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ZGPAT zinc finger CCCH-type and G-patch domain containing [ Homo sapiens (human) ]

Gene ID: 84619, updated on 5-Mar-2024

Summary

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Official Symbol
ZGPATprovided by HGNC
Official Full Name
zinc finger CCCH-type and G-patch domain containingprovided by HGNC
Primary source
HGNC:HGNC:15948
See related
Ensembl:ENSG00000197114 MIM:619577; AllianceGenome:HGNC:15948
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
ZIP; ZC3H9; GPATC6; GPATCH6; ZC3HDC9; KIAA1847
Summary
Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of epidermal growth factor-activated receptor activity and negative regulation of transcription by RNA polymerase II. Located in nucleoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver (RPKM 22.1), kidney (RPKM 17.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
20q13.33
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (63707442..63736142)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65527749..65556418)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62338794..62367494)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RTEL1-TNFRSF6B readthrough (NMD candidate) Neighboring gene uncharacterized LOC124904954 Neighboring gene regulator of telomere elongation helicase 1 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62307938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62313341-62314065 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62314792-62315516 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 20:62320674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62330893-62331773 Neighboring gene TNF receptor superfamily member 6b Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62339316-62340276 Neighboring gene ADP ribosylation factor related protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62347847-62348348 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:62359961-62360460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363158-62363701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62363702-62364244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62368201-62369118 Neighboring gene LIME1 eExon liver enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13186 Neighboring gene ZBTB46 antisense RNA 2 Neighboring gene SLC2A4 regulator Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62383144-62384094 Neighboring gene Lck interacting transmembrane adaptor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62384095-62385046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62385047-62385996 Neighboring gene zinc finger and BTB domain containing 46 Neighboring gene uncharacterized LOC124904956 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62401989-62402163

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. sZIP, an alternative splice variant of ZIP, antagonizes transcription repression and growth inhibition by ZIP. Yu W, et al. J Biol Chem, 2010 May 7. PMID 20233718, Free PMC Article
  2. Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Ordway JM, et al. Carcinogenesis, 2006 Dec. PMID 16952911
  3. Investigation of reported associations between the 20q13 and 21q22 loci and pediatric-onset Crohn's disease in Canadian children. Amre DK, et al. Am J Gastroenterol, 2009 Nov. PMID 19623168
  4. Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. Kugathasan S, et al. Nat Genet, 2008 Oct. PMID 18758464, Free PMC Article
  5. HIV-1 Vpr induces the degradation of ZIP and sZIP, adaptors of the NuRD chromatin remodeling complex, by hijacking DCAF1/VprBP. Maudet C, et al. PLoS One, 2013. PMID 24116224, Free PMC Article

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Data suggest that ZIP, USP39, Prp24/p100/SART3, and Prp43 associate to form complex instrumental in spliceosome assembly; ZIP regulates pre-mRNA splicing of USP39 independent of RNA binding; stable 35S tri-snRNP particles are enriched in Cajal body. (USP39 = ubiquitin specific peptidase 39; SART3 = squamous cell carcinoma antigen recognised by T cells 3; Prp43 = RNA helicase Prp43)
    Title: Identification of a 35S U4/U6.U5 tri-small nuclear ribonucleoprotein (tri-snRNP) complex intermediate in spliceosome assembly.
  2. sZIP, an alternative splice variant of ZIP, antagonizes transcription repression and growth inhibition by ZIP in liver neoplasms.
    Title: sZIP, an alternative splice variant of ZIP, antagonizes transcription repression and growth inhibition by ZIP.
  3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Genome-wide searching of rare genetic variants in WTCCC data.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Investigation of reported associations between the 20q13 and 21q22 loci and pediatric-onset Crohn's disease in Canadian children.
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
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
EBI GWAS Catalog
Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease.
EBI GWAS Catalog
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of zinc finger, CCCH-type with G patch domain (ZGPAT) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr induces the degradation of ZIP/sZIP through the DCAF1 ubiquitin ligase, while VprQ65R mutant impairs the Vpr-induced degradation of ZIP/sZIP PubMed
vpr HIV-1 Vpr forms a complex by recruiting RbAp46, HAT1, ZIP/sZIP, and Cul4A PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: LIME1

Homology

Clone Names

  • KIAA1847, MGC44880

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of epidermal growth factor-activated receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
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
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
zinc finger CCCH-type with G patch domain-containing protein
Names
g patch domain-containing protein 6
zinc finger CCCH domain-containing protein 9
zinc finger and G patch domain-containing protein
zinc finger, CCCH-type with G patch domain

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_001083113.2 → NP_001076582.1  zinc finger CCCH-type with G patch domain-containing protein isoform c

    See identical proteins and their annotated locations for NP_001076582.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a. Variants 3, 4 and 5 encode the same isoform (c).
    Source sequence(s)
    AB058750, BC019338, DA252406
    Consensus CDS
    CCDS13535.1
    UniProtKB/TrEMBL
    A0A0S2Z5X3, A0A0S2Z6H0
    Related
    ENSP00000391176.1, ENST00000448100.6
    Conserved Domains (3) summary
    cd04508
    Location:221 → 251
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
    smart00356
    Location:178 → 199
    ZnF_C3H1; zinc finger
    pfam01585
    Location:313 → 354
    G-patch; G-patch domain

  2. NM_001195653.2 → NP_001182582.1  zinc finger CCCH-type with G patch domain-containing protein isoform c

    See identical proteins and their annotated locations for NP_001182582.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a. Variants 3, 4 and 5 encode the same isoform (c).
    Source sequence(s)
    AK314726, BC019338, BC032612
    Consensus CDS
    CCDS13535.1
    UniProtKB/TrEMBL
    A0A0S2Z5X3, A0A0S2Z6H0
    Related
    ENSP00000358984.3, ENST00000369967.7
    Conserved Domains (3) summary
    cd04508
    Location:221 → 251
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
    smart00356
    Location:178 → 199
    ZnF_C3H1; zinc finger
    pfam01585
    Location:313 → 354
    G-patch; G-patch domain

  3. NM_001195654.2 → NP_001182583.1  zinc finger CCCH-type with G patch domain-containing protein isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses two alternate in-frame splice sites in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform d), compared to isoform a.
    Source sequence(s)
    BC019338, BC032612, DA055150
    Consensus CDS
    CCDS56203.1
    UniProtKB/TrEMBL
    A0A0S2Z6H0
    Related
    ENSP00000349634.4, ENST00000357119.8
    Conserved Domains (3) summary
    cd04508
    Location:221 → 251
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
    smart00356
    Location:178 → 199
    ZnF_C3H1; zinc finger
    pfam01585
    Location:304 → 345
    G-patch; G-patch domain

  4. NM_032527.5 → NP_115916.3  zinc finger CCCH-type with G patch domain-containing protein isoform a

    See identical proteins and their annotated locations for NP_115916.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AK027878, BC019338, BC032612, DA055150
    Consensus CDS
    CCDS13534.1
    UniProtKB/Swiss-Prot
    E1P5K1, Q4VXN9, Q5JWI9, Q5JWJ0, Q8N5A5, Q8NC55, Q8WUV4, Q96JI0, Q96JU4, Q9H401
    UniProtKB/TrEMBL
    A0A0S2Z6H0
    Related
    ENSP00000332013.5, ENST00000328969.5
    Conserved Domains (3) summary
    cd04508
    Location:221 → 251
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
    smart00356
    Location:178 → 199
    ZnF_C3H1; zinc finger
    pfam01585
    Location:333 → 374
    G-patch; G-patch domain

  5. NM_181485.3 → NP_852150.2  zinc finger CCCH-type with G patch domain-containing protein isoform c

    See identical proteins and their annotated locations for NP_852150.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a. Variants 3, 4 and 5 encode the same isoform (c).
    Source sequence(s)
    AL121845, BC019338, BC032612, DA848516
    Consensus CDS
    CCDS13535.1
    UniProtKB/TrEMBL
    A0A0S2Z5X3, A0A0S2Z6H0
    Related
    ENSP00000348242.6, ENST00000355969.11
    Conserved Domains (3) summary
    cd04508
    Location:221 → 251
    TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
    smart00356
    Location:178 → 199
    ZnF_C3H1; zinc finger
    pfam01585
    Location:313 → 354
    G-patch; G-patch domain

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    63707442..63736142
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65527749..65556418
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_181484.1: Suppressed sequence

    Description
    NM_181484.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N5A5.3 GenPept UniProtKB/Swiss-Prot:Q8N5A5

Gene LinkOut

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

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