2024-09-28 09:28:00, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
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:277088" 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:460476" 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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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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