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    ZC3H4 zinc finger CCCH-type containing 4 [ Homo sapiens (human) ]

    Gene ID: 23211, updated on 3-Nov-2024

    Summary

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    Official Symbol
    ZC3H4provided by HGNC
    Official Full Name
    zinc finger CCCH-type containing 4provided by HGNC
    Primary source
    HGNC:HGNC:17808
    See related
    Ensembl:ENSG00000130749 MIM:619498; AllianceGenome:HGNC:17808
    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
    C19orf7
    Summary
    This gene encodes a member of a family of CCCH (C-x8-C-x5-C-x3-H type) zinc finger domain-containing proteins. These zinc finger domains, which coordinate zinc finger binding and are characterized by three cysteine residues and one histidine residue, are nucleic acid-binding. Other family members are known to function in post-transcriptional regulation. [provided by RefSeq, Aug 2011]
    Expression
    Ubiquitous expression in spleen (RPKM 3.8), ovary (RPKM 2.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZC3H4 in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (47064187..47113776, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (49889484..49939121, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (47567444..47617033, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr19:47533967-47534068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47534993-47535494 Neighboring gene neuronal PAS domain protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10836 Neighboring gene Sharpr-MPRA regulatory region 8906 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:47552307-47552824 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:47552825-47553342 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:47557751-47558307 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:47562983-47563503 Neighboring gene transmembrane protein 160 Neighboring gene MPRA-validated peak3531 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14856 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:47613025-47613752 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47615210-47615938 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47615939-47616666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14858 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47633866-47634480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47638584-47639354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47639355-47640124 Neighboring gene SUMO1 activating enzyme subunit 1 Neighboring gene uncharacterized LOC124904730 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr19:47660297-47660840 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47660841-47661382 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47661383-47661925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47692347-47693113 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47712248-47712997 Neighboring gene Sharpr-MPRA regulatory region 12080 Neighboring gene MPRA-validated peak3532 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47728631-47729130 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:47729258-47729424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10840 Neighboring gene microRNA 3190 Neighboring gene microRNA 3191 Neighboring gene BCL2 binding component 3

    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 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. Zinc finger proteins as potential targets for toxic metal ions: differential effects on structure and function. Hartwig A. Antioxid Redox Signal, 2001 Aug. PMID 11554449
    2. Multiple modes of RNA recognition by zinc finger proteins. Hall TM. Curr Opin Struct Biol, 2005 Jun. PMID 15963892
    3. ZC3H4 restricts non-coding transcription in human cells. Estell C, et al. Elife, 2021 Apr 29. PMID 33913806, Free PMC Article
    4. A first exon termination checkpoint preferentially suppresses extragenic transcription. Austenaa LMI, et al. Nat Struct Mol Biol, 2021 Apr. PMID 33767452, Free PMC Article
    5. Zinc finger proteins: getting a grip on RNA. Brown RS. Curr Opin Struct Biol, 2005 Feb. PMID 15718139

    See all (89) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters.
      Title: ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters.
    2. ZC3H4 restricts non-coding transcription in human cells.
      Title: ZC3H4 restricts non-coding transcription in human cells.
    3. A first exon termination checkpoint preferentially suppresses extragenic transcription.
      Title: A first exon termination checkpoint preferentially suppresses extragenic transcription.
    4. ZC3H4 controls termination of extragenic transcription in human and mouse cells. Cells depleted of ZC3H4 show greatly enhanced synthesis of long and spliced extragenic transcripts.
      Title: A first exon termination checkpoint preferentially suppresses extragenic transcription.
    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
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    • KIAA1064

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables promoter-specific chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA-templated transcription termination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lncRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription, elongation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of lncRNA transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nuclear RNA surveillance IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    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_055983.1
    XP_005258733.1
    XP_005258734.1
    XP_005258735.1
    XP_006723176.1
    XP_011524970.1
    XP_011524971.1
    XP_011524972.1
    XP_016882019.1
    XP_047294470.1
    XP_047294471.1
    XP_047294472.1
    XP_047294473.1
    XP_047294474.1
    XP_054176319.1
    XP_054176320.1
    XP_054176321.1
    XP_054176322.1
    XP_054176323.1
    XP_054176324.1
    XP_054176325.1
    XP_054176326.1
    XP_054176327.1
    XP_054176328.1
    XP_054176329.1
    XP_054176330.1

    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.

    Genomic

    1. NG_027798.1 RefSeqGene

      Range
      4977..54566
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015168.2 → NP_055983.1  zinc finger CCCH domain-containing protein 4

      See identical proteins and their annotated locations for NP_055983.1

      Status: VALIDATED

      Source sequence(s)
      AB028987, AC008755, AK074282, AK125279, AW603637, CN300565
      Consensus CDS
      CCDS42582.1
      UniProtKB/Swiss-Prot
      Q9UPT8, Q9Y420
      Related
      ENSP00000253048.4, ENST00000253048.10
      Conserved Domains (1) summary
      smart00356
      Location:421 → 445
      ZnF_C3H1; zinc finger

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      47064187..47113776 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438517.1 → XP_047294473.1  zinc finger CCCH domain-containing protein 4 isoform X11

    2. XM_017026530.3 → XP_016882019.1  zinc finger CCCH domain-containing protein 4 isoform X7

    3. XM_006723113.4 → XP_006723176.1  zinc finger CCCH domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006723176.1

      UniProtKB/Swiss-Prot
      Q9UPT8, Q9Y420
      Conserved Domains (1) summary
      smart00356
      Location:421 → 445
      ZnF_C3H1; zinc finger

    4. XM_011526668.4 → XP_011524970.1  zinc finger CCCH domain-containing protein 4 isoform X3

      See identical proteins and their annotated locations for XP_011524970.1

      Conserved Domains (1) summary
      smart00356
      Location:380 → 404
      ZnF_C3H1; zinc finger

    5. XM_047438516.1 → XP_047294472.1  zinc finger CCCH domain-containing protein 4 isoform X10

    6. XM_005258678.3 → XP_005258735.1  zinc finger CCCH domain-containing protein 4 isoform X5

      Conserved Domains (1) summary
      smart00356
      Location:372 → 396
      ZnF_C3H1; zinc finger

    7. XM_005258677.5 → XP_005258734.1  zinc finger CCCH domain-containing protein 4 isoform X3

      See identical proteins and their annotated locations for XP_005258734.1

      Conserved Domains (1) summary
      smart00356
      Location:380 → 404
      ZnF_C3H1; zinc finger

    8. XM_047438515.1 → XP_047294471.1  zinc finger CCCH domain-containing protein 4 isoform X9

    9. XM_011526669.4 → XP_011524971.1  zinc finger CCCH domain-containing protein 4 isoform X4

      Conserved Domains (1) summary
      smart00356
      Location:375 → 399
      ZnF_C3H1; zinc finger

    10. XM_011526670.4 → XP_011524972.1  zinc finger CCCH domain-containing protein 4 isoform X6

      Conserved Domains (1) summary
      smart00356
      Location:371 → 395
      ZnF_C3H1; zinc finger

    11. XM_047438514.1 → XP_047294470.1  zinc finger CCCH domain-containing protein 4 isoform X8

    12. XM_005258676.4 → XP_005258733.1  zinc finger CCCH domain-containing protein 4 isoform X2

      Conserved Domains (1) summary
      smart00356
      Location:385 → 409
      ZnF_C3H1; zinc finger

    13. XM_047438518.1 → XP_047294474.1  zinc finger CCCH domain-containing protein 4 isoform X12

      Related
      ENSP00000469684.1, ENST00000601973.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      49889484..49939121 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320344.1 → XP_054176319.1  zinc finger CCCH domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      Q9UPT8, Q9Y420

    2. XM_054320351.1 → XP_054176326.1  zinc finger CCCH domain-containing protein 4 isoform X7

    3. XM_054320347.1 → XP_054176322.1  zinc finger CCCH domain-containing protein 4 isoform X3

    4. XM_054320346.1 → XP_054176321.1  zinc finger CCCH domain-containing protein 4 isoform X3

    5. XM_054320354.1 → XP_054176329.1  zinc finger CCCH domain-containing protein 4 isoform X10

    6. XM_054320349.1 → XP_054176324.1  zinc finger CCCH domain-containing protein 4 isoform X5

    7. XM_054320353.1 → XP_054176328.1  zinc finger CCCH domain-containing protein 4 isoform X9

    8. XM_054320348.1 → XP_054176323.1  zinc finger CCCH domain-containing protein 4 isoform X4

    9. XM_054320350.1 → XP_054176325.1  zinc finger CCCH domain-containing protein 4 isoform X6

    10. XM_054320352.1 → XP_054176327.1  zinc finger CCCH domain-containing protein 4 isoform X8

    11. XM_054320345.1 → XP_054176320.1  zinc finger CCCH domain-containing protein 4 isoform X2

    12. XM_054320355.1 → XP_054176330.1  zinc finger CCCH domain-containing protein 4 isoform X12

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPT8.3 GenPept UniProtKB/Swiss-Prot:Q9UPT8

    Gene LinkOut

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

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