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ZC3H3 zinc finger CCCH-type containing 3 [ Homo sapiens (human) ]

Gene ID: 23144, updated on 3-Apr-2024

Summary

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Official Symbol
ZC3H3provided by HGNC
Official Full Name
zinc finger CCCH-type containing 3provided by HGNC
Primary source
HGNC:HGNC:28972
See related
Ensembl:ENSG00000014164 MIM:618640; AllianceGenome:HGNC:28972
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SMICL; ZC3HDC3
Summary
Predicted to enable SMAD binding activity. Involved in regulation of mRNA polyadenylation. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 6.1), testis (RPKM 5.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
8q24.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (143437659..143541447, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (144587223..144699075, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (144519829..144623617, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19621 Neighboring gene MAFA antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144504663-144505250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144517937-144518722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144518723-144519506 Neighboring gene MAF bZIP transcription factor A Neighboring gene Sharpr-MPRA regulatory region 10662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144544126-144544839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144544840-144545552 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144547684-144548592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144550408-144551314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144552747-144553448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144561253-144561753 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144569950-144570487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144570488-144571024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144583622-144584122 Neighboring gene small nucleolar RNA, C/D box 149 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:144597771-144597965 Neighboring gene RN7SK pseudogene 175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144631415-144632004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144632005-144632593 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144635671-144636416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144636417-144637160 Neighboring gene uncharacterized LOC100310756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144640331-144640972 Neighboring gene gasdermin D

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The human ZC3H3 and RBM26/27 proteins are critical for PAXT-mediated nuclear RNA decay. Silla T, et al. Nucleic Acids Res, 2020 Mar 18. PMID 31950173, Free PMC Article
  2. Smicl is a novel Smad interacting protein and cleavage and polyadenylation specificity factor associated protein. Collart C, et al. Genes Cells, 2005 Sep. PMID 16115198
  3. A conserved CCCH-type zinc finger protein regulates mRNA nuclear adenylation and export. Hurt JA, et al. J Cell Biol, 2009 Apr 20. PMID 19364924, Free PMC Article
  4. In Vitro Identification of Histatin 5 Salivary Complexes. Moffa EB, et al. PLoS One, 2015. PMID 26544073, Free PMC Article
  5. A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis. Greliche N, et al. BMC Med Genet, 2013 Mar 20. PMID 23509962, Free PMC Article

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. three additional proteins required for Poly(A) Tail eXosome Targeting (PAXT) function: ZC3H3, RBM26 and RBM27 along with the known PAXT-associated protein, PABPN1, were identified.
    Title: The human ZC3H3 and RBM26/27 proteins are critical for PAXT-mediated nuclear RNA decay.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0150

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables R-SMAD binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in mRNA 3'-end processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA transport IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of activin receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of mRNA cleavage and polyadenylation specificity factor complex IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
zinc finger CCCH domain-containing protein 3
Names
smad-interacting CPSF-like factor
zinc finger CCCH-type domain containing 3

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_015117.3 → NP_055932.2  zinc finger CCCH domain-containing protein 3

    See identical proteins and their annotated locations for NP_055932.2

    Status: VALIDATED

    Source sequence(s)
    AA806585, AC067930, BM148116, D63484
    Consensus CDS
    CCDS6402.1
    UniProtKB/Swiss-Prot
    Q14163, Q8IXZ2, Q8N4E2, Q9BUS4
    Related
    ENSP00000262577.5, ENST00000262577.6
    Conserved Domains (2) summary
    smart00356
    Location:750 → 776
    ZnF_C3H1; zinc finger
    pfam00642
    Location:668 → 694
    zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    143437659..143541447 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516943.3 → XP_011515245.2  zinc finger CCCH domain-containing protein 3 isoform X1

  2. XM_011516944.3 → XP_011515246.2  zinc finger CCCH domain-containing protein 3 isoform X2

RNA

  1. XR_928313.4 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187571.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    5375..31487 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    144587223..144699075 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054360168.1 → XP_054216143.1  zinc finger CCCH domain-containing protein 3 isoform X3

  2. XM_054360169.1 → XP_054216144.1  zinc finger CCCH domain-containing protein 3 isoform X1

  3. XM_054360170.1 → XP_054216145.1  zinc finger CCCH domain-containing protein 3 isoform X2

RNA

  1. XR_008487828.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IXZ2.3 GenPept UniProtKB/Swiss-Prot:Q8IXZ2

Gene LinkOut

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