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

Gene ID: 55094, updated on 23-Nov-2023

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, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 3.8), testis (RPKM 3.4) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (33081181..33130542)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (35599866..35649224)
105.20220307 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
  • 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 (40) 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_2023_10

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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