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

    Gene ID: 54865, updated on 10-Dec-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. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    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
    mouse all
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    Genomic context

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    See GPATCH4 in Genome Data Viewer
    Location:
    1q22-q23.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156594301..156601479, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155730677..155737859, complement)
    RS_2024_09 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. GPATCH4 contributes to nucleolus morphology and its dysfunction impairs cell viability. Kodera K, et al. Biochem Biophys Res Commun, 2024 Jan 22. PMID 38113722
    2. 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
    3. GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners. Kanwal N, et al. Nucleic Acids Res, 2024 Feb 28. PMID 38113271, Free PMC Article
    4. 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
    5. 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

    See all (94) 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)

    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_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
      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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