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

    Gene ID: 55105, updated on 27-Nov-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
    mouse all
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    Genomic context

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    See GPATCH2 in Genome Data Viewer
    Location:
    1q41
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (217426992..217631090, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (216668052..216872104, complement)
    RS_2024_09 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. 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
    3. Involvement of G-patch domain containing 2 overexpression in breast carcinogenesis. Lin ML, et al. Cancer Sci, 2009 Aug. PMID 19432882, Free PMC Article
    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)

    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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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_2024_08

    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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