Encodes a Dicer-like protein that functions in the
antiviral silencing response in turnip-crinkle
virus-infected plants but not in TMV or
CMV-strain-Y-infected plants. Involved in the production
of ta-siRNAs. Partially antagonizes the production of
miRNAs by DCL1. Substitutes for DCL4 to produce viral
siRNA when DCL4 is missing or inhibited. Able to produce
siRNAs but not miRNAs."
/db_xref="Araport:AT3G03300"
/db_xref="GeneID:821300"
/db_xref="TAIR:AT3G03300"
CDS 1..4125
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/inference="Similar to RNA sequence,
EST:INSD:EG523966.1,INSD:ES138108.1,INSD:EG470520.1,
INSD:EG523965.1,INSD:ES072351.1,INSD:ES189211.1,
INSD:ES204888.1,INSD:ES135198.1,INSD:ES171321.1,
INSD:ES202797.1,INSD:BE524988.1,INSD:ES126577.1,
INSD:BE529383.1"
/inference="Similar to RNA sequence, mRNA:INSD:DQ479971.1"
/note="dicer-like 2 (DCL2); FUNCTIONS IN: in 7 functions;
INVOLVED IN: defense response to virus, maintenance of DNA
methylation, production of ta-siRNAs involved in RNA
interference; LOCATED IN: intracellular; EXPRESSED IN: 23
plant structures; EXPRESSED DURING: 13 growth stages;
CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH
box type, N-terminal (InterPro:IPR011545), Double-stranded
RNA-binding (InterPro:IPR001159), Argonaute/Dicer protein,
PAZ (InterPro:IPR003100), Ribonuclease III
(InterPro:IPR000999), DNA/RNA helicase, C-terminal
(InterPro:IPR001650), Dicer double-stranded RNA-binding
fold (InterPro:IPR005034), Helicase, superfamily 1/2,
ATP-binding domain (InterPro:IPR014021); BEST Arabidopsis
thaliana protein match is: dicer-like 4
(TAIR:AT5G20320.1); Has 11820 Blast hits to 10882 proteins
in 2832 species: Archae - 232; Bacteria - 5768; Metazoa -
1870; Fungi - 1100; Plants - 675; Viruses - 26; Other
Eukaryotes - 2149 (source: NCBI BLink)."
/codon_start=1
/product="dicer-like 2"
/protein_id="NP_001078101.1"
/db_xref="GeneID:821300"
/db_xref="TAIR:AT3G03300"
/db_xref="Araport:AT3G03300"
/translation="
MLLCLLGSSSGSCHSGIGVRIGVVDKGIHQYTDLSFVLQFLHYYTCSFSKFRNFSVTFSIISAFFLVCFTQQAEALKMHTDLKVGMYWGDMGVDFWDSSTWKQEVDKYEVLVMTPAILLDALRHSFLSLSMIKVLIVDECHHAGGKHPYACIMREFYHKELNSGTSNVPRIFGMTASLVKTKGENLDSYWKKIHELETLMNSKVYTCENESVLAGFVPFSTPSFKYYQHIKIPSPKRASLVEKLERLTIKHRLSLGTLDLNSSTVDSVEKRLLRISSTLTYCLDDLGILLAQKAAQSLSASQNDSFLWGELNMFSVALVKKFCSDASQEFLAEIPQGLNWSVANINGNAEAGLLTLKTVCLIETLLGYSSLENIRCIIFVDRVITAIVLESLLAEILPNCNNWKTKYVAGNNSGLQNQTRKKQNEIVEDFRRGLVNIIVATSILEEGLDVQSCNLVIRFDPASNICSFIQSRGRARMQNSDYLMMVESGDLLTQSRLMKYLSGGKRMREESLDHSLVPCPPLPDDSDEPLFRVESTGATVTLSSSVSLIYHYCSRLPSDEYFKPAPRFDVNKDQGSCTLYLPKSCPVKEVKAEANNKVLKQAVCLKACIQLHKVGALSDHLVPDMVVAETVSQKLEKIQYNTEQPCYFPPELVSQFSAQPETTYHFYLIRMKPNSPRNFHLNDVLLGTRVVLEDDIGNTSFRLEDHRGTIAVTLSYVGAFHLTQEEVLFCRRFQITLFRVLLDHSVENLMEALNGLHLRDGVALDYLLVPSTHSHETSLIDWEVIRSVNLTSHEVLEKHENCSTNGASRILHTKDGLFCTCVVQNALVYTPHNGYVYCTKGVLNNLNGNSLLTKRNSGDQTYIEYYEERHGIQLNFVDEPLLNGRHIFTLHSYLHMAKKKKEKEHDREFVELPPELCHVILSPISVDMIYSYTFIPSVMQRIESLLIAYNLKKSIPKVNIPTIKVLEAITTKKCEDQFHLESLETLGDSFLKYAVCQQLFQHCHTHHEGLLSTKKDGMISNVMLCQFGCQQKLQGFIRDECFEPKGWMVPGQSSAAYSLVNDTLPESRNIYVASRRNLKRKSVADVVESLIGAYLSEGGELAALMFMNWVGIKVDFTTTKIQRDSPIQAEKLVNVGYMESLLNYSFEDKSLLVEALTHGSYMMPEIPRCYQRLEFLGDSVLDYLITKHLYDKYPCLSPGLLTDMRSASVNNECYALVAVKANLHKHILYASHHLHKHISRTVSEFEQSSLQSTFGWESDISFPKVLGDVIESLAGAIFVDSGYNKEVVFASIKPLLGCMITPETVKLHPVRELTELCQKWQFELSKAKDFDSFTVEVKAKEMSFAHTAKASDKKMAKKLAYKEVLNLLKNSLDY"
misc_feature <187..624
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="DEXH-box helicase domain of endoribonuclease Dicer;
Region: DEXHc_dicer; cd18034"
/db_xref="CDD:350792"
misc_feature order(262..267,340..342,346..351,358..360,433..441)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="nucleic acid binding site [nucleotide binding];
other site"
/db_xref="CDD:350792"
misc_feature 1069..1458
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="C-terminal helicase domain of the endoribonuclease
Dicer; Region: SF2_C_dicer; cd18802"
/db_xref="CDD:350189"
misc_feature order(1141..1149,1327..1329,1384..1386,1390..1392)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="DNA binding site [nucleotide binding]"
/db_xref="CDD:350189"
misc_feature order(1339..1341,1345..1347,1420..1422,1426..1428)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="ATP binding site [chemical binding]; other site"
/db_xref="CDD:350189"
misc_feature 1633..1869
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="Dicer dimerization domain; Region: Dicer_dimer;
pfam03368"
/db_xref="CDD:427264"
misc_feature 2377..2769
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="PAZ domain, named PAZ after the proteins Piwi
Argonaut and Zwille. PAZ is found in two families of
proteins that are essential components of RNA-mediated
gene-silencing pathways, including RNA interference, the
piwi and Dicer families. PAZ functions as a...; Region:
PAZ; cl00301"
/db_xref="CDD:444818"
misc_feature order(2509..2511,2584..2586,2596..2598,2650..2652,
2728..2730,2734..2736)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="nucleic acid-binding interface [nucleotide
binding]; other site"
/db_xref="CDD:239207"
misc_feature 2896..3327
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/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(2941..2946,2953..2958,2965..2967,2974..2979,
2986..2991,2995..3003,3031..3033,3283..3285,3310..3312)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="dimerization interface [polypeptide binding]; other
site"
/db_xref="CDD:238333"
misc_feature order(2941..2943,2950..2952,2962..2964,3253..3255,
3262..3264)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="active site"
/db_xref="CDD:238333"
misc_feature order(2950..2952,3253..3255,3262..3264)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="metal binding site [ion binding]; metal-binding
site"
/db_xref="CDD:238333"
misc_feature 3448..3912
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/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(3511..3516,3523..3528,3535..3537,3544..3549,
3556..3561,3565..3573,3601..3603,3832..3834,3865..3867)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="dimerization interface [polypeptide binding]; other
site"
/db_xref="CDD:238333"
misc_feature order(3511..3513,3520..3522,3532..3534,3802..3804,
3811..3813)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="active site"
/db_xref="CDD:238333"
misc_feature order(3520..3522,3802..3804,3811..3813)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="metal binding site [ion binding]; metal-binding
site"
/db_xref="CDD:238333"
misc_feature 3919..4104
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="double-stranded RNA binding motif (DSRM)
superfamily; Region: DSRM_SF; cl00054"
/db_xref="CDD:444671"
misc_feature order(3940..3945,3949..3951,3997..3999,4054..4062,
4069..4071)
/gene="DCL2"
/locus_tag="AT3G03300"
/gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2;
T17B22.28"
/note="RNA binding site [nucleotide binding]; other site"
/db_xref="CDD:380679"
ORIGIN
atgcttctgtgtcttcttggttcctcaagtggttcttgtcactcaggtattggtgttaggattggagttgtggacaaagggattcaccaatatacggacttgtcctttgttctacaatttctgcattattacacgtgctccttttccaaatttagaaactttagtgttactttctccattatttctgcatttttccttgtgtgttttacgcagcaagcagaagccctgaagatgcatactgatctaaaagttggtatgtattggggagacatgggggtggacttttgggattcttcaacatggaaacaagaagttgataaatatgaggttctggtgatgacccctgccattttgctcgacgcgttgaggcatagttttctgagcttgagcatgatcaaggttctaatagttgatgagtgtcatcatgcagggggaaagcacccttatgcttgtatcatgagggagttctatcataaggagttaaattctggaacttccaatgttccacggatatttgggatgactgcttcacttgtgaaaacaaagggtgaaaatctggatagctactggaaaaaaattcatgaactcgaaactctaatgaattcaaaggtctatacctgtgagaatgagtctgtgctggctgggtttgtccccttttctacaccaagcttcaagtattaccagcacataaaaataccaagtcccaaacgagcaagcttggtagagaagctagaaagactaacgataaagcatcgcttatcccttggaaccttggatctcaactcctctactgttgattctgtagagaagagactgttgaggataagttcaactctaacatattgtttggatgatctcggaattttgctggcccagaaggctgctcagtcattgtcagccagtcagaatgactctttcttgtggggcgaactaaatatgtttagcgtggccttggtaaaaaaattctgctctgatgcttcacaggagtttttggctgagatacctcaaggtcttaattggagtgttgcaaacataaatggaaatgcggaggcaggtctcctaactttaaaaactgtctgcctcattgagactcttcttggttatagctccttggagaacatacggtgcatcatttttgtggatagggtgataacagccatcgttctggaatcccttttggctgagattcttccaaactgtaataactggaaaaccaagtacgttgcaggaaataactctggtctgcaaaatcaaactcggaagaagcaaaatgaaattgtggaagacttccggagaggcttggttaacatcattgtagcaacatctattctagaggagggtctagatgttcaaagttgcaacctggttatcagatttgaccctgcatccaacatttgcagtttcatacagtctcgtgggcgtgctagaatgcaaaattcagattatttgatgatggtggaaagcggagatctgttaacacaatctcgattaatgaaatatctttctggtgggaaaagaatgcgcgaagagtctttggatcattctcttgttccctgtccacctcttccagatgattcagatgaaccactcttccgtgtcgaaagtactggagcaactgtaactcttagctcaagcgtcagcttaatatatcattactgctcaaggcttccttcagatgagtacttcaaaccagcccctagatttgatgtaaacaaggatcaggggagttgcaccctttaccttcctaagagttgcccagtaaaagaagttaaagctgaagcaaataataaagtgttaaaacaagctgtctgtcttaaagcttgcattcaactgcacaaagttggagctctaagtgatcatcttgtgcctgacatggttgtggcggaaactgtctcacaaaaactcgagaaaatccaatataacacagagcagccatgttacttccccccagagctagtctcccagttttcagcacagccggagacaacataccacttctacttaataagaatgaagccaaactctccaagaaattttcatttaaacgatgttttactaggcaccagagttgtgcttgaagatgacattgggaacacaagcttccggttggaagatcataggggtacaatagctgtgacattgagttatgtgggagcttttcaccttacacaagaagaggtccttttctgtagaagatttcagataactctattccgagttcttttagatcacagtgtggaaaatttgatggaggcattgaatggattgcatctcagagatggggtggcacttgattatctactagttccatccactcattcacatgaaacatctcttattgattgggaagtgatcagatccgtgaatctaacttctcatgaggttttggaaaaacacgaaaattgttctaccaacggtgcttctcgcattctacacacaaaagacggcttgttttgtacttgtgtcgtacaaaatgcattggtttacacaccacataatggatacgtctactgcacaaaaggtgttctcaacaatctaaacggaaattcattattgaccaagagaaattctggcgatcagacttacattgagtactacgaggaaaggcatgggattcaattaaattttgtggatgaacctcttctaaatggaagacacattttcacgttgcatagttatcttcacatggccaagaagaagaaggagaaagagcatgacagggaatttgttgaactacctcctgagctttgtcatgtcattttgtccccaatatcagttgatatgatctattcatatacttttatcccatctgttatgcaacgcattgaatctttgcttatagcatacaacctgaagaaaagcatcccaaaagtcaatattccaaccattaaggttttggaagctattacgacaaagaagtgcgaagatcagttccacttggaatcactagaaactcttggtgactcttttctgaaatatgctgtttgtcagcaactattccaacactgtcatactcaccatgagggtcttcttagcacgaagaaagatggaatgatttcaaatgtcatgctctgccaatttggatgtcagcagaaacttcagggatttatccgcgatgagtgttttgaacccaaaggttggatggttccaggtcaatcatctgcagcttattcacttgtaaacgatactctacccgagtctagaaacatatacgttgctagtaggaggaatctgaaacgcaagagtgtggccgatgttgtagaatcattaattggagcatatctcagcgagggaggtgaacttgcagctttgatgttcatgaattgggttggaataaaggtcgactttacaactacgaagatccagagagattccccaatacaagcagagaagcttgtgaatgtaggttatatggagtcgctgttgaattacagttttgaggataagtctcttctagttgaagcattgactcatggttcatacatgatgcctgaaattccaagatgctatcagcggttggagttcctcggtgactctgtattggattatctcataaccaagcatctatacgacaaatatccttgtctgtcccctggactattaaccgacatgcgatcagcttctgttaacaatgaatgttatgccctagtggcggtgaaagcaaacctgcacaaacacatcctgtacgcctctcatcatctccataagcacatctctagaactgtcagtgagtttgaacagtcttctttgcaatccactttcggatgggaatccgatatatcttttccaaaggttcttggagatgtgatagaatctctagcaggcgcgatatttgttgactcaggttacaacaaggaagtagtgtttgcaagtattaaaccacttttgggttgtatgataactccagagactgtcaagttgcatcctgtgagagagttgacagaattatgtcagaagtggcagttcgagttgagtaaagctaaagatttcgattctttcacggttgaggtgaaagctaaggagatgagttttgctcacacagcaaaggcctctgataagaaaatggccaagaaattggcttacaaagaagtcttgaacttacttaagaacagcctggactactaa
//
by
@meso_cacase at
DBCLS
This page is licensed under a
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.
[Full Text]