LOCUS       NM_001336818            6509 bp    mRNA    linear   PLN 20-OCT-2022
DEFINITION  Arabidopsis thaliana nuclear RNA polymerase D1B (NRPD1B), mRNA.
ACCESSION   NM_001336818
VERSION     NM_001336818.1
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 6509)
  AUTHORS   Lin,X., Kaul,S., Rounsley,S., Shea,T.P., Benito,M.I., Town,C.D.,
            Fujii,C.Y., Mason,T., Bowman,C.L., Barnstead,M., Feldblyum,T.V.,
            Buell,C.R., Ketchum,K.A., Lee,J., Ronning,C.M., Koo,H.L.,
            Moffat,K.S., Cronin,L.A., Shen,M., Pai,G., Van Aken,S., Umayam,L.,
            Tallon,L.J., Gill,J.E., Adams,M.D., Carrera,A.J., Creasy,T.H.,
            Goodman,H.M., Somerville,C.R., Copenhaver,G.P., Preuss,D.,
            Nierman,W.C., White,O., Eisen,J.A., Salzberg,S.L., Fraser,C.M. and
            Venter,J.C.
  TITLE     Sequence and analysis of chromosome 2 of the plant Arabidopsis
            thaliana
  JOURNAL   Nature 402 (6763), 761-768 (1999)
   PUBMED   10617197
REFERENCE   2  (bases 1 to 6509)
  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 6509)
  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 6509)
  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_003071).
FEATURES             Location/Qualifiers
     source          1..6509
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /chromosome="2"
                     /ecotype="Columbia"
     gene            1..6509
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="Encodes the unique largest subunit of nuclear
                     DNA-dependent RNA polymerase V; homologous to budding
                     yeast RPB1 and the E. coli RNA polymerase beta prime
                     subunit. Required for normal RNA-directed DNA methylation
                     at non-CG methylation sites and transgene silencing."
                     /db_xref="Araport:AT2G40030"
                     /db_xref="GeneID:818591"
                     /db_xref="TAIR:AT2G40030"
     CDS             275..5602
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /codon_start=1
                     /product="nuclear RNA polymerase D1B"
                     /protein_id="NP_001323985.1"
                     /db_xref="Araport:AT2G40030"
                     /db_xref="GeneID:818591"
                     /db_xref="TAIR:AT2G40030"
                     /translation="

MEEESTSEILDGEIVGITFALASHHEICIQSISESAINHPSQLTNAFLGLPLEFGKCESCGATEPDKCEGHFGYIQLPVPIYHPAHVNELKQMLSLLCLKCLKIKKAKGTSGGLADRLLGVCCEEASQISIKDRASDGASYLELKLPSRSRLQPGCWNFLERYGYRYGSDYTRPLLAREVKEILRRIPEESRKKLTAKGHIPQEGYILEYLPVPPNCLSVPEASDGFSTMSVDPSRIELKDVLKKVIAIKSSRSGETNFESHKAEASEMFRVVDTYLQVRGTAKAARNIDMRYGVSKISDSSSSKAWTEKMRTLFIRKGSGFSSRSVITGDAYRHVNEVGIPIEIAQRITFEERVSVHNRGYLQKLVDDKLCLSYTQGSTTYSLRDGSKGHTELKPGQVVHRRVMDGDVVFINRPPTTHKHSLQALRVYVHEDNTVKINPLMCSPLSADFDGDCVHLFYPQSLSAKAEVMELFSVEKQLLSSHTGQLILQMGSDSLLSLRVMLERVFLDKATAQQLAMYGSLSLPPPALRKSSKSGPAWTVFQILQLAFPERLSCKGDRFLVDGSDLLKFDFGVDAMGSIINEIVTSIFLEKGPKETLGFFDSLQPLLMESLFAEGFSLSLEDLSMSRADMDVIHNLIIREISPMVSRLRLSYRDELQLENSIHKVKEVAANFMLKSYSIRNLIDIKSNSAITKLVQQTGFLGLQLSDKKKFYTKTLVEDMAIFCKRKYGRISSSGDFGIVKGCFFHGLDPYEEMAHSIAAREVIVRSSRGLAEPGTLFKNLMAVLRDIVITNDGTVRNTCSNSVIQFKYGVDSERGHQGLFEAGEPVGVLAATAMSNPAYKAVLDSSPNSNSSWELMKEVLLCKVNFQNTTNDRRVILYLNECHCGKRFCQENAACTVRNKLNKVSLKDTAVEFLVEYRKQPTISEIFGIDSCLHGHIHLNKTLLQDWNISMQDIHQKCEDVINSLGQKKKKKATDDFKRTSLSVSECCSFRDPCGSKGSDMPCLTFSYNATDPDLERTLDVLCNTVYPVLLEIVIKGDSRICSANIIWNSSDMTTWIRNRHASRRGEWVLDVTVEKSAVKQSGDAWRVVIDSCLSVLHLIDTKRSIPYSVKQVQELLGLSCAFEQAVQRLSASVRMVSKGVLKEHIILLANNMTCSGTMLGFNSGGYKALTRSLNIKAPFTEATLIAPRKCFEKAAEKCHTDSLSTVVGSCSWGKRVDVGTGSQFELLWNQKETGLDDKEETDVYSFLQMVISTTNADAFVSSPGFDVTEEEMAEWAESPERDSALGEPKFEDSADFQNLHDEGKPSGANWEKSSSWDNGCSGGSEWGVSKSTGGEANPESNWEKTTNVEKEDAWSSWNTRKDAQESSKSDSGGAWGIKTKDADADTTPNWETSPAPKDSIVPENNEPTSDVWGHKSVSDKSWDKKNWGTESAPAAWGSTDAAVWGSSDKKNSETESDAAAWGSRDKNNSDVGSGAGVLGPWNKKSSETESNGATWGSSDKTKSGAAAWNSWDKKNIETDSEPAAWGSQGKKNSETESGPAAWGAWDKKKSETEPGPAGWGMGDKKNSETELGPAAMGNWDKKKSDTKSGPAAWGSTDAAAWGSSDKNNSETESDAAAWGSRNKKTSEIESGAGAWGSWGQPSPTAEDKDTNEDDRNPWVSLKETKSREKDDKERSQWGNPAKKFPSSGGWSNGGGADWKGNRNHTPRPPRSEDNLAPMFTATRQRLDSFTSEEQELLSDVEPVMRTLRKIMHPSAYAFLVLTLCLYNFQFYV"

     misc_feature    344..2668
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="Largest subunit (NRPD1) of higher plant RNA
                     polymerase IV, N-terminal domain; Region: RNAP_IV_RPD1_N;
                     cd10506"
                     /db_xref="CDD:259849"
     misc_feature    order(443..445,452..454,476..478,485..487)
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="Zn-binding [ion binding]; other site"
                     /db_xref="CDD:259849"
     misc_feature    order(1196..1198,1211..1213,1229..1231,1247..1249,
                     1514..1522,1619..1621,1625..1627,1631..1633,2600..2605)
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="putative active site region [active]"
                     /db_xref="CDD:259849"
     misc_feature    2747..3967
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="Largest subunit (NRPD1) of Higher plant RNA
                     polymerase IV, C-terminal domain; Region: RNAP_IV_NRPD1_C;
                     cd02737"
                     /db_xref="CDD:132724"
     misc_feature    order(2747..2830,2834..2911,3479..3511,3536..3685,
                     3695..3778)
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="cleft [active]"
                     /db_xref="CDD:132724"
     misc_feature    order(2750..2752,3941..3943,3950..3961,3965..3967)
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="Rpb1 (NRPD1) - Rpb6 interaction site [polypeptide
                     binding]; other site"
                     /db_xref="CDD:132724"
     misc_feature    order(2753..2755,2762..2764,3857..3859,3887..3895,
                     3911..3916,3920..3922,3926..3928,3941..3943)
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="putative Rpb1 (NRPD1) - Rpb2 interaction site
                     [polypeptide binding]; other site"
                     /db_xref="CDD:132724"
     misc_feature    order(3566..3568,3584..3589,3593..3595,3623..3643,
                     3647..3649,3707..3709,3740..3745,3749..3751)
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="putative Rpb1 (NRPD1) - Rpb5 interaction site
                     [polypeptide binding]; other site"
                     /db_xref="CDD:132724"
     misc_feature    3812..3937
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="clamp [active]"
                     /db_xref="CDD:132724"
     misc_feature    <4658..5020
                     /gene="NRPD1B"
                     /locus_tag="AT2G40030"
                     /gene_synonym="ATNRPD1B; DEFECTIVE IN MERISTEM SILENCING
                     5; DMS5; DRD3; NRPE1; nuclear RNA polymerase D1B;
                     T28M21.19; T28M21_19"
                     /note="Argonaute hook; Region: Ago_hook; pfam10427"
                     /db_xref="CDD:463088"
ORIGIN      

gcaatgtgggttttaaagacggaagctgaagagtgaagaagaacaaaagatttttgagagagaaaagtagagtcactccaaaattgttctctcgcaatcttctttctcggtttcctcttttaagaaaaagtccgccattttcactctcactcagatttcttccctcttctcacctgcaaaaacccttgtttcccgctgtttcgtttcttctccggttgaggaaccaaaacgggtcaaatacgcagctgaatcatcgaattcttagggttttttcatggaggaagaatctacatcagagattcttgacggagagattgttggaatcacatttgctcttgctagtcaccatgaaatatgtattcaatcgattagtgaatccgcaattaatcatcccagtcaactcactaacgcattcttggggttacctcttgaatttggtaaatgtgaatcttgcggtgcgacagaaccagataaatgtgaaggtcattttggttatattcagcttccagtgccaatataccatcctgctcatgttaatgagttgaaacaaatgctgagccttctgtgcttgaaatgtctgaagataaagaaggcaaagggcacaagtggtggtctggcggatcgcttgttgggtgtctgttgtgaggaagcttcgcaaatctcaatcaaagatagagcatcagatggtgcctcatatctagaactgaagctcccatctaggtcaagactgcagcctggttgctggaatttcctggaaagatatggttatcgctatggaagcgattacacgcgtcccctgctggcaagagaggttaaggaaattctaagacggatccccgaagaatcaagaaagaaactcacggcaaagggacatattcctcaagaaggatacatactagagtatcttcctgtcccgcctaactgtttgtcagtgccagaggcttctgatggtttcagcaccatgtcagtggatccttccagaattgagctaaaggacgttctgaagaaagtcatagccataaaaagctctaggtctggcgagacaaactttgagtcgcataaggctgaagccagtgagatgtttagagtggtggatacctatctccaggtgaggggtactgcaaaagcggcaagaaacattgatatgagatacggggtgtctaagatctcggatagttcatcttcaaaagcttggacagaaaaaatgagaacacttttcatccgtaagggttcaggtttctcttcccgtagcgtcatcactggagatgcttaccgacatgtgaatgaggtagggatcccaatagaaattgcgcagagaatcacatttgaggaaagggttagtgtccacaatagaggttatctacaaaagttggtagacgacaagttgtgtttgagttatactcaaggttctacgacctattctttaagggatggatccaaggggcacactgagcttaaacccgggcaggttgttcatcgcagggtcatggatggggatgttgtgtttatcaacagacccccgacaacacataaacattctcttcaagcgcttcgggtgtatgttcatgaagacaacaccgtgaagattaaccctctgatgtgtagccccctcagtgctgattttgatggtgattgtgtccatttgttctaccctcagtctcttagtgctaaggcagaggttatggagctcttctctgtggagaagcaactgcttagctcacatactggacagctgattttgcagatgggtagtgattctttactgtctttgagggtaatgctggagcgggtatttctggacaaggcaactgctcaacagttagctatgtatggctctctgtccctgccaccaccagcactaaggaagtccagtaaatctggcccagcttggacagttttccagattctacagcttgcctttccagaacgtctgagttgcaaaggagacagattcctggttgatggaagtgatttgctgaagtttgatttcggggttgacgcgatggggtccatcatcaatgaaattgtaacttcaatcttcctggagaagggtccaaaggagacacttggattctttgattcgctgcagcctctattgatggaaagtctgtttgctgagggatttagtctaagtttggaagacttatccatgtctagggcagacatggatgtaattcacaacctaataatccgagagatttcacctatggtgtctcgcttgagattatcatatagagatgaattgcagctagagaacagcatccacaaagtgaaggaagtggctgctaactttatgctgaagtcatattccattcggaacttgattgatatcaagagtaactcagcaatcaccaagctggtgcagcagacaggcttcttgggtcttcagctttctgacaagaagaagttttacacgaagactctggtagaggacatggctatcttttgtaagagaaagtatggcaggatttcttcatctggtgattttggaatagtgaagggctgcttctttcatgggctggatccgtatgaagagatggctcattcaattgcagctagggaggtaattgttcgctcttcaaggggattagctgagcctggaaccctctttaagaacctgatggctgttcttcgggatatcgtgattacaaacgatggaactgtaagaaacacctgtagtaactcagtcatccagttcaaatatggagttgattctgaacgtggacatcaaggtctgtttgaagctggagaacctgttggagtattggcagctactgccatgtcaaatcctgcatataaggcagtgcttgattcctctccaaatagtaattcatcatgggagctaatgaaggaagttctgctctgcaaagtcaatttccaaaacactactaatgatcggcgcgtaatcctttatttaaacgaatgccattgtggaaaaaggttttgccaggaaaatgctgcttgcacagtcaggaacaagctgaataaagttagtcttaaagatactgcagtggaattcctagtcgaatatagaaagcaaccaactatatcagaaatttttggaattgattcatgcctacatggccatattcatcttaataagacattgctgcaagattggaacatcagtatgcaggatatacatcaaaagtgtgaggatgtaattaactcactaggacaaaagaaaaagaagaaagctactgatgatttcaagagaacaagtttgtctgtcagtgagtgctgctctttccgagatccttgtgggagcaaaggttcggatatgccttgtttgacgttctcctacaatgccaccgatcccgatctagaacgaactcttgatgttctttgcaatacagtttacccagttctgctggaaatagtgatcaaaggtgattcacggatttgctcagcaaatataatctggaatagttcagacatgacaacgtggatccggaatcgtcatgcatcccgccgaggggaatgggttttggatgtcactgttgaaaaatctgctgtcaagcaaagtggtgatgcatggagggttgtgatagactcatgtctttcagtgcttcatctaatagacacaaaacggtcaatcccttattctgtaaaacaagtgcaagaattgcttgggttatcctgtgcttttgagcaagcagtacagcgtctatcagcttcagtgagaatggtctccaagggagttttgaaagaacacatcattctcctagcaaacaacatgacttgttcagggactatgttgggtttcaattctggaggttacaaagctttgacccgatccttaaacatcaaggctccattcacagaagcaactctgattgcaccaagaaaatgttttgagaaagcggctgagaaatgtcatacagattcactatcaacagtcgttgggtcttgttcttggggaaaacgcgtggatgttggtacaggctcacagtttgagctcctatggaaccaaaaagagactggtctagatgataaagaagaaacagatgtgtacagcttccttcaaatggtcatatccacgacaaacgcagatgcatttgtttcttcccctggttttgatgttacagaggaagaaatggctgaatgggctgaatcgcccgagcgagactctgctcttggagagcccaagtttgaggacagtgccgacttccaaaatttacatgacgaaggcaagccatcaggagccaactgggagaaaagctcttcgtgggacaatggttgcagtggtggttcagagtggggagtctcaaaaagtacaggtggtgaggcaaacccggagtctaattgggaaaagactacaaatgttgagaaggaagatgcttggtctagttggaacactagaaaagatgctcaagaatcttccaagtcagattcagggggtgcttggggtataaagacaaaggatgctgatgcagatacaacaccaaactgggaaacaagtccagctccgaaggattccattgtcccagaaaataatgagccgacttctgacgtttggggacacaaatctgtttcagacaaatcgtgggacaaaaagaactggggaactgaatcagctcctgctgcatggggttctacagatgctgctgtttggggttctagtgataaaaagaactcggaaacagaatcagatgctgctgcttggggttccagggacaaaaataattctgacgttgggtcaggtgctggtgttttaggtccctggaacaagaagagctcggaaactgagtcaaatggtgctacttggggttctagtgacaaaaccaaatcaggtgctgctgcatggaattcttgggacaaaaagaacatagaaactgactcagaacctgctgcttggggttctcagggaaaaaagaattctgaaactgagtcaggtcctgctgcttggggtgcttgggacaaaaagaaatcggaaactgaaccaggtcctgctggttggggtatgggggacaaaaagaattctgaaactgaattaggccctgctgctatgggtaattgggacaaaaagaaatcggatacgaaatcaggtccagctgcttggggatctacagatgctgctgcttggggttctagtgacaaaaacaactcggaaactgaatcagatgctgctgcttggggttctaggaacaaaaagacttctgaaattgaatcaggtgctggcgcttggggttcgtggggacagccaagtcccactgcagaagacaaggataccaatgaggatgatagaaatccgtgggtttccttgaaggagaccaaaagtagagagaaggatgataaagagagaagccagtggggaaatccagccaagaaatttccatctagtggtggctggtccaatggtggtggtgcagactggaaaggaaataggaaccatactcctaggccacctagatctgaggataatttggctcccatgtttacagcaacgagacagcgcttggactcattcacctctgaggagcaagagctgctctcagatgttgagccagtcatgaggactctcaggaaaattatgcatccgtctgcgtatgcctttctagttcttacgctctgtttatacaatttccagttctatgtataattaattatgctgtttcacatgccatatacttgttatgcttcatctatctaaaactatcttctttcgatgaaggtaccctgatggagacccaatttctgatgatgacaagacgtttgtcctggagaagattttgaacttccatccccaaaaagagacaaagcttggttctggcgttgacttcatcacggttgataagcacaccatcttctcagacagcaggtgcttctttgttgtctcaactgatggggccaaacaggacttttcataccgaaaatccctcaacaactatttgatgaagaaataccctgaccgtgctgaagaattcattgacaagtactttacgaaacctcggcctagcggaaacagagacaggaacaaccaagatgccacaccacctggggaagaacagtctcagcctccgaatcagtctataggtaatggaggtgacgactttcagacacagactcagtctcagtctccatctcagactcgggctcagtctccatctcaggctcaggctcagtctccatctcagacgcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctcagtctccatcccagactcagactcagtctccgtctcagactcaggctcaggctcagtctccatcatctcagtctccgtcccagacgcagacataaactcttgagaaccaaagaagatttggttcgtttaggtaaaccattcagtctccactgttttgttttgatgtacataaagagtggagagaatggcggtttttatcattaaaagactctgatgtgaagtgcaaaacaatgtgtaaatgcagttctctagtttcagatcgtttgtcctaa

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