2024-09-28 09:30:29, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
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:277019" 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:460476" 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
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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.
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