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    ARFGAP2 ARF GTPase activating protein 2 [ Homo sapiens (human) ]

    Gene ID: 84364, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ARFGAP2provided by HGNC
    Official Full Name
    ARF GTPase activating protein 2provided by HGNC
    Primary source
    HGNC:HGNC:13504
    See related
    Ensembl:ENSG00000149182 MIM:606908; AllianceGenome:HGNC:13504
    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
    IRZ; ZFP289; ZNF289; NBLA10535
    Summary
    Predicted to enable GTPase activator activity. Predicted to be involved in COPI coating of Golgi vesicle. Located in Golgi apparatus; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in skin (RPKM 24.0), brain (RPKM 23.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARFGAP2 in Genome Data Viewer
    Location:
    11p11.2
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (47164301..47176879, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (47321070..47333633, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (47185852..47198430, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene centriolar satellite-associated tubulin polyglutamylase complex regulator 1 Neighboring gene uncharacterized LOC124902671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4687 Neighboring gene uncharacterized LOC124902672 Neighboring gene Sharpr-MPRA regulatory region 11477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3321 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47198949-47199530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:47207755-47208641 Neighboring gene protein kinase C and casein kinase substrate in neurons 3 Neighboring gene microRNA 6745 Neighboring gene ribosomal protein S20 pseudogene 26

    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. ARFGAP2 and ARFGAP3 are essential for COPI coat assembly on the Golgi membrane of living cells. Kartberg F, et al. J Biol Chem, 2010 Nov 19. PMID 20858901, Free PMC Article
    2. Distinct role of subcomplexes of the COPI coat in the regulation of ArfGAP2 activity. Pevzner I, et al. Traffic, 2012 Jun. PMID 22375848
    3. Molecular cloning and characterization of a zinc finger protein involved in Id-1-stimulated mammary epithelial cell growth. Singh J, et al. J Biol Chem, 2001 Apr 13. PMID 11278321
    4. Two human ARFGAPs associated with COP-I-coated vesicles. Frigerio G, et al. Traffic, 2007 Nov. PMID 17760859, Free PMC Article
    5. Three homologous ArfGAPs participate in coat protein I-mediated transport. Saitoh A, et al. J Biol Chem, 2009 May 15. PMID 19299515, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. analysis of the distinct role of subcomplexes of the COPI coat in the regulation of ArfGAP2 activity
      Title: Distinct role of subcomplexes of the COPI coat in the regulation of ArfGAP2 activity.
    2. ARFGAP2 and ARFGAP3 are essential for COPI coat assembly on the Golgi membrane of living cells.
      Title: ARFGAP2 and ARFGAP3 are essential for COPI coat assembly on the Golgi membrane of living cells.
    3. 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.
    4. Differential roles of ArfGAP1, ArfGAP2, and ArfGAP3 in COPI trafficking
      Title: Differential roles of ArfGAP1, ArfGAP2, and ArfGAP3 in COPI trafficking.
    5. 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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Genome-wide shRNA screening identifies ARFGAP2, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells 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

    Clone Names

    • FLJ14576, FLJ26000

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in COPI coating of Golgi vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ADP-ribosylation factor GTPase-activating protein 2
    Names
    ADP ribosylation factor GTPase activating protein 2
    GTPase-activating protein ZNF289
    zinc finger protein 289, ID1 regulated

    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_001242832.2 → NP_001229761.1  ADP-ribosylation factor GTPase-activating protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001229761.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AC090589
      Consensus CDS
      CCDS73283.1
      UniProtKB/TrEMBL
      G5E9L0
      Related
      ENSP00000400226.3, ENST00000426335.6
      Conserved Domains (2) summary
      PLN03114
      Location:1 → 443
      PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
      pfam01412
      Location:11 → 117
      ArfGap; Putative GTPase activating protein for Arf

    2. NM_001410995.1 → NP_001397924.1  ADP-ribosylation factor GTPase-activating protein 2 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC090589
      Consensus CDS
      CCDS91467.1
      UniProtKB/TrEMBL
      E9PN48
      Related
      ENSP00000434809.2, ENST00000525314.6

    3. NM_032389.6 → NP_115765.2  ADP-ribosylation factor GTPase-activating protein 2 isoform 1

      See identical proteins and their annotated locations for NP_115765.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC090589
      Consensus CDS
      CCDS7926.1
      UniProtKB/Swiss-Prot
      B4DX29, B7Z9M7, D3DQQ9, Q3LIF2, Q8N3I1, Q8N6H7, Q96SX7
      Related
      ENSP00000434442.1, ENST00000524782.6
      Conserved Domains (2) summary
      PLN03114
      Location:1 → 471
      PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
      cd09029
      Location:5 → 124
      ArfGap_ArfGap2; Arf1 GTPase-activating protein 2

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      47164301..47176879 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017018413.2 → XP_016873902.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X4

      Conserved Domains (2) summary
      PLN03114
      Location:1 → 485
      PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
      cd09029
      Location:5 → 124
      ArfGap_ArfGap2; Arf1 GTPase-activating protein 2

    2. XM_005253167.2 → XP_005253224.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X2

      Conserved Domains (3) summary
      PLN03114
      Location:1 → 499
      PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
      pfam01412
      Location:11 → 117
      ArfGap; Putative GTPase activating protein for Arf
      cl23720
      Location:255 → 327
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    3. XM_006718346.3 → XP_006718409.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X3

      Conserved Domains (3) summary
      PLN03114
      Location:1 → 496
      PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
      pfam01412
      Location:11 → 117
      ArfGap; Putative GTPase activating protein for Arf
      cl23720
      Location:252 → 324
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    4. XM_005253166.3 → XP_005253223.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X1

      Conserved Domains (3) summary
      PLN03114
      Location:1 → 510
      PLN03114; ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
      pfam01412
      Location:11 → 117
      ArfGap; Putative GTPase activating protein for Arf
      cl23720
      Location:266 → 338
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      47321070..47333633 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370184.1 → XP_054226159.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X4

    2. XM_054370182.1 → XP_054226157.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X2

    3. XM_054370183.1 → XP_054226158.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X3

    4. XM_054370181.1 → XP_054226156.1  ADP-ribosylation factor GTPase-activating protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N6H7.1 GenPept UniProtKB/Swiss-Prot:Q8N6H7

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