LOCUS       NM_202316               2136 bp    mRNA    linear   PLN 20-OCT-2022
DEFINITION  Arabidopsis thaliana Zinc finger (C3HC4-type RING finger) family
            protein (VIM1), mRNA.
ACCESSION   NM_202316
VERSION     NM_202316.2
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 2136)
  AUTHORS   Theologis,A., Ecker,J.R., Palm,C.J., Federspiel,N.A., Kaul,S.,
            White,O., Alonso,J., Altafi,H., Araujo,R., Bowman,C.L.,
            Brooks,S.Y., Buehler,E., Chan,A., Chao,Q., Chen,H., Cheuk,R.F.,
            Chin,C.W., Chung,M.K., Conn,L., Conway,A.B., Conway,A.R.,
            Creasy,T.H., Dewar,K., Dunn,P., Etgu,P., Feldblyum,T.V., Feng,J.,
            Fong,B., Fujii,C.Y., Gill,J.E., Goldsmith,A.D., Haas,B.,
            Hansen,N.F., Hughes,B., Huizar,L., Hunter,J.L., Jenkins,J.,
            Johnson-Hopson,C., Khan,S., Khaykin,E., Kim,C.J., Koo,H.L.,
            Kremenetskaia,I., Kurtz,D.B., Kwan,A., Lam,B., Langin-Hooper,S.,
            Lee,A., Lee,J.M., Lenz,C.A., Li,J.H., Li,Y., Lin,X., Liu,S.X.,
            Liu,Z.A., Luros,J.S., Maiti,R., Marziali,A., Militscher,J.,
            Miranda,M., Nguyen,M., Nierman,W.C., Osborne,B.I., Pai,G.,
            Peterson,J., Pham,P.K., Rizzo,M., Rooney,T., Rowley,D., Sakano,H.,
            Salzberg,S.L., Schwartz,J.R., Shinn,P., Southwick,A.M., Sun,H.,
            Tallon,L.J., Tambunga,G., Toriumi,M.J., Town,C.D., Utterback,T.,
            Van Aken,S., Vaysberg,M., Vysotskaia,V.S., Walker,M., Wu,D., Yu,G.,
            Fraser,C.M., Venter,J.C. and Davis,R.W.
  TITLE     Sequence and analysis of chromosome 1 of the plant Arabidopsis
            thaliana
  JOURNAL   Nature 408 (6814), 816-820 (2000)
   PUBMED   11130712
REFERENCE   2  (bases 1 to 2136)
  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 2136)
  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 (18-JUL-2017) Plant Genomics, J. Craig Venter Institute,
            9704 Medical Center Dr, Rockville, MD 20850, USA
  REMARK    Protein update by submitter
REFERENCE   4  (bases 1 to 2136)
  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   5  (bases 1 to 2136)
  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_003070).
            
            On Apr 18, 2007 this sequence version replaced NM_202316.1.
FEATURES             Location/Qualifiers
     source          1..2136
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /chromosome="1"
                     /ecotype="Columbia"
     gene            1..2136
                     /gene="VIM1"
                     /locus_tag="AT1G57820"
                     /gene_synonym="F12K22.14; F12K22_14; ORTH2; ORTHRUS 2;
                     VARIANT IN METHYLATION 1"
                     /note="Encodes a 645-amino acid methylcytosine-binding
                     protein with a PHD domain, two RING finger domains, and an
                     SRA domain that is involved in centromere
                     heterochromatinization. This protein functions as an E3
                     ubiquitin ligase in vitro. The protein has been shown to
                     bind to methylated cytosines of CG, CNG and CNN motifs via
                     its SRA domain but has a preference for the former. It
                     plays a role in the establishment/maintenance of chromatin
                     structure during cell division and is localized in the
                     nucleus. Plants over-expressing VIM1/ORTH2 show an
                     inhibition in root growth and a delay in flowering. Both
                     over-expression of GFP:ORTH2 and loss of ORTH2/VIM1 lead
                     to decreased levels of DNA methylation. GFP:ORTH2
                     over-expressers also have increased levels of FWA
                     transcripts."
                     /db_xref="Araport:AT1G57820"
                     /db_xref="GeneID:842157"
                     /db_xref="TAIR:AT1G57820"
     CDS             36..1964
                     /gene="VIM1"
                     /locus_tag="AT1G57820"
                     /gene_synonym="F12K22.14; F12K22_14; ORTH2; ORTHRUS 2;
                     VARIANT IN METHYLATION 1"
                     /inference="Similar to RNA sequence,
                     EST:INSD:AV803882.1,INSD:EL977407.1,INSD:ES186848.1,
                     INSD:BP641015.1,INSD:BP832344.1,INSD:DR383765.1,
                     INSD:AV811223.1,INSD:DR369931.1,INSD:BP838633.1,
                     INSD:BP823873.1,INSD:BX836555.1,INSD:ES065233.1,
                     INSD:EL166291.1,INSD:BP829501.1,INSD:AV829002.1,
                     INSD:BP822637.1,INSD:ES033393.1,INSD:ES125996.1,
                     INSD:ES111806.1,INSD:EL250292.1,INSD:BX836533.1,
                     INSD:BP834236.1,INSD:ES197839.1,INSD:BP651766.1,
                     INSD:BP836756.1,INSD:ES199679.1,INSD:ES106136.1,
                     INSD:BX840837.1,INSD:ES136852.1,INSD:ES134737.1,
                     INSD:BP828072.1,INSD:ES034591.1"
                     /inference="similar to RNA sequence, mRNA:INSD:BX813373.1"
                     /note="VARIANT IN METHYLATION 1 (VIM1); CONTAINS InterPro
                     DOMAIN/s: Zinc finger, RING-type, conserved site
                     (InterPro:IPR017907), Zinc finger, PHD-type, conserved
                     site (InterPro:IPR019786), Zinc finger, RING-type
                     (InterPro:IPR001841), Zinc finger, PHD-type
                     (InterPro:IPR001965), SRA-YDG (InterPro:IPR003105), Zinc
                     finger, C3HC4 RING-type (InterPro:IPR018957), Zinc finger,
                     FYVE/PHD-type (InterPro:IPR011011), Zinc finger,
                     PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana
                     protein match is: zinc finger (C3HC4-type RING finger)
                     family protein (TAIR:AT1G57800.1); Has 35333 Blast hits to
                     34131 proteins in 2444 species: Archae - 798; Bacteria -
                     22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses -
                     0; Other Eukaryotes - 9610 (source: NCBI BLink)."
                     /codon_start=1
                     /product="Zinc finger (C3HC4-type RING finger) family
                     protein"
                     /protein_id="NP_974045.1"
                     /db_xref="Araport:AT1G57820"
                     /db_xref="GeneID:842157"
                     /db_xref="TAIR:AT1G57820"
                     /translation="

MARDIQLPCDGDGVCMRCKSNPPPEESLTCGTCVTPWHVSCLSSPPKTLASTLQWHCPDCSGEIDPLPVSGGATGFESAGSDLVAAIRAIEADESLSTEEKAKMRQRLLSGKGVEEDDEEEKRKKKGKGKNPNLDVLSALGDNLMCSFCMQLPERPVTKPCGHNACLKCFEKWMGQGKRTCGKCRSIIPEKMAKNPRINSSLVAAIRLAKVSKSAAATTSKVFHFISNQDRPDKAFTTERAKKTGKANAASGKIYVTIPPDHFGPIPAENDPVRNQGLLVGESWEDRLECRQWGAHFPHVAGIAGQSTYGAQSVALSGGYKDDEDHGEWFLYTGRDLSGNKRTNKEQSFDQKFEKSNAALKLSCKLGYPVRVVRSHKEKRSAYAPEEGVRYDGVYRIEKCWRKVGVQGSFKVCRYLFVRCDNEPAPWTSDENGDRPRPIPNIPELNMATDLFERKETPSWDFDEGEGCWKWMKPPPASKKSVNVLAPEERKNLRKAIKAAHSNTMRARLLKEFKCQICQQVLTLPVTTPCAHNFCKACLEAKFAGKTLVRERSTGGRTLRSRKNVLNCPCCPTDISDFLQNPQVNREVAEVIEKLKTQEEDTAELEDEDEGECSGTTPEEDSEQPKKRIKLDTDATVSATIR"

     misc_feature    75..215
                     /gene="VIM1"
                     /locus_tag="AT1G57820"
                     /gene_synonym="F12K22.14; F12K22_14; ORTH2; ORTHRUS 2;
                     VARIANT IN METHYLATION 1"
                     /note="PHD zinc finger; Region: PHD; smart00249"
                     /db_xref="CDD:214584"
     misc_feature    order(114..125,135..137,198..200)
                     /gene="VIM1"
                     /locus_tag="AT1G57820"
                     /gene_synonym="F12K22.14; F12K22_14; ORTH2; ORTHRUS 2;
                     VARIANT IN METHYLATION 1"
                     /note="histone H3 binding site [polypeptide binding];
                     other site"
                     /db_xref="CDD:276966"
     misc_feature    459..602
                     /gene="VIM1"
                     /locus_tag="AT1G57820"
                     /gene_synonym="F12K22.14; F12K22_14; ORTH2; ORTHRUS 2;
                     VARIANT IN METHYLATION 1"
                     /note="first RING finger, HC subclass, found in
                     Arabidopsis thaliana ORTHRUS and similar proteins; Region:
                     RING-HC_ORTHRUS_rpt1; cd23138"
                     /db_xref="CDD:438500"
     misc_feature    819..1298
                     /gene="VIM1"
                     /locus_tag="AT1G57820"
                     /gene_synonym="F12K22.14; F12K22_14; ORTH2; ORTHRUS 2;
                     VARIANT IN METHYLATION 1"
                     /note="SAD/SRA domain; Region: SAD_SRA; pfam02182"
                     /db_xref="CDD:426640"
     misc_feature    1557..1772
                     /gene="VIM1"
                     /locus_tag="AT1G57820"
                     /gene_synonym="F12K22.14; F12K22_14; ORTH2; ORTHRUS 2;
                     VARIANT IN METHYLATION 1"
                     /note="second RING finger, HC subclass, found in
                     Arabidopsis thaliana ORTHRUS and similar proteins; Region:
                     RING-HC_ORTHRUS_rpt2; cd23139"
                     /db_xref="CDD:438501"
ORIGIN      

cattttctcactctctgatcttttttcccccaaaaatggcgcgtgacatccaactcccctgcgacggcgacggcgtatgcatgcgatgcaaatccaaccctccgcctgaagaatctctcacttgcggcacgtgcgttacaccgtggcacgtgtcctgtctctcttcacctcccaaaaccctagcttccactctacagtggcattgtcctgattgctccggcgaaatcgatcctcttcctgtttccggcggtgctactggtttcgaatctgctgggtcagatcttgtagctgcgattcgtgcgattgaggctgatgagtcgttgagtactgaagagaaagctaagatgaggcaacggttactgagtggtaaaggtgttgaggaggatgatgaagaagagaagaggaagaagaaggggaaagggaagaatccgaatctggatgtgttatctgctcttggagataacttgatgtgttctttctgtatgcagttgcctgagagacctgtgacgaaaccatgtgggcacaacgcttgcttaaaatgttttgagaaatggatggggcagggaaagagaacttgtggtaaatgccgcagcataattcctgaaaaaatggctaagaatccccgtatcaactcgtctcttgttgctgccattcgattagcaaaagtctctaaaagtgctgctgcgaccacttcaaaggtctttcatttcatcagcaaccaagaccgaccagataaagcatttacaaccgagcgtgcaaagaaaactggcaaggcaaacgctgctagtggaaagatttatgttacaataccaccagatcattttggtcctattccagctgaaaatgaccctgtcaggaaccaaggtcttttggttggagaatcctgggaggacagactcgagtgtaggcagtggggtgctcatttcccacatgttgctggcattgctggacaatctacttatggcgctcaatctgtagcactctctggaggttataaggatgatgaggatcatggagaatggtttctatacacaggaagagatctcagtggcaacaaaaggactaacaaggagcagtcttttgaccaaaagtttgagaagtctaatgcagcattaaaactcagctgcaaattggggtatcctgttcgagttgtcaggtctcacaaggagaagcgttctgcatacgcccctgaggaaggagtgagatatgatggggtttacaggattgagaagtgctggcgcaaagttggagtacagggttcttttaaggtctgtcgttacctgttcgttagatgtgacaatgagccagctccatggaccagtgatgagaatggagatcgtccaagacctatccctaatattccagagcttaatatggccaccgacctgtttgagagaaaagaaactccatcatgggattttgatgaaggtgagggttgttggaaatggatgaagccgccacctgcaagtaaaaagtcagtgaatgttttggctcctgaggagaggaaaaatttgaggaaagccataaaggcggcacactcgaataccatgagggcaagacttctgaaagaatttaagtgccagatctgtcagcaagtgttgactcttcctgtgacaacaccctgtgctcataacttctgcaaggcttgcttagaagcgaaatttgctgggaaaactcttgtgagagagagaagcacaggtggacggacactacgctcaaggaagaatgtcctgaactgcccttgttgcccaacagacatatctgattttctgcagaaccctcaggtcaacagagaagtagcggaggtgatagagaagctaaagacccaggaagaggacaccgcagagcttgaagatgaagatgaaggtgaatgctcaggcaccacccctgaagaagattctgagcaaccgaagaaaaggatcaagttggacactgacgcaacagtttctgcgaccatcaggtgaagttggtaccaaagaactctttagtaaaaaaaaactctagtgccttattttgtacgcaatatttgtggaacgtacctattgcgatgtgttattttggatcttacaacaactaagttattaatatggaacgtaaactatggttctcaggttttcaatttttctcttattttgg

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