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    Zc3h4 zinc finger CCCH-type containing 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 678741, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Zc3h4provided by RGD
    Official Full Name
    zinc finger CCCH-type containing 4provided by RGD
    Primary source
    RGD:1596943
    See related
    Ensembl:ENSRNOG00000015229 AllianceGenome:RGD:1596943
    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
    Summary
    Predicted to enable RNA binding activity and metal ion binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human ZC3H4 (zinc finger CCCH-type containing 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 59.3), Spleen (RPKM 55.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Zc3h4 in Genome Data Viewer
    Location:
    1q21
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (86234457..86271963)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (77106309..77143827)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (78352833..78390906)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene Bcl-2 binding component 3 Neighboring gene SUMO1 activating enzyme subunit 1 Neighboring gene ferritin light chain 1, pseudogene 12 Neighboring gene transmembrane protein 160 Neighboring gene neuronal PAS domain protein 1

    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. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    2. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in lncRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription, elongation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of lncRNA transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear RNA surveillance ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger CCCH domain-containing protein 4
    NP_001414244.1
    NP_001414245.1
    XP_063129249.1

    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_001427315.2 → NP_001414244.1  zinc finger CCCH domain-containing protein 4 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A0A8I6G746

    2. NM_001427316.2 → NP_001414245.1  zinc finger CCCH domain-containing protein 4 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A0A8I6G746, D3ZVW3

    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_086019.1 Reference GRCr8

      Range
      86234457..86271963
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063273179.1 → XP_063129249.1  zinc finger CCCH domain-containing protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A8I6G746
    Nucleotide Protein Strain
    Heading Accession and Version

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