LOCUS       NM_105276               2227 bp    mRNA    linear   PLN 20-OCT-2022
DEFINITION  Arabidopsis thaliana Zinc finger (C3HC4-type RING finger) family
            protein (VIM2), mRNA.
ACCESSION   NM_105276
VERSION     NM_105276.4
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 2227)
  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 2227)
  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 2227)
  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 2227)
  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 2227)
  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_105276.3.
FEATURES             Location/Qualifiers
     source          1..2227
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /chromosome="1"
                     /ecotype="Columbia"
     gene            1..2227
                     /gene="VIM2"
                     /locus_tag="AT1G66050"
                     /gene_synonym="F15E12.5; F15E12_5; ORTH5; ORTHRUS 5;
                     VARIANT IN METHYLATION 2"
                     /note="Encodes a protein that is similar to VIM1 but is
                     not involved in cytosine methylation. This protein has an
                     N-terminal PHD domain and two RING domains surrounding an
                     SRA domain. ORTH5/VIM2 has E3 ubiquitin ligase activity in
                     vitro."
                     /db_xref="Araport:AT1G66050"
                     /db_xref="GeneID:842919"
                     /db_xref="TAIR:AT1G66050"
     CDS             192..2063
                     /gene="VIM2"
                     /locus_tag="AT1G66050"
                     /gene_synonym="F15E12.5; F15E12_5; ORTH5; ORTHRUS 5;
                     VARIANT IN METHYLATION 2"
                     /inference="Similar to RNA sequence,
                     EST:INSD:T21607.1,INSD:EL188966.1,INSD:T21332.1,
                     INSD:BP837874.1,INSD:BP784533.1,INSD:BP787025.1,
                     INSD:BP659920.1,INSD:EH967657.1,INSD:BP659512.1,
                     INSD:AI993860.1,INSD:BP781169.1,INSD:BP826270.1,
                     INSD:BP819932.1"
                     /inference="similar to RNA sequence,
                     mRNA:INSD:BT010568.1,INSD:AK176012.1,INSD:AK175694.1,
                     INSD:AK175887.1"
                     /note="VARIANT IN METHYLATION 2 (VIM2); 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:AT1G66040.1); Has 6271 Blast
                     hits to 5010 proteins in 428 species: Archae - 0; Bacteria
                     - 14; Metazoa - 4526; Fungi - 407; Plants - 903; Viruses -
                     19; Other Eukaryotes - 402 (source: NCBI BLink)."
                     /codon_start=1
                     /product="Zinc finger (C3HC4-type RING finger) family
                     protein"
                     /protein_id="NP_176779.2"
                     /db_xref="Araport:AT1G66050"
                     /db_xref="GeneID:842919"
                     /db_xref="TAIR:AT1G66050"
                     /translation="

MAIQTQLPCDGDGVCMRCQVNPPSEETLTCGTCVTPWHVSCLLPESLASSTGDWECPDCSGVVVPSAAPGTGISGPESSGSVLVTAIRAIQADVTLTEAEKAKKRQRLMSGGGDDGVDDEEKKKLEIFCSICIQLPERPVTTPCGHNFCLKCFEKWAVGQGKLTCMICRSKIPRHVAKNPRINLALVSAIRLANVTKCSGEATAAKVHHIIRNQDRPDKAFTTERAVKTGKANAASGKFFVTIPRDHFGPIPAANDVTRNQGVLVGESWEDRQECRQWGVHFPHVAGIAGQAAVGAQSVALSGGYDDDEDHGEWFLYTGSGGRDLSGNKRVNKIQSSDQAFKNMNEALRLSCKMGYPVRVVRSWKEKRSAYAPAEGVRYDGVYRIEKCWSNVGVQGLHKMCRYLFVRCDNEPAPWTSDEHGDRPRPLPDVPELENATDLFVRKESPSWGFDEAEGRWKWMKSPPVSRMALDTEERKKNKRAKKGNNAMKARLLKEFSCQICRKVLSLPVTTPCAHNFCKACLEAKFAGITQLRDRSNGVRKLRAKKNIMTCPCCTTDLSEFLQNPQVNREMMEIIENFKKSEEEAEVAESSNISEEEGEEESEPPTKKIKMDKNSVGGTSLSA"

     misc_feature    231..368
                     /gene="VIM2"
                     /locus_tag="AT1G66050"
                     /gene_synonym="F15E12.5; F15E12_5; ORTH5; ORTHRUS 5;
                     VARIANT IN METHYLATION 2"
                     /note="PHD zinc finger; Region: PHD; smart00249"
                     /db_xref="CDD:214584"
     misc_feature    order(270..281,291..293,351..353)
                     /gene="VIM2"
                     /locus_tag="AT1G66050"
                     /gene_synonym="F15E12.5; F15E12_5; ORTH5; ORTHRUS 5;
                     VARIANT IN METHYLATION 2"
                     /note="histone H3 binding site [polypeptide binding];
                     other site"
                     /db_xref="CDD:276966"
     misc_feature    564..710
                     /gene="VIM2"
                     /locus_tag="AT1G66050"
                     /gene_synonym="F15E12.5; F15E12_5; ORTH5; ORTHRUS 5;
                     VARIANT IN METHYLATION 2"
                     /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    930..1418
                     /gene="VIM2"
                     /locus_tag="AT1G66050"
                     /gene_synonym="F15E12.5; F15E12_5; ORTH5; ORTHRUS 5;
                     VARIANT IN METHYLATION 2"
                     /note="SAD/SRA domain; Region: SAD_SRA; pfam02182"
                     /db_xref="CDD:426640"
     misc_feature    1662..1877
                     /gene="VIM2"
                     /locus_tag="AT1G66050"
                     /gene_synonym="F15E12.5; F15E12_5; ORTH5; ORTHRUS 5;
                     VARIANT IN METHYLATION 2"
                     /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      

tcttatctctttgtgagatttttttctttttttgaaggatttttacaaatcattttgaattcgtcttcccaaaatttcaaaacccgcctcttcacttttcgccttcctctacttatttagcctaaatctctcacaaatctcgacaacaccattttctctctaaatctctctctcactcactcgtttcaacaatggcgattcaaactcagcttccttgcgacggagacggtgtatgtatgcggtgccaggtgaatcctccgtcagaagagactctcacgtgtggcacctgtgtcactccatggcacgtgtcgtgtctccttcctgaatcactcgcttcttccactggagactgggagtgtcccgattgctccggcgttgttgttccctccgccgctccgggtaccggaatctccggacctgaatcttccggttcagttctcgttactgcgatccgtgcgattcaggctgatgtgactttgaccgaagctgagaaagccaaaaagaggcagagactgatgagtggtggtggtgacgatggtgtcgatgatgaagaaaagaagaagttagaaatcttttgttctatttgcattcaattgccagagagacctgttacgacaccgtgtgggcacaatttctgtttgaaatgtttcgagaaatgggcagtaggtcaagggaagctaacttgtatgatatgccgaagcaaaattccgagacatgtggcgaaaaatcctcgcatcaacttagctctagtttctgctattcgtttagcaaatgttaccaaatgttctggtgaggcaactgcggccaaggttcatcatattatccgcaaccaagaccgtcctgacaaagcatttactaccgagcgggcagtaaaaactgggaaagctaatgctgctagcggtaagttttttgtgacaatacctcgtgatcattttggtcccataccagctgcgaatgatgtcactagaaaccaaggtgttttggttggagaatcttgggaggacaggcaagagtgtaggcagtggggagttcatttcccgcatgttgctggcattgccgggcaagcagcggttggagctcagtctgtggccctctctggaggttatgacgatgatgaggatcatggtgaatggtttctctacacaggaagtggtggaagggatctcagtggaaacaaaagagttaacaagatacagtcttctgaccaggcgtttaaaaacatgaatgaagctctaagacttagttgcaaaatgggctatcctgtccgagttgtaaggtcttggaaggagaagcgttctgcatatgcccctgcggaaggagtgagatacgatggggtctacagaattgaaaagtgctggagtaatgttggcgtacagggtttgcataagatgtgtcgttacctgtttgttagatgtgacaatgagccagctccatggaccagtgatgagcatggcgatcgtccaagacctttgcctgatgttccagagctggagaatgctactgacctgtttgtgagaaaggagagtccatcatggggtttcgatgaagctgagggtcgttggaagtggatgaagtctccacctgttagcagaatggctttggatactgaggagaggaagaagaataagagagcaaaaaaaggaaataatgctatgaaggccagacttctgaaagaattcagttgccaaatctgtcggaaagtgctgagtcttccagtgacgacaccttgtgcacacaacttctgcaaagcatgcttagaagcgaagtttgctgggataactcaactgagagacagaagcaatggcgtgcgtaaactacgtgcaaagaaaaacatcatgacctgcccttgctgcacaaccgatctctccgagtttctccaaaacccgcaggtgaacagagagatgatggagataatagagaattttaagaagagtgaggaagaggctgaagttgcggagtcatcaaacatttctgaagaagaaggagaagaagaatccgaacctccaactaagaagattaagatggataaaaactctgttggtggtacaagtctctcagcttaaggagctctttagtttttccaaacaaacttcctttctgtgaagtgcattgcgacttatcatttttattttaaaacttatcagaaattgctcgaatctttttttcccgttagatattgattcaacattactacaacatattactctaaaatttcgtggtcagtgag

//