GGRNA ver.2 Home | Help | Advanced search    Previous release (v1)

2024-03-28 20:12:04, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       NM_001170471            6199 bp    mRNA    linear   ROD 22-MAR-2023
DEFINITION  Rattus norvegicus zinc finger CCCH type containing 13 (Zc3h13),
            mRNA.
ACCESSION   NM_001170471 XM_001072035 XM_224295
VERSION     NM_001170471.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 6199)
  AUTHORS   Wen J, Lv R, Ma H, Shen H, He C, Wang J, Jiao F, Liu H, Yang P, Tan
            L, Lan F, Shi YG, He C, Shi Y and Diao J.
  TITLE     Zc3h13 Regulates Nuclear RNA m6A Methylation and Mouse Embryonic
            Stem Cell Self-Renewal
  JOURNAL   Mol Cell 69 (6), 1028-1038 (2018)
   PUBMED   29547716
REFERENCE   2  (bases 1 to 6199)
  AUTHORS   Yue Y, Liu J, Cui X, Cao J, Luo G, Zhang Z, Cheng T, Gao M, Shu X,
            Ma H, Wang F, Wang X, Shen B, Wang Y, Feng X, He C and Liu J.
  TITLE     VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near
            stop codon and associates with alternative polyadenylation
  JOURNAL   Cell Discov 4, 10 (2018)
   PUBMED   29507755
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 6199)
  AUTHORS   Horiuchi K, Kawamura T, Iwanari H, Ohashi R, Naito M, Kodama T and
            Hamakubo T.
  TITLE     Identification of Wilms' tumor 1-associating protein complex and
            its role in alternative splicing and the cell cycle
  JOURNAL   J Biol Chem 288 (46), 33292-33302 (2013)
   PUBMED   24100041
REFERENCE   4  (bases 1 to 6199)
  AUTHORS   Baltz AG, Munschauer M, Schwanhausser B, Vasile A, Murakawa Y,
            Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, Wyler E,
            Bonneau R, Selbach M, Dieterich C and Landthaler M.
  TITLE     The mRNA-bound proteome and its global occupancy profile on
            protein-coding transcripts
  JOURNAL   Mol Cell 46 (5), 674-690 (2012)
   PUBMED   22681889
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BC158717.1 and JACYVU010000272.1.
            
            On or before Dec 20, 2009 this sequence version replaced
            XM_001072035.1, XM_224295.4.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data because no single transcript was available
            for the full length of the gene. The extent of this transcript is
            supported by transcript alignments and orthologous data.
            
            ##Evidence-Data-START##
            RNAseq introns :: single sample supports all introns SAMD00132261,
                              SAMD00132262 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1137              BC158717.1         1-1137
            1138-1244           JACYVU010000272.1  7127255-7127361
            1245-1552           JACYVU010000272.1  7132786-7133093
            1553-2194           JACYVU010000272.1  7134335-7134976
            2195-2386           JACYVU010000272.1  7135421-7135612
            2387-2987           JACYVU010000272.1  7138543-7139143
            2988-3091           JACYVU010000272.1  7140670-7140773
            3092-4288           JACYVU010000272.1  7141059-7142255
            4289-4801           JACYVU010000272.1  7142688-7143200
            4802-4954           JACYVU010000272.1  7146639-7146791
            4955-5155           JACYVU010000272.1  7147706-7147906
            5156-5319           JACYVU010000272.1  7149862-7150025
            5320-6199           JACYVU010000272.1  7154084-7154963
FEATURES             Location/Qualifiers
     source          1..6199
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10116"
                     /chromosome="15"
                     /map="15q11"
     gene            1..6199
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /note="zinc finger CCCH type containing 13"
                     /db_xref="GeneID:305955"
                     /db_xref="RGD:1307729"
     exon            1..294
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            295..420
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    295..297
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /note="upstream in-frame stop codon"
     CDS             304..5490
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /codon_start=1
                     /product="zinc finger CCCH domain-containing protein 13"
                     /protein_id="NP_001163942.1"
                     /db_xref="GeneID:305955"
                     /db_xref="RGD:1307729"
                     /translation="
MSKIRRKVTVENTKTISESTSRRPSVFERLGPSTGSTTETQCRNWLKTGSCLYGNTCRFIHGPSPRGKGYSSNYRRSPERPTGDLRERMKNKRQDVDSESQKRNTEESSSPVRKESSRGRHRDKEDIKIVKERTPESEEENVEWETNRDDSDNGDINYDYVHELSLEMKRQKIQRELMKLEQENMDKREEIIIQKEVSPEVVRSKLSPSPLRKSSKSPKRKSSPKASSAGKKERKAAVVASPLLDQQRNSKSNQSKKKGPRTPSPPPPILEDIILGKKYKEKYKVKDKIEEKPRDGKDRGRDFERQREKRDKPRSSSPGQHHSPLSSRHHSSSSQSGSSIQRHSPSPRRKRTPSPSYQRTLTPSLRRSASPYPTHCLSSPQRKQSPPRHRSPMREKGRHDHERTSQSHDRRHERREEARGKRDREKDTREERESEHDHRDDREPRDSRDRRDTRDRRELRDSRDMRDSREIRDYSRDTKESRDPRDSRSARDVHDYRDREARDAHARDVRDVRDARDARDVRDVRDVRDARDVRDVRDARDVRDARDVRDVRDVRDVRDTRDARDARDARDGHRKEDVYQEEARSYGRNHLREESSRVELRNDSRNESRSEIRNDRMGRSRGRGPELPEKGGRSTRGSQMDSHSSGSNYHDSWETRSSYPERDRYPERDTRDQARDSSFERRHGERDRRDNRERDQRPSSPIRHQGRSEELEREERREERRIDRVDERRDERVRDRDRERERERERERDREREREREKERERELERERAREREREREKERERERERERDQRDRDHDREREREREREREKEREREERERERERERERERERERERERERERERERERAREREKERERQREWEDKDKGRDDRREKREDVHVREDRIPRDGHEERKSKKRYRNEGSPSPRQSPKRRREHSPDSDTYHSGDDKNEKHRLLSQVVRPQESRSLSPSHLTEDRQGRWKEEERKSERKESSRRYEEQELKEKLSCGDRQREQTESVDGGSRARSAQDLLSHRQAEDRDRDGSDRAHDEKKKAKAPKKPVKKKREEDVGIERGNPETHEDSQVFSPKKGQKKKNIEKKRKRSKGDSDVSDEEAAPQSKKKRGPRTPPLAIKEELIEISTDKEGILEDPLKKEDTAFSDWSDEDVPDRTDGLEAEHTAAAATPGSTPSPMSSLLPPPPPVAAAGTAATALAASAISATTSTTISSSGATSNINASEDSHRKCHRARGEKVEVSHVTLEDTPHRKLVDQKRSSSLGSNRSHRSHTSGRLRSPSNDSAHRSGDDQGGRKRVLHSGSRDREKTKSLELTGERKSRIDQLKRGEPSRSTSSDRQDSRSHSSRRSSPESDRQVHSRSGSFDSRDRLQERDRYEHDRERERERRDPRQREWDREADKEWPRTRDRDRLRERERDRDKRRDLDRERERLVADPMERDRERDRTFETSQLESVKRSEVKLESEHDRDLEGSSRDSVALDKERMDRDLGSAQGFEDVSKAERTESLEAGDDESKLDDAHSLGSGAGEGYEPISDDELDEILAGDAEKREDQQEEEKMPDPLDVIDVDWSGLMPKHRKEPREPGAALLKFTPGAVLLRVGISKKLAGSELFTKVKETCQQLLEKPKDADSLFEHELGALNMAALLRKEERASLLSDLGPCCKALCFRRDSAIRKQLVKNEKGTVKQAYTNTPMVDNELLRLSLRLLKRKTSCHTPGQEKTEDGKLAPCSGQQELCVS"
     misc_feature    427..492
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /note="Zinc finger C-x8-C-x5-C-x3-H type (and similar);
                     Region: zf-CCCH; pfam00642"
                     /db_xref="CDD:425793"
     exon            421..530
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            531..642
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            643..751
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            752..891
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            892..1046
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            1047..1244
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            1245..1552
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            1553..2194
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            2195..2386
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            2387..2987
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            2988..3091
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            3092..4288
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            4289..4801
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            4802..4954
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            4955..5155
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            5156..5319
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
     exon            5320..6199
                     /gene="Zc3h13"
                     /gene_synonym="RGD1307729"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
cttttagatgcttcctatgtagaggcccgatggagttgcgggtttagcgcgttgctctgcagcggcctctgtacgtctcatctggtgtccggagctccctggagcttggcgaagatctgggcggctccgctgctctctgttcccggcgtccgcccggttgaggagagcgggcccctgggagtcgcgcgtgcacgtcttctccgtcgtcctcccggggcggggcgcggggacagcggagctgaggcgtccgggacatcctgaagactgcgcttactaagggtgcttagagaggagtagttcaaaatgtcaaaaattaggaggaaggtcacagtggaaaacaccaagaccatatctgaaagcacatcccgaagacctagtgtgtttgagaggcttggacccagcactggaagcacaacagagacacagtgccgtaactggctgaagaccggcagctgcctctatggaaacacatgtaggttcatacatggcccttcacctcgtgggaaaggttacagcagcaattacagaaggtcaccggaaaggcctacaggtgatctcagagaaagaatgaagaataagcgtcaggatgtggattctgaatcccagaaacggaacacagaggagtcatcctcacctgttaggaaagaatcttcaagagggagacatagagacaaggaagacataaaaattgttaaagagagaactccagaaagcgaagaagaaaacgtagaatgggaaaccaacagagatgattctgacaatggagatattaattacgattatgttcatgagttatcattggaaatgaagcgtcagaaaatacagagagaattaatgaagttggaacaagaaaacatggataaaagagaagaaattattattcaaaaggaggtttccccagaagtggtgagatcaaagttgtctccatcacctctgagaaagtcgagtaaatctccaaagcggaagtccagccccaaggcatcttcagctggcaagaaagagcggaaggctgctgtggtggcttccccgctgctggaccagcagagaaattcaaaaagcaaccaaagtaaaaagaaagggccacgcactcctagtccacctcctcctatactagaagatatcattctgggaaaaaaatacaaagaaaagtataaagtgaaagacaagatagaagaaaaaccaagagatggaaaggacagaggacgggattttgaaaggcaaagagaaaaacgagacaaaccaaggtcttcctccccgggacagcaccattctcctctgtcttctagacatcactcgtcgtcctcacagtcagggtcatctattcagagacattctccctctcctcgccggaaaagaactccttccccatcctaccagaggactttaactccatctttacgacgttctgcatctccttatccaacccattgtctgtcttctcctcagagaaagcaaagtcctccaagacatcgctctccaatgagagagaaagggaggcatgatcatgaacggacttcacagtcacatgatcggcgtcatgaaaggagggaagaagctcgaggcaaaagggatagagaaaaggacaccagagaagagcgagagtctgaacatgaccacagggatgacagagaaccgcgagacagtcgggaccggagagacactagagaccgcagggaacttagagactccagagacatgcgggactccagagagataagggattatagcagagacaccaaggagagccgtgatcccagagattcccggtcagctcgggatgtccatgactacagggaccgtgaagctcgggatgctcatgctcgagatgttcgggatgtcagggatgctcgagatgctcgagatgttcgggatgtccgggatgtcagggatgctcgagatgtccgggatgttcgggatgctcgagatgtccgggatgcccgggatgtccgggatgttcgggatgtccgggatgtccgggacaccagagatgcccgggatgcccgggatgctcgagatggtcatcgaaaggaggatgtataccaggaagaagcccgtagttatggcagaaaccacctgagagaagagagttctagagttgaactaaggaatgactctagaaatgagtctcgaagtgaaattagaaatgaccgcatgggcagaagtagggggagaggtccagaactgcctgaaaagggaggtcgaagcacaagaggttcccaaatggatagccacagtagtggcagcaactaccatgacagctgggaaactcgaagtagctatcctgaaagagacagataccctgagagagataccagagatcaagcaagggattcttcctttgagagaaggcatggagaaagagaccgtcgggataacagagaacgagatcaaagaccaagctcacctattcgccatcaggggaggagtgaggagcttgagcgagaggaaagaagagaggaaagacgaatagacagagtggatgagagacgagatgaaagggtcagagacagagatagggagagagagagagagcgggagagggagagagatcgggaacgggagcgggagcgggaaaaggaaagagaaagagaactagaaagagagagagctagagagcgggagagagagagagagaaagagagggagagagagcgagaaagagaaagagatcagagagatcgtgaccatgatcgagagcgagaaagagagagggagcgagagagggaaaaagaacgggagcgagaagagagagagagggagagagaaagggaaagggaacgggaaagagaaagggaacgggagcgggagagagagcgagaacgtgagcgggagcgagaaagggccagagaaagagaaaaagaacgagagcggcaaagagaatgggaggataaagacaagggacgcgatgaccggagggagaagcgcgaggacgttcatgttcgagaggacaggatccccagagacggccacgaggagagaaagtccaagaaacgctatagaaatgaagggagtcccagcccccggcagtcccccaagcgccggcgggagcattctcctgacagtgacacctaccacagtggggatgacaaaaatgaaaagcatagactcttgagccaggtcgtacggccacaggaatctcgttctctcagcccgtcccacctcacagaagacaggcagggtagatggaaagaggaggagcgtaaatcggaaaggaaggagagttcaaggcgctatgaagaacaagaactcaaagagaagctttcttgtggcgacaggcaaagggagcagacagaaagcgtggacggcggctcgagagcgcgcagcgcgcaagacctgctcagccatcgccaggctgaagaccgcgaccgagatgggtctgatcgagcccatgatgaaaagaaaaaagcaaaagctccgaagaaacccgtaaagaaaaagagggaggaggatgttggaatagagaggggcaaccctgagacacacgaggatagtcaagtgttttcaccaaaaaaaggacagaaaaagaaaaacattgaaaaaaagcgtaaaagatccaagggggattctgatgtttctgacgaagaggcagccccgcagagtaagaagaagaggggtccacgcacaccccctcttgccatcaaggaggagctgattgagatttccactgacaaggaaggcatccttgaggatcccctgaagaaagaagataccgcctttagtgactggtctgatgaggatgtgcctgaccgcacagacggcttggaagctgagcacactgcagccgcggccactcccgggagcaccccttcccccatgtcgtctcttctccctcccccgccccctgtggctgctgccggtactgcagccactgctcttgccgcctcagccatttctgccaccacctctaccaccatttcaagctctggtgccacctccaatatcaatgccagtgaagactcacacagaaaatgccacagggcacgaggggagaaggtagaggtgtctcatgtgaccctggaagatacaccacatcgcaaactggtggatcaaaagagaagcagcagcctgggaagcaatcggagtcaccgcagccatacctctggtcgcctgcgctccccatctaatgattctgcacatcgaagtggggacgatcagggtggtcggaagagagtgctccacagtggctccagagatagagaaaagacaaagagcctagagctcacaggagagagaaaatctaggatcgatcagttaaagcgtggagagcccagtcggagtacttcttcagatcgccaggattccagaagccacagctccagaagaagctctcctgagtcagaccgacaggttcactccaggtctgggtcatttgacagcagagaccggcttcaagaacgagataggtatgagcatgacagagagcgtgagagggagcggagagatcccagacaaagggagtgggaccgggaagcagacaaagagtggcctcggacccgagaccgtgatagacttcgggaacgcgagagagaccgagacaaaaggagagacttggacagagagagagagagactggtcgccgaccccatggaaagagacagagaacgagatagaacttttgagacgtctcagttggaatctgtgaagcgaagtgaagtcaaattggagagtgaacacgacagagacctggagggcagctcccgggactctgtggccttggacaaagaaaggatggacagagacctggggtctgcgcaggggtttgaggatgtgagtaaagcggagagaacagagagtctggaagcaggagatgacgagtccaagttagatgatgcgcattcgttagggtctggtgctggggaaggctatgagcccatcagtgacgacgagctagatgaaattctggcaggggatgcagaaaagagagaggaccagcaggaagaggagaagatgccagatccattagatgtgatagatgtggactggtctggactaatgccaaagcatcggaaagagccgagagagcccggggctgcactcttaaagttcacacccggagccgtgctactacgagttgggatttctaaaaagttggccggttctgagctctttacaaaagttaaagaaacatgtcaacaacttctagagaaacccaaagatgcagacagcctttttgaacatgaactaggggctctcaacatggctgctttacttcgaaaagaagagcgggcgagtctccttagtgacctgggaccatgttgtaaagcattatgtttcagacgggattctgcaatccggaagcagcttgtgaagaacgaaaagggaaccgtgaagcaggcgtacaccaacactccgatggtggacaacgagctgcttcggctgagtcttcggttactcaagaggaagacttcctgccacacccctgggcaggaaaagactgaagatgggaaattagccccgtgcagtggccagcaggagctgtgtgtgtcctaggcagagattgaggacggcccgtttgctctctcttcacaggagtgcataatctttctcaaagttttttgttttgagacattgctaattacagagacagaagagtcaccggccacatcagatgtgaagaacttcagtcttcagagacaccagttttggttcatttaagattttacattaatttttatacagtaattgacactcaggcaaaataatgtgaaaatgtctagatttagtaatttcgtctgtgtcttcattaaaattgaagattttaagtaaccaggtcacccctgctcttccagcctatgaatacttcctatgaaataaaagcactgatttttattctggatcaccacgcagaactgaccgtagtcagaaaggtgtgtcgctagaggctgctgcacaggctgcagtgccgtgtacagagctctgaggtgcgccggccttgcgagtgcgcccggaggcagtcttcacaaggaaaccccagtgggtttgcttttttcttttgaaaattctaaaataaatgactccatgggatttttttttacacatgtacattgctacattatatattggaagtctttggacttttgagtggggtttaattgttcattatcagagactgtgtgctattttatttttaataaatgtacgttcccttttcttgttgtagattttccttgctctttattaatcagactccagacactga
//

by @meso_cacase at DBCLS
This page is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

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. [Full Text]