LOCUS       NM_105275               2028 bp    mRNA    linear   PLN 20-OCT-2022
DEFINITION  Arabidopsis thaliana Zinc finger (C3HC4-type RING finger) family
            protein (VIM4), mRNA.
ACCESSION   NM_105275
VERSION     NM_105275.2
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 2028)
  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 2028)
  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 2028)
  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 2028)
  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 2028)
  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 Sep 12, 2016 this sequence version replaced NM_105275.1.
FEATURES             Location/Qualifiers
     source          1..2028
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /chromosome="1"
                     /ecotype="Columbia"
     gene            1..2028
                     /gene="VIM4"
                     /locus_tag="AT1G66040"
                     /gene_synonym="F15E12.8; F15E12_8; ORTH4; ORTHRUS 4;
                     VARIANT IN METHYLATION 4"
                     /note="predicted to encode a protein with an N-terminal
                     PHD domain and two RING domains surrounding an SRA domain.
                     Attempts to isolate ORTH4/VIM4 cDNA through RT-PCR were
                     unsuccessful and analysis of the expression of this gene
                     is difficult since it shares 99% nucleotide identity with
                     ORTH5/VIM2."
                     /db_xref="Araport:AT1G66040"
                     /db_xref="GeneID:842917"
                     /db_xref="TAIR:AT1G66040"
     CDS             80..1948
                     /gene="VIM4"
                     /locus_tag="AT1G66040"
                     /gene_synonym="F15E12.8; F15E12_8; ORTH4; ORTHRUS 4;
                     VARIANT IN METHYLATION 4"
                     /inference="Similar to RNA sequence,
                     EST:INSD:EL177826.1,INSD:EL265513.1"
                     /note="VARIANT IN METHYLATION 4 (VIM4); FUNCTIONS IN: zinc
                     ion binding; LOCATED IN: cellular_component unknown;
                     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); BEST Arabidopsis thaliana protein
                     match is: Zinc finger (C3HC4-type RING finger) family
                     protein (TAIR:AT1G66050.1); Has 6297 Blast hits to 5041
                     proteins in 427 species: Archae - 0; Bacteria - 14;
                     Metazoa - 4562; Fungi - 413; Plants - 874; Viruses - 19;
                     Other Eukaryotes - 415 (source: NCBI BLink)."
                     /codon_start=1
                     /product="Zinc finger (C3HC4-type RING finger) family
                     protein"
                     /protein_id="NP_176778.1"
                     /db_xref="Araport:AT1G66040"
                     /db_xref="GeneID:842917"
                     /db_xref="TAIR:AT1G66040"
                     /translation="

MAIQTQLPCDGDGVCMRCQVTPPSEETLTCGTCVTPWHVSCLLPESLASSTGDWECPDCSGVVVPSAAPGTGISGPESSGSVLVAAIRAIQADVTLTEAEKAKKRQRLMSGGGDDGVDDEEKKKLEIFCSICIQLPERPVTTPCGHNFCLKCFEKWAVGQGKLTCMICRSKIPRHVAKNPRINLALVSAIRLANVTKCSGEATAAKVHHIIRNQDRPDKAFTTERAVKTGKANAASGKFFVTIPRDHFGPIPAANDVTRNQGVLVGESWEDRQECRQWGVHFPHVAGIAGQAAVGAQSVALSGGYDDDEDHGEWFLYTGSGGRDLSGNKRVNKIQSSDQAFKNMNEALRLSCKMGYPVRVVRSWKEKRSAYAPAEGVRYDGVYRIEKCWSNVGVQGLHKMCRYLFVRCDNEPAPWTSDEHGDRPRPLPDVPELENATDLFVRKESPSWGFDEAEGRWKWMKSPPVSRMALDTEERKKNKRAKKGNNAMKARLLKEFSCQICRKVLSLPVTTPCAHNFCKACLEAKFAGITQLRDRSNGVRKLRAKKNIMTCPCCTTDLSEFLQNPQVNREMMEIIENFKKSEEEAEVAESSNISEEEEEESEPPTKKIKMDNNSVGDTSLSA"

     misc_feature    119..256
                     /gene="VIM4"
                     /locus_tag="AT1G66040"
                     /gene_synonym="F15E12.8; F15E12_8; ORTH4; ORTHRUS 4;
                     VARIANT IN METHYLATION 4"
                     /note="PHD zinc finger; Region: PHD; smart00249"
                     /db_xref="CDD:214584"
     misc_feature    order(158..169,179..181,239..241)
                     /gene="VIM4"
                     /locus_tag="AT1G66040"
                     /gene_synonym="F15E12.8; F15E12_8; ORTH4; ORTHRUS 4;
                     VARIANT IN METHYLATION 4"
                     /note="histone H3 binding site [polypeptide binding];
                     other site"
                     /db_xref="CDD:276966"
     misc_feature    452..598
                     /gene="VIM4"
                     /locus_tag="AT1G66040"
                     /gene_synonym="F15E12.8; F15E12_8; ORTH4; ORTHRUS 4;
                     VARIANT IN METHYLATION 4"
                     /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    818..1306
                     /gene="VIM4"
                     /locus_tag="AT1G66040"
                     /gene_synonym="F15E12.8; F15E12_8; ORTH4; ORTHRUS 4;
                     VARIANT IN METHYLATION 4"
                     /note="SAD/SRA domain; Region: SAD_SRA; pfam02182"
                     /db_xref="CDD:426640"
     misc_feature    1550..1765
                     /gene="VIM4"
                     /locus_tag="AT1G66040"
                     /gene_synonym="F15E12.8; F15E12_8; ORTH4; ORTHRUS 4;
                     VARIANT IN METHYLATION 4"
                     /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      

cacgcctcttcatttttccccttcctcttctcatctctcgataacacctctctctctatctctcacactcgtttcaacaatggcgattcaaactcagcttccttgcgacggagacggtgtatgtatgcggtgccaggtgacacctccgtcagaagagactctcacgtgtggcacctgtgtcactccatggcacgtgtcgtgtctccttcctgaatcactcgcttcttccactggagattgggagtgtcccgattgctccggcgttgtcgttccctccgccgctccgggtaccggaatctccggacctgaatcttccggttcagttctcgttgctgcgatccgtgcgattcaggctgatgtgactttgaccgaagctgagaaagccaaaaagaggcagagactgatgagtggtggtggtgacgatggtgtcgatgatgaagaaaagaagaagttagaaatcttttgttctatttgcattcaattgccagagagacctgtcacgacaccgtgtgggcacaatttctgtttgaaatgtttcgagaaatgggcagtaggtcaagggaagctaacttgtatgatatgccgaagcaaaattccgagacatgtggcgaaaaatcctcgcatcaacttagctctagtttctgctattcgtttagcaaatgttaccaaatgttctggtgaggcaactgcggccaaggttcatcatattatccgcaaccaagaccgtcctgacaaagcatttactaccgagcgggcagtaaaaactgggaaagctaatgctgctagcggtaagttttttgtgacaatacctcgtgatcattttggtcccataccagctgcgaatgatgtcactagaaaccaaggtgttttggttggagaatcttgggaggacaggcaagagtgtaggcagtggggagttcatttcccgcatgttgctggcattgccgggcaagcagcggttggagctcagtctgtggccctctctggaggttatgacgatgatgaggatcatggtgaatggtttctctacacaggaagtggtggaagggatctcagtggaaacaaaagagttaacaagatacagtcttctgaccaggcgtttaaaaacatgaatgaagctctaagacttagttgcaaaatgggctatcctgtccgagttgtaaggtcttggaaggagaagcgttctgcatatgcccctgcggaaggagtgagatacgatggggtctacagaattgaaaagtgctggagtaatgttggcgtacagggtttgcataagatgtgtcgttacctgtttgttagatgtgacaatgagccagctccatggaccagtgatgagcatggcgatcgtccaagacctttgcctgatgttccagagctggagaatgctactgacctgtttgtgagaaaggagagtccatcatggggtttcgatgaagctgagggtcgttggaagtggatgaagtctccacctgttagcagaatggctttggatactgaggagaggaagaagaataagagagcaaaaaaaggaaataatgctatgaaggccagacttctgaaagaattcagttgccaaatctgtcggaaagtgctgagtcttccagtgacgacaccttgtgcacacaacttctgcaaagcatgcttagaagcgaagtttgctgggataactcaactgagagacagaagcaatggcgtgcgtaaactacgtgcaaagaaaaacatcatgacctgcccttgctgcacaaccgatctctccgagtttctccaaaacccgcaggtgaacagagaaatgatggagataatagagaattttaagaagagtgaggaagaggctgaagttgcggagtcatcaaacatttctgaagaagaagaagaagaatccgaacctccaactaagaagattaagatggataacaactctgttggtgatacaagtctctcagcttaaggagctctttagtttttccaaacaaacttcctttctttttttggtaatattccgcaaacgtctgaagttatgcattgcga

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