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GPATCH4 G-patch domain containing 4 (gene/pseudogene) [ Homo sapiens (human) ]

Gene ID: 54865, updated on 5-Mar-2024

Summary

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Official Symbol
GPATCH4provided by HGNC
Official Full Name
G-patch domain containing 4 (gene/pseudogene)provided by HGNC
Primary source
HGNC:HGNC:25982
See related
Ensembl:ENSG00000160818 AllianceGenome:HGNC:25982
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
GPATC4
Summary
Enables RNA binding activity. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. [provided by Alliance of Genome Resources, Apr 2022]
Annotation information
Annotation category: suggests misassembly
Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Expression
Ubiquitous expression in appendix (RPKM 11.6), brain (RPKM 10.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1q22-q23.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156594301..156601479, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155730677..155737859, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156564093..156571271, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1873 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156554411-156554912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156554913-156555412 Neighboring gene tetratricopeptide repeat domain 24 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156561722-156562568 Neighboring gene NAD(P)HX epimerase Neighboring gene hyaluronan and proteoglycan link protein 2 Neighboring gene uncharacterized LOC101928177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156616142-156616665 Neighboring gene BCAN antisense RNA 2 Neighboring gene brevican Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156624901-156625401 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156626597-156627098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156627099-156627599 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156628979-156629479

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. G-patch domain-containing protein 4 localizes to both the nucleoli and Cajal bodies and regulates cell growth and nucleolar structure. Hirawake-Mogi H, et al. Biochem Biophys Res Commun, 2021 Jun 25. PMID 33933995
  2. EZH2 and BCL6 Cooperate to Assemble CBX8-BCOR Complex to Repress Bivalent Promoters, Mediate Germinal Center Formation and Lymphomagenesis. Béguelin W, et al. Cancer Cell, 2016 Aug 8. PMID 27505670, Free PMC Article
  3. USP53 plays an antitumor role in hepatocellular carcinoma through deubiquitination of cytochrome c. Yao Y, et al. Oncogenesis, 2022 Jun 2. PMID 35654790, Free PMC Article
  4. KSHV episome tethering sites on host chromosomes and regulation of latency-lytic switch by CHD4. Kumar A, et al. Cell Rep, 2022 May 10. PMID 35545047, Free PMC Article
  5. HIV-1 Vpr induces cell cycle arrest and enhances viral gene expression by depleting CCDC137. Zhang F, et al. Elife, 2020 Jun 15. PMID 32538781, Free PMC Article

See all (78) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners.
    Title: GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners.
  2. GPATCH4 contributes to nucleolus morphology and its dysfunction impairs cell viability.
    Title: GPATCH4 contributes to nucleolus morphology and its dysfunction impairs cell viability.
  3. G-patch domain-containing protein 4 localizes to both the nucleoli and Cajal bodies and regulates cell growth and nucleolar structure.
    Title: G-patch domain-containing protein 4 localizes to both the nucleoli and Cajal bodies and regulates cell growth and nucleolar structure.
  4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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

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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Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev is identified to have a physical interaction with G patch domain containing 4 (GPATCH4) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
G patch domain-containing protein 4

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_001396855.1 → NP_001383784.1  G patch domain-containing protein 4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AK293026, AL365181
    UniProtKB/Swiss-Prot
    Q5T3I0, Q5T3I1, Q6ZUE7, Q8IWG8, Q9NXH4
    UniProtKB/TrEMBL
    A8KAG1
    Conserved Domains (1) summary
    pfam01585
    Location:8 → 55
    G-patch; G-patch domain

  2. NM_001396861.1 → NP_001383790.1  G patch domain-containing protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AK293026, AL365181
    UniProtKB/TrEMBL
    A8KAG1
    Conserved Domains (1) summary
    pfam01585
    Location:13 → 60
    G-patch; G-patch domain

  3. NM_015590.4 → NP_056405.2  G patch domain-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_056405.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks an internal segment in the 5' region, resulting in an upstream AUG start codon, as compared to variant 2. The resulting isoform (1) has a longer and distinct N-terminus, as compared to isoform 2.
    Source sequence(s)
    AK293026, AL365181, BC056904, BE326312, CB109133, DA087471
    UniProtKB/TrEMBL
    E9PAV9
    Conserved Domains (1) summary
    pfam01585
    Location:13 → 60
    G-patch; G-patch domain

  4. NM_182679.3 → NP_872620.1  G patch domain-containing protein 4 isoform 2

    See identical proteins and their annotated locations for NP_872620.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) is the longer and predominant transcript, which encodes a shorter isoform (2).
    Source sequence(s)
    AK293026, AL365181, BC056904, BE326312, DA087471
    UniProtKB/TrEMBL
    A0A0A0MRK1
    Related
    ENSP00000357215.5, ENST00000368232.9
    Conserved Domains (1) summary
    pfam01585
    Location:8 → 55
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    156594301..156601479 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791758.1 Reference GRCh38.p14 PATCHES

    Range
    152858..160038 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    155730677..155737859 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_017725.1: Suppressed sequence

    Description
    NM_017725.1: 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
Q5T3I0.2 GenPept UniProtKB/Swiss-Prot:Q5T3I0

Gene LinkOut

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

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