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2024-11-01 08:31:32, GGRNA.v2 : RefSeq release 226 (Sep, 2024)

LOCUS       NM_001170471            6199 bp    mRNA    linear   ROD 30-MAR-2024
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,Y.G., 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,A.G., 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 JAXUCZ010000015.1.
            
            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##
            Transcript exon combination :: SRR26360194.374363.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760383, SAMEA5760386
                                           [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           JAXUCZ010000015.1  57053493-57053599
            1245-1552           JAXUCZ010000015.1  57059024-57059331
            1553-2194           JAXUCZ010000015.1  57060573-57061214
            2195-2386           JAXUCZ010000015.1  57061659-57061850
            2387-2987           JAXUCZ010000015.1  57064781-57065381
            2988-3091           JAXUCZ010000015.1  57066908-57067011
            3092-4288           JAXUCZ010000015.1  57067297-57068493
            4289-4801           JAXUCZ010000015.1  57068926-57069438
            4802-4954           JAXUCZ010000015.1  57072877-57073029
            4955-5155           JAXUCZ010000015.1  57073944-57074144
            5156-5319           JAXUCZ010000015.1  57076100-57076263
            5320-6199           JAXUCZ010000015.1  57080322-57081201
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:459885"
     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]