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

    Gene ID: 23144, updated on 10-Dec-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 DNA binding activity; R-SMAD binding activity; and metal ion binding activity. Predicted to be involved in mRNA transport. Predicted to act upstream of or within mRNA 3'-end processing and positive regulation of activin receptor signaling pathway. Located in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 6.1), testis (RPKM 5.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZC3H3 in Genome Data Viewer
    Location:
    8q24.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (143437659..143541447, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (144587223..144699075, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1. Nagase T, et al. DNA Res, 1995 Aug 31. PMID 8590280

    See all (27) 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)

    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
    		  
    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_2024_08

    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

      UniProtKB/TrEMBL
      A0A0J9YYE2

    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

      UniProtKB/TrEMBL
      A0A0J9YYE2

    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

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