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GPATCH2 G-patch domain containing 2 [ Homo sapiens (human) ]

Gene ID: 55105, updated on 3-Apr-2024

Summary

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Official Symbol
GPATCH2provided by HGNC
Official Full Name
G-patch domain containing 2provided by HGNC
Primary source
HGNC:HGNC:25499
See related
Ensembl:ENSG00000092978 MIM:616836; AllianceGenome:HGNC:25499
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Pfa1; CT110; GPATC2; PPP1R30
Summary
The gene encodes a nuclear factor that may play a role in spermatogenesis and in tumor growth during breast cancer. The encoded protein contains a G-patch domain with an RNA binding motif. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
Expression
Ubiquitous expression in testis (RPKM 2.6), thyroid (RPKM 1.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1q41
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (217426992..217631090, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (216668052..216872104, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (217600334..217804432, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372920 Neighboring gene small nucleolar RNA SNORD45 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:217555074-217555725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:217610119-217610638 Neighboring gene Sharpr-MPRA regulatory region 1921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1818 Neighboring gene Sharpr-MPRA regulatory region 7160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2538 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:217833249-217834448 Neighboring gene spermatogenesis associated 17 Neighboring gene SPATA17 antisense RNA 1 Neighboring gene ubiquitin B pseudogene 2

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 2, a gene highly expressed in testes, inhibits nuclear factor-κB and cell proliferation. Hu F, et al. Mol Med Rep, 2015 Feb. PMID 25376275
  2. Involvement of G-patch domain containing 2 overexpression in breast carcinogenesis. Lin ML, et al. Cancer Sci, 2009 Aug. PMID 19432882
  3. Genome-wide gene-expression profiles of breast-cancer cells purified with laser microbeam microdissection: identification of genes associated with progression and metastasis. Nishidate T, et al. Int J Oncol, 2004 Oct. PMID 15375528
  4. Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes. Murea M, et al. Am J Nephrol, 2011. PMID 21546767, Free PMC Article
  5. Docking motif-guided mapping of the interactome of protein phosphatase-1. Hendrickx A, et al. Chem Biol, 2009 Apr 24. PMID 19389623

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. GPATC2 may be involved in inhibiting G1-S phase transition in 293T cells.
    Title: G-patch domain containing 2, a gene highly expressed in testes, inhibits nuclear factor-κB and cell proliferation.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. Involvement of GPATCH2 overexpression in breast carcinogensis is reported.
    Title: Involvement of G-patch domain containing 2 overexpression in breast carcinogenesis.
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 association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
EBI GWAS Catalog
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
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

  • FLJ10252, FLJ21048, FLJ33578, FLJ41751, MGC74998, DKFZp686H07113

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
G patch domain-containing protein 2
Names
cancer/testis antigen 110
protein phosphatase 1, regulatory subunit 30

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_053034.1 RefSeqGene

    Range
    5013..209111
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001297754.3 → NP_001284683.1  G patch domain-containing protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001284683.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences in the 3' coding region and differs in the 3' UTR, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK001114, BC042193, BC063474, DB074192
    Consensus CDS
    CCDS73031.1
    UniProtKB/TrEMBL
    A8K5C3
    Related
    ENSP00000355901.3, ENST00000366934.3

  2. NM_018040.5 → NP_060510.1  G patch domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_060510.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC096641, AK001114, AL354659, CA311820
    Consensus CDS
    CCDS1518.1
    UniProtKB/Swiss-Prot
    Q5VYK7, Q5VYK8, Q86YE7, Q9NW75
    Related
    ENSP00000355902.3, ENST00000366935.8
    Conserved Domains (1) summary
    pfam01585
    Location:468 → 511
    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
    217426992..217631090 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017001592.3 → XP_016857081.1  G patch domain-containing protein 2 isoform X3

  2. XM_011509690.4 → XP_011507992.1  G patch domain-containing protein 2 isoform X2

    Conserved Domains (1) summary
    pfam01585
    Location:454 → 497
    G-patch; G-patch domain

  3. XM_011509689.4 → XP_011507991.1  G patch domain-containing protein 2 isoform X1

    Conserved Domains (1) summary
    pfam01585
    Location:491 → 534
    G-patch; G-patch domain

  4. XM_047423792.1 → XP_047279748.1  G patch domain-containing protein 2 isoform X4

  5. XM_047423801.1 → XP_047279757.1  G patch domain-containing protein 2 isoform X6

  6. XM_017001593.3 → XP_016857082.1  G patch domain-containing protein 2 isoform X4

    UniProtKB/TrEMBL
    A8K5C3

  7. XM_047423800.1 → XP_047279756.1  G patch domain-containing protein 2 isoform X5

  8. XM_011509694.4 → XP_011507996.1  G patch domain-containing protein 2 isoform X7

    UniProtKB/TrEMBL
    A8K5C3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    216668052..216872104 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337319.1 → XP_054193294.1  G patch domain-containing protein 2 isoform X3

  2. XM_054337318.1 → XP_054193293.1  G patch domain-containing protein 2 isoform X2

  3. XM_054337317.1 → XP_054193292.1  G patch domain-containing protein 2 isoform X1

  4. XM_054337321.1 → XP_054193296.1  G patch domain-containing protein 2 isoform X4

  5. XM_054337323.1 → XP_054193298.1  G patch domain-containing protein 2 isoform X6

  6. XM_054337320.1 → XP_054193295.1  G patch domain-containing protein 2 isoform X4

  7. XM_054337322.1 → XP_054193297.1  G patch domain-containing protein 2 isoform X5

  8. XM_054337324.1 → XP_054193299.1  G patch domain-containing protein 2 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NW75.1 GenPept UniProtKB/Swiss-Prot:Q9NW75

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