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    Zc3h13 zinc finger CCCH type containing 13 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 305955, updated on 2-May-2024

    Summary

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    Official Symbol
    Zc3h13provided by RGD
    Official Full Name
    zinc finger CCCH type containing 13provided by RGD
    Primary source
    RGD:1307729
    See related
    Ensembl:ENSRNOG00000011237 AllianceGenome:RGD:1307729
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1307729
    Summary
    Predicted to enable metal ion binding activity. Predicted to be involved in mRNA methylation and regulation of stem cell population maintenance. Predicted to be located in nucleoplasm. Predicted to be part of RNA N6-methyladenosine methyltransferase complex. Predicted to be active in nuclear speck. Orthologous to human ZC3H13 (zinc finger CCCH-type containing 13). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 75.7), Spleen (RPKM 72.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Zc3h13 in Genome Data Viewer
    Location:
    15q11
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (57016686..57081201)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (50607335..50671802)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (57340522..57405287)

    Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene tRNA methyltransferase 10A, pseudogene 1 Neighboring gene U6 spliceosomal RNA Neighboring gene carboxypeptidase B2 Neighboring gene siah E3 ubiquitin protein ligase family member 3 Neighboring gene uncharacterized LOC120097040 Neighboring gene chibby family member 2 Neighboring gene GABA type A receptor associated protein like 2, pseudogene 2 Neighboring gene glutamate-rich 6B Neighboring gene component of oligomeric golgi complex 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Zc3h13 Regulates Nuclear RNA m(6)A Methylation and Mouse Embryonic Stem Cell Self-Renewal. Wen J, et al. Mol Cell, 2018 Mar 15. PMID 29547716, Free PMC Article
    2. Identification of Wilms' tumor 1-associating protein complex and its role in alternative splicing and the cell cycle. Horiuchi K, et al. J Biol Chem, 2013 Nov 15. PMID 24100041, Free PMC Article
    3. Phosphorylation and degradation of tomosyn-2 de-represses insulin secretion. Bhatnagar S, et al. J Biol Chem, 2014 Sep 5. PMID 25002582, Free PMC Article
    4. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    5. VIRMA mediates preferential m(6)A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Yue Y, et al. Cell Discov, 2018. PMID 29507755, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of stem cell population maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of RNA N6-methyladenosine methyltransferase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nuclear speck IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger CCCH domain-containing protein 13

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001170471.1 → NP_001163942.1  zinc finger CCCH domain-containing protein 13

      See identical proteins and their annotated locations for NP_001163942.1

      Status: VALIDATED

      Source sequence(s)
      BC158717, JAXUCZ010000015
      UniProtKB/TrEMBL
      E9PSN4
      Related
      ENSRNOP00000015467.5, ENSRNOT00000015467.6
      Conserved Domains (1) summary
      pfam00642
      Location:42 → 63
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086033.1 Reference GRCr8

      Range
      57016686..57081201
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063274280.1 → XP_063130350.1  zinc finger CCCH domain-containing protein 13 isoform X2

    2. XM_063274281.1 → XP_063130351.1  zinc finger CCCH domain-containing protein 13 isoform X3

    3. XM_006252316.5 → XP_006252378.1  zinc finger CCCH domain-containing protein 13 isoform X1

      See identical proteins and their annotated locations for XP_006252378.1

      UniProtKB/TrEMBL
      E9PSN4
      Conserved Domains (1) summary
      pfam00642
      Location:42 → 63
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

    4. XM_017599690.3 → XP_017455179.1  zinc finger CCCH domain-containing protein 13 isoform X4

    Nucleotide Protein Strain
    Heading Accession and Version

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