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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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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)

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

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