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    ARFGAP3 ARF GTPase activating protein 3 [ Homo sapiens (human) ]

    Gene ID: 26286, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ARFGAP3provided by HGNC
    Official Full Name
    ARF GTPase activating protein 3provided by HGNC
    Primary source
    HGNC:HGNC:661
    See related
    Ensembl:ENSG00000242247 MIM:612439; AllianceGenome:HGNC:661
    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
    ARFGAP1
    Summary
    The protein encoded by this gene is a GTPase-activating protein (GAP) that associates with the Golgi apparatus and regulates the early secretory pathway of proteins. The encoded protein promotes hydrolysis of ADP-ribosylation factor 1 (ARF1)-bound GTP, which is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is a prerequisite for the fusion of these vesicles with target compartments. The activity of this protein is sensitive to phospholipids. Multiple transcript variants encoding different isoforms have been found for this gene. This gene was originally known as ARFGAP1, but that is now the name of a related but different gene. [provided by RefSeq, Nov 2008]
    Expression
    Ubiquitous expression in adrenal (RPKM 47.6), prostate (RPKM 36.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARFGAP3 in Genome Data Viewer
    Location:
    22q13.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42796502..42857273, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (43277420..43338189, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (43192508..43253279, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9313 Neighboring gene ADAMTS7 pseudogene 5 Neighboring gene dynamin 1 pseudogene 18 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:43252438-43253282 Neighboring gene uncharacterized LOC101927393 Neighboring gene COA1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43277300-43277874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43277875-43278449 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43278450-43279023 Neighboring gene protein kinase C and casein kinase substrate in neurons 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43293568-43294344 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43294345-43295119 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43300517-43301037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43301932-43302607 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43311964-43312742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43321567-43322365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43330023-43330539 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43330540-43331055 Neighboring gene uncharacterized LOC124905128 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:43335396-43335896

    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. ArfGAP3 regulates the transport of cation-independent mannose 6-phosphate receptor in the post-Golgi compartment. Shiba Y, et al. Curr Biol, 2013 Oct 7. PMID 24076238, Free PMC Article
    2. Expression of ArfGAP3 in Vaginal Anterior Wall of Patients With Pelvic Floor Organ Prolapse in Pelvic Organ Prolapse and Non-Pelvic Organ Prolapse Patients. Sun Y, et al. Female Pelvic Med Reconstr Surg, 2021 Jan 1. PMID 31868832, Free PMC Article
    3. ARFGAP3, an androgen target gene, promotes prostate cancer cell proliferation and migration. Obinata D, et al. Int J Cancer, 2012 May 15. PMID 21647875
    4. Characterization, chromosomal assignment, and tissue expression of a novel human gene belonging to the ARF GAP family. Zhang C, et al. Genomics, 2000 Feb 1. PMID 10704287
    5. Two human ARFGAPs associated with COP-I-coated vesicles. Frigerio G, et al. Traffic, 2007 Nov. PMID 17760859, Free PMC Article

    See all (60) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression of ArfGAP3 in Vaginal Anterior Wall of Patients With Pelvic Floor Organ Prolapse in Pelvic Organ Prolapse and Non-Pelvic Organ Prolapse Patients.
      Title: Expression of ArfGAP3 in Vaginal Anterior Wall of Patients With Pelvic Floor Organ Prolapse in Pelvic Organ Prolapse and Non-Pelvic Organ Prolapse Patients.
    2. We suggest a model in which ArfGAP3 regulates Golgi association of GGA clathrin adaptors.
      Title: ArfGAP3 regulates the transport of cation-independent mannose 6-phosphate receptor in the post-Golgi compartment.
    3. our results suggest that ARFGAP3 is a novel androgen-regulated gene that can promote prostate cancer cell proliferation and migration in collaboration with paxillin.
      Title: ARFGAP3, an androgen target gene, promotes prostate cancer cell proliferation and migration.
    4. 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.
    5. ArfGAP1, ArfGAP2, and ArfGAP3 have overlapping roles in regulating COPI function in Golgi-to-ER retrograde transport.
      Title: Three homologous ArfGAPs participate in coat protein I-mediated transport.
    6. Differential roles of ArfGAP1, ArfGAP2, and ArfGAP3 in COPI trafficking
      Title: Differential roles of ArfGAP1, ArfGAP2, and ArfGAP3 in COPI trafficking.
    7. human ARFGAP2 and ARFGAP3 are associated with COP-I-coated vesicles and function in COP I traffic
      Title: Two human ARFGAPs associated with COP-I-coated vesicles.
    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)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ45618

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in COPI coating of Golgi vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular protein transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein secretion IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in vesicle-mediated transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    ADP-ribosylation factor GTPase-activating protein 3
    Names
    ADP ribosylation factor GTPase activating protein 3
    ADP-ribosylation factor GTPase activating protein 1
    ARF GAP 3

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001142293.2 → NP_001135765.1  ADP-ribosylation factor GTPase-activating protein 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting protein (isoform 2) has the same N- and C-termini but is shorter than isoform 1.
      Source sequence(s)
      AF111847, AK307967, AL049757, BQ019944, DB458974
      Consensus CDS
      CCDS46722.1
      UniProtKB/TrEMBL
      B7Z4Q0
      Related
      ENSP00000388791.2, ENST00000437119.6
      Conserved Domains (3) summary
      PLN03114
      Location:1 → 420
      PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
      pfam01412
      Location:12 → 106
      ArfGap; Putative GTPase activating protein for Arf
      pfam12329
      Location:202 → 257
      TMF_DNA_bd; TATA element modulatory factor 1 DNA binding

    2. NM_014570.5 → NP_055385.3  ADP-ribosylation factor GTPase-activating protein 3 isoform 1

      See identical proteins and their annotated locations for NP_055385.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AF111847, AL049757, BC005122, BQ019944, DB458974
      Consensus CDS
      CCDS14042.1
      UniProtKB/Swiss-Prot
      E9PB03, Q9BSC6, Q9H9J0, Q9NP61, Q9NT10, Q9NUP5, Q9Y4V3, Q9Y4V4
      UniProtKB/TrEMBL
      B7Z4Q0, B7Z6L2
      Related
      ENSP00000263245.5, ENST00000263245.10
      Conserved Domains (3) summary
      PLN03114
      Location:1 → 464
      PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
      pfam01412
      Location:12 → 116
      ArfGap; Putative GTPase activating protein for Arf
      pfam12329
      Location:246 → 301
      TMF_DNA_bd; TATA element modulatory factor 1 DNA binding

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      42796502..42857273 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005261525.5 → XP_005261582.1  ADP-ribosylation factor GTPase-activating protein 3 isoform X1

      UniProtKB/TrEMBL
      B7Z4Q0
      Conserved Domains (3) summary
      PLN03114
      Location:1 → 420
      PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
      pfam01412
      Location:12 → 116
      ArfGap; Putative GTPase activating protein for Arf
      pfam12329
      Location:246 → 301
      TMF_DNA_bd; TATA element modulatory factor 1 DNA binding

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      43277420..43338189 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325525.1 → XP_054181500.1  ADP-ribosylation factor GTPase-activating protein 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NP61.1 GenPept UniProtKB/Swiss-Prot:Q9NP61

    Gene LinkOut

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