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    GPATCH1 G-patch domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 55094, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GPATCH1provided by HGNC
    Official Full Name
    G-patch domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:24658
    See related
    Ensembl:ENSG00000076650 AllianceGenome:HGNC:24658
    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
    ECGP; GPATC1
    Summary
    Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 3.8), testis (RPKM 3.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GPATCH1 in Genome Data Viewer
    Location:
    19q13.11
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (33081181..33130542)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (35599866..35649224)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (33572087..33621448)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14436 Neighboring gene FA core complex associated protein 24 Neighboring gene rhophilin Rho GTPase binding protein 2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33522974-33523845 Neighboring gene HNF1 motif-containing MPRA enhancer 165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33532539-33533040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33534226-33534776 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:33539186-33539904 Neighboring gene uncharacterized LOC124904805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33545753-33546253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33547387-33547910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33547911-33548434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33554488-33555116 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10488 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10489 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:33556329-33556828 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51002 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14437 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33573947-33574447 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51021 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51032 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51043 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51054 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51091 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:33619955-33620099 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14439 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51125 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51126 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51137 Neighboring gene WD repeat domain 88 Neighboring gene uncharacterized LOC124904691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14440 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33666856-33667620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10492 Neighboring gene tRNA-Thr (anticodon AGT) 1-3

    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 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. Regulation of Toll-like receptor 2 interaction with Ecgp96 controls Escherichia coli K1 invasion of brain endothelial cells. Krishnan S, et al. Cell Microbiol, 2013 Jan. PMID 22963587, Free PMC Article
    2. Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium. Moayyeri A, et al. Hum Mol Genet, 2014 Jun 1. PMID 24430505, Free PMC Article
    3. Identification of susceptibility loci for colorectal cancer in a genome-wide meta-analysis. Whiffin N, et al. Hum Mol Genet, 2014 Sep 1. PMID 24737748, Free PMC Article
    4. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Estrada K, et al. Nat Genet, 2012 Apr 15. PMID 22504420, Free PMC Article
    5. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. Roux KJ, et al. J Cell Biol, 2012 Mar 19. PMID 22412018, Free PMC Article

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. In vitro, OmpA+ Escherichia coli infection selectively upregulates Ecgp96 and TLR2 in human brain microvascular endothelial cells (HBMEC), whereas OmpA- E. coli upregulates TLR4 in these cells.
      Title: Regulation of Toll-like receptor 2 interaction with Ecgp96 controls Escherichia coli K1 invasion of brain endothelial cells.
    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.
    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
    Genetic determinants of heel bone properties: genome-wide association meta-analysis and replication in the GEFOS/GENOMOS consortium.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Identification of susceptibility loci for colorectal cancer in a genome-wide meta-analysis.
    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

    • FLJ10206, FLJ34516, FLJ38686

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    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 1
    Names
    evolutionarily conserved G patch domain containing
    evolutionarily conserved G-patch domain-containing protein

    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_018025.3 → NP_060495.2  G patch domain-containing protein 1

      See identical proteins and their annotated locations for NP_060495.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is the protein-coding transcript.
      Source sequence(s)
      AC008521, BC006108
      Consensus CDS
      CCDS12428.1
      UniProtKB/Swiss-Prot
      Q8IZV6, Q8N3B7, Q9BRR8, Q9NW94
      UniProtKB/TrEMBL
      A8K8Y8
      Related
      ENSP00000170564.1, ENST00000170564.7
      Conserved Domains (3) summary
      pfam01585
      Location:154 → 181
      G-patch; G-patch domain
      pfam07713
      Location:31 → 116
      DUF1604; Protein of unknown function (DUF1604)
      cl01255
      Location:403 → 486
      DAGK_cat; Diacylglycerol kinase catalytic domain

    RNA

    1. NR_135270.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate exon compared to variant (1). This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).z
      Source sequence(s)
      AC008521, BC006108

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      33081181..33130542
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006723255.5 → XP_006723318.1  G patch domain-containing protein 1 isoform X1

      Conserved Domains (3) summary
      pfam01585
      Location:154 → 181
      G-patch; G-patch domain
      pfam07713
      Location:31 → 116
      DUF1604; Protein of unknown function (DUF1604)
      cl01255
      Location:403 → 486
      DAGK_cat; Diacylglycerol kinase catalytic domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      35599866..35649224
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321348.1 → XP_054177323.1  G patch domain-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRR8.1 GenPept UniProtKB/Swiss-Prot:Q9BRR8

    Gene LinkOut

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

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