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Zc3h13 zinc finger CCCH type containing 13 [ Mus musculus (house mouse) ]

Gene ID: 67302, updated on 2-Nov-2024

Summary

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Official Symbol
Zc3h13provided by MGI
Official Full Name
zinc finger CCCH type containing 13provided by MGI
Primary source
MGI:MGI:1914552
See related
Ensembl:ENSMUSG00000022000 AllianceGenome:MGI:1914552
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
2600010B19Rik; 3110050K21Rik; 4930570G11Rik
Summary
Predicted to enable metal ion binding activity. Involved in regulation of stem cell population maintenance. Located in nuclear speck. Part of RNA N6-methyladenosine methyltransferase complex. Is expressed in early conceptus; inner cell mass; and oocyte. Orthologous to human ZC3H13 (zinc finger CCCH-type containing 13). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 8.3), frontal lobe adult (RPKM 5.8) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Zc3h13 in Genome Data Viewer
Location:
14 D3; 14 39.8 cM
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (75521746..75581873)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (75284306..75344433)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene predicted gene 15628 Neighboring gene lymphocyte cytosolic protein 1 Neighboring gene STARR-positive B cell enhancer mm9_chr14:75576489-75576789 Neighboring gene STARR-seq mESC enhancer starr_37136 Neighboring gene STARR-positive B cell enhancer ABC_E4120 Neighboring gene STARR-positive B cell enhancer ABC_E8899 Neighboring gene STARR-positive B cell enhancer ABC_E7338 Neighboring gene predicted gene, 35679 Neighboring gene STARR-positive B cell enhancer ABC_E7339 Neighboring gene carboxypeptidase B2 Neighboring gene ribosomal protein L17 pseudogene Neighboring gene STARR-seq mESC enhancer starr_37139 Neighboring gene predicted gene, 46470 Neighboring gene STARR-seq mESC enhancer starr_37142 Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:75845484-75845692 Neighboring gene predicted gene, 41212 Neighboring gene siah E3 ubiquitin protein ligase family member 3 Neighboring gene predicted gene, 35966

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

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. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m(6)A machinery component Wtap/Fl(2)d. Knuckles P, et al. Genes Dev, 2018 Mar 1. PMID 29535189, Free PMC Article
  3. The interactome of CLUH reveals its association to SPAG5 and its co-translational proximity to mitochondrial proteins. Hémono M, et al. BMC Biol, 2022 Jan 10. PMID 35012549, Free PMC Article
  4. Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue. Chavez JD, et al. Cell Syst, 2018 Jan 24. PMID 29199018, Free PMC Article
  5. New roles for the de-ubiquitylating enzyme OTUD4 in an RNA-protein network and RNA granules. Das R, et al. J Cell Sci, 2019 Jun 17. PMID 31138677, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (4) 

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 MGI

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of RNA N6-methyladenosine methyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear speck ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

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_001359875.1 → NP_001346804.1  zinc finger CCCH domain-containing protein 13 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AW536655, BC082576, BC138264, BY127373
    Consensus CDS
    CCDS88715.1
    UniProtKB/TrEMBL
    A0A2I3BPQ5
    Related
    ENSMUSP00000153882.2, ENSMUST00000227049.2
    Conserved Domains (1) summary
    pfam00642
    Location:42 → 62
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

  2. NM_026083.2 → NP_080359.2  zinc finger CCCH domain-containing protein 13 isoform 2

    See identical proteins and their annotated locations for NP_080359.2

    Status: VALIDATED

    Source sequence(s)
    AK078225, AW536655, BB619434, BC038882, BG062845, CAAA01056772, CF731340, CF742012
    Consensus CDS
    CCDS27278.1
    UniProtKB/Swiss-Prot
    B9EHN9, E9Q784
    Related
    ENSMUSP00000022577.6, ENSMUST00000022577.6
    Conserved Domains (1) summary
    pfam00642
    Location:42 → 62
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000080.7 Reference GRCm39 C57BL/6J

    Range
    75521746..75581873
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006519447.5 → XP_006519510.1  zinc finger CCCH domain-containing protein 13 isoform X3

    See identical proteins and their annotated locations for XP_006519510.1

    UniProtKB/Swiss-Prot
    B9EHN9, E9Q784
    Conserved Domains (1) summary
    pfam00642
    Location:42 → 62
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

  2. XM_030247971.2 → XP_030103831.1  zinc finger CCCH domain-containing protein 13 isoform X2

    UniProtKB/TrEMBL
    A0A2I3BPQ5
    Conserved Domains (1) summary
    pfam00642
    Location:42 → 62
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

  3. XM_011245157.4 → XP_011243459.1  zinc finger CCCH domain-containing protein 13 isoform X4

  4. XM_006519446.5 → XP_006519509.1  zinc finger CCCH domain-containing protein 13 isoform X2

    See identical proteins and their annotated locations for XP_006519509.1

    UniProtKB/TrEMBL
    A0A2I3BPQ5
    Conserved Domains (1) summary
    pfam00642
    Location:42 → 62
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

  5. XM_036158826.1 → XP_036014719.1  zinc finger CCCH domain-containing protein 13 isoform X1

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

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_027377.1: Suppressed sequence

    Description
    NM_027377.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
E9Q784.1 GenPept UniProtKB/Swiss-Prot:E9Q784

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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