2024-09-29 03:53:24, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
LOCUS NM_104575 2107 bp mRNA linear PLN 20-OCT-2022 DEFINITION Arabidopsis thaliana zinc finger (C3HC4-type RING finger) family protein (VIM5), partial mRNA. ACCESSION NM_104575 VERSION NM_104575.3 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 2107) 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 2107) 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 2107) 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 2107) 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 2107) 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 Feb 17, 2004 this sequence version replaced NM_104575.2. COMPLETENESS: incomplete on the 5' end. FEATURES Location/Qualifiers source 1..2107 /organism="Arabidopsis thaliana" /mol_type="mRNA" /db_xref="taxon:3702" /chromosome="1" /ecotype="Columbia" gene <1..2107 /gene="VIM5" /locus_tag="AT1G57800" /gene_synonym="F12K22.15; F12K22_15; ORTH3; ORTHRUS 3; VARIANT IN METHYLATION 5" /note="predicted to encode a protein with an N-terminal PHD domain and two RING domains surrounding an SRA domain. Attempts to isolate ORTH3/VIM5 cDNA through RT-PCR were unsuccessful and only one Arabidopsis EST is associated with this locus. A paternally expressed imprinted gene." /db_xref="Araport:AT1G57800" /db_xref="GeneID:842155" /db_xref="TAIR:AT1G57800" CDS 1..1983 /gene="VIM5" /locus_tag="AT1G57800" /gene_synonym="F12K22.15; F12K22_15; ORTH3; ORTHRUS 3; VARIANT IN METHYLATION 5" /inference="Similar to RNA sequence, EST:INSD:Z35066.1" /note="VARIANT IN METHYLATION 5 (VIM5); FUNCTIONS IN: zinc ion binding; LOCATED IN: cellular_component unknown; CONTAINS InterPro DOMAIN/s: SRA-YDG (InterPro:IPR003105), Zinc finger, RING-type, conserved site (InterPro:IPR017907), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011); BEST Arabidopsis thaliana protein match is: Zinc finger (C3HC4-type RING finger) family protein (TAIR:AT1G57820.1); Has 5254 Blast hits to 5127 proteins in 1563 species: Archae - 0; Bacteria - 14; Metazoa - 4362; Fungi - 258; Plants - 447; Viruses - 0; Other Eukaryotes - 173 (source: NCBI BLink)." /codon_start=1 /product="zinc finger (C3HC4-type RING finger) family protein" /protein_id="NP_176091.2" /db_xref="Araport:AT1G57800" /db_xref="GeneID:842155" /db_xref="TAIR:AT1G57800" /translation="
MTPATQYPCDPEGVCMRCKSMPPPEESLTCGTCVTPWHVSCLLSPPETLSATLQWLCPDCSGETNPLPVSGVAAGYGSVGSDLVAAIHSIEADETLSAEEKAKKKQQLLSGKGVVDEDDEEEKKKTSKGKKPIDVLSHFECSFCMQSLQKPVSVRVLFALALMLVWFLESTPCGHNACLKCFLKWMGQGHRSCGTCRSVIPESMVTNPRINLSIVSAIRLARVSEKADARTSKVVHYVDNEDRPDKAFTTERAKKTGNANASSGKIFVTIPRDHFGPIPAENDPVRNQGLLVGESWKGRLACRQWGAHFPHVSGIAGQASYGAQSVVLAGGYDDDEDHGEWFLYTGSGGRILKGNKRTNTVQAFDQVFLNFNEALRLSCKLGYPVRVVRSTKDKRSPYAPQGGLLRYDGVYRIEKCWRIVGIQMCRFLFVRCDNEPAPWTSDEHGDRPRPLPNVPELNMATDLFERKESPSWDFDEGEDRWRWMKPPPASKKAVKNVLDPEERKLLREAIKSANPNTMRARLLKEFKCQICQKVMTNPVTTPCAHNFCKACLESKFAGTALVRERGSGGRKLRSQKSVMKCPCCPTDIAEFVQNPQVNREVAEVIEKLKKQEEEENAKSLDEGQCSGTSHEEEDDEQPKKRIKLDTDAEVSATVVESDMK"
misc_feature 40..180 /gene="VIM5" /locus_tag="AT1G57800" /gene_synonym="F12K22.15; F12K22_15; ORTH3; ORTHRUS 3; VARIANT IN METHYLATION 5" /note="PHD zinc finger; Region: PHD; smart00249" /db_xref="CDD:214584" misc_feature order(79..90,100..102,163..165) /gene="VIM5" /locus_tag="AT1G57800" /gene_synonym="F12K22.15; F12K22_15; ORTH3; ORTHRUS 3; VARIANT IN METHYLATION 5" /note="histone H3 binding site [polypeptide binding]; other site" /db_xref="CDD:277088" misc_feature 409..603 /gene="VIM5" /locus_tag="AT1G57800" /gene_synonym="F12K22.15; F12K22_15; ORTH3; ORTHRUS 3; VARIANT IN METHYLATION 5" /note="RING finger (Really Interesting New Gene) domain and U-box domain superfamily; Region: RING_Ubox; cl17238" /db_xref="CDD:473075" misc_feature order(421..423,430..432,517..519,523..525,532..534, 541..543,577..579,586..588) /gene="VIM5" /locus_tag="AT1G57800" /gene_synonym="F12K22.15; F12K22_15; ORTH3; ORTHRUS 3; VARIANT IN METHYLATION 5" /note="cross-brace motif; other site" /db_xref="CDD:438111" misc_feature 820..1299 /gene="VIM5" /locus_tag="AT1G57800" /gene_synonym="F12K22.15; F12K22_15; ORTH3; ORTHRUS 3; VARIANT IN METHYLATION 5" /note="SAD/SRA domain; Region: SAD_SRA; pfam02182" /db_xref="CDD:460476" misc_feature 1561..1776 /gene="VIM5" /locus_tag="AT1G57800" /gene_synonym="F12K22.15; F12K22_15; ORTH3; ORTHRUS 3; VARIANT IN METHYLATION 5" /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
atgacgcctgccacccagtacccatgcgaccccgaaggtgtatgcatgcgatgcaaatcgatgcctccaccggaggaatctctcacttgcggcacgtgcgtcacgccttggcacgtgtcctgccttttgtccccgcccgaaaccctaagtgctactttacagtggctttgtcctgattgctccggtgaaaccaatcctcttcctgtttccggtgttgcggctggatatggatctgttggttcagatcttgtagcggcgatccactcgattgaggcggatgaaactctctctgctgaagagaaggctaagaagaagcagcagttactgagtggtaagggggtcgtcgatgaggatgacgaagaagagaagaagaagacgagtaaaggaaagaaacccatcgatgtgctatctcacttcgagtgttctttctgcatgcagtcgctacaaaaacccgtctcggttcgtgtactctttgctttggctcttatgcttgtgtggtttctcgaatctacaccatgtgggcacaacgcttgcttgaaatgtttcttgaagtggatggggcagggacaccgcagttgtggaacatgccgcagcgtaattcctgaaagcatggttaccaatccccgtatcaacttgtccattgtgtctgctattaggttagcaagagtatccgaaaaggctgatgcgcgtacttcaaaagttgttcactatgttgacaatgaagatcgtccagataaagcatttacaactgagcgcgctaagaaaacagggaatgcaaatgcttccagtggcaagatttttgttacaatccctcgagatcattttggtcctataccagctgaaaatgatcctgttaggaaccaaggtcttttggttggagaatcctggaagggccgacttgcttgtcggcagtggggggctcacttcccacatgtttccggcattgctggacaagcgagttatggagctcaatctgttgtgctcgctggaggttatgatgatgatgaggatcatggagaatggtttctatacacaggaagtgggggaagaattctcaaaggcaacaaaaggactaacacggttcaagcttttgatcaagtatttctaaactttaatgaagctttaagacttagttgtaaactagggtatcctgttcgagttgtcaggtctaccaaggacaagcgttctccatacgcccctcaaggaggactactaaggtatgatggtgtttaccggatagagaaatgctggaggatagttggaatacagatgtgccgtttcctgtttgttagatgtgacaatgagccagctccatggaccagtgatgagcatggagatcgcccaagacctttgcctaatgttcctgagcttaatatggccacagacctgtttgagagaaaagaaagtccatcatgggattttgatgaaggtgaggatcgttggagatggatgaagccaccacctgctagtaaaaaggcagttaaaaatgttttggatcctgaggagaggaaacttttgagggaagccataaagtcggcaaacccgaataccatgagggcaagacttttgaaagaatttaagtgccagatctgtcagaaagtgatgactaatcctgtgacaacgccttgtgctcataacttctgcaaggcttgtttggaatcgaagtttgctgggacagctctagtgagagagagaggcagcggtggacgaaaattacgttcacaaaagagtgtcatgaagtgcccttgttgcccaacggacattgccgagtttgtccagaaccctcaggtcaatagagaagtagcggaggtgatagagaagctgaagaaacaggaagaggaggaaaacgcaaagtctttagatgaaggtcaatgctcaggtaccagccatgaagaagaagatgatgagcaaccaaagaaacggattaagttggacactgacgcagaagtttctgcgactgttgtggaatctgacatgaagtaagtaagtaggggcctttccaatggctcttttggacaagtaaacttggagactatgtttatgttttggtaccaaagactggaaaaactctcttaccttatttagtacgcaacatttgtggaacgta
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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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