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AGFG1 ArfGAP with FG repeats 1 [ Homo sapiens (human) ]

Gene ID: 3267, updated on 6-Jan-2019

Summary

Official Symbol
AGFG1provided by HGNC
Official Full Name
ArfGAP with FG repeats 1provided by HGNC
Primary source
HGNC:HGNC:5175
See related
Ensembl:ENSG00000173744 MIM:600862
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
HRB; RAB; RIP
Summary
The protein encoded by this gene is related to nucleoporins, a class of proteins that mediate nucleocytoplasmic transport. The encoded protein binds the activation domain of the human immunodeficiency virus Rev protein when Rev is assembled onto its RNA target, and is required for the nuclear export of Rev-directed RNAs. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
Expression
Broad expression in bone marrow (RPKM 27.1), testis (RPKM 16.3) and 24 other tissues See more
Orthologs

Genomic context

See AGFG1 in Genome Data Viewer
Location:
2q36.3
Exon count:
16
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (227472169..227561222)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (228336853..228425938)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene stress induced phosphoprotein 1 pseudogene 2 Neighboring gene mitochondrial fission factor Neighboring gene transmembrane 4 L six family member 20 Neighboring gene microRNA 5703 Neighboring gene spore coat protein SP96 Neighboring gene chromosome 2 open reading frame 83 Neighboring gene solute carrier family 19 member 3 pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Rev rev Depletion of endogenous HIV-1 Rev binding protein (hRIP) by RNA interference results in the loss of viral replication in human cell lines and primary macrophages; virus production is restored to wild-type levels after reintroduction of hRIP protein PubMed
rev hRIP/Rab is known to interact with CRM1 (exportin 1) as part of its cofactor involvement with Rev-mediated nuclear export of HIV-1 mRNA PubMed
rev hRIP/Rab is a nucleoporin like protein that binds to the activation domain of HIV-1 Rev (amino acids 75-83) and acts as a cofactor for Rev-mediated nuclear export of HIV-1 mRNA PubMed
rev hRIP is an essential cellular HIV-1 Rev cofactor; abolishing hRIP activity with a dominant-negative mutant or RNA interference causes Rev-directed mRNAs to mislocalize and aberrantly accumulate at the nuclear periphery PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystemRecruitment of plasma membrane-localized cargo into clathrin-coated endocytic vesicles is mediated by interaction with a variety of clathrin-interacting proteins collectively called CLASPs (clathrin-...
  • Clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Clathrin-mediated endocytosis, organism-specific biosystemClathrin-mediated endocytosis (CME) is one of a number of process that control the uptake of material from the plasma membrane, and leads to the formation of clathrin-coated vesicles (Pearse et al, 1...
  • Influenza A, organism-specific biosystem (from KEGG)
    Influenza A, organism-specific biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Influenza A, conserved biosystem (from KEGG)
    Influenza A, conserved biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC116938, MGC116940, DKFZp686I15205

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
GTPase activator activity IEA
Inferred from Electronic Annotation
more info
 
RNA binding TAS
Traceable Author Statement
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acrosome assembly IEA
Inferred from Electronic Annotation
more info
 
intermediate filament organization IEA
Inferred from Electronic Annotation
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
PubMed 
membrane organization TAS
Traceable Author Statement
more info
 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
spermatid nucleus differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell projection IEA
Inferred from Electronic Annotation
more info
 
cytoplasmic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
nuclear pore TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
arf-GAP domain and FG repeat-containing protein 1
Names
HIV-1 Rev-binding protein
Rab, Rev/Rex activation domain-binding protein
arf-GAP domain and FG repeats-containing protein 1
hRIP, Rev interacting protein
nucleoporin-like protein RIP
rev-interacting protein
rev/Rex activation domain-binding protein

NCBI Reference Sequences (RefSeq)

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_001135187.1NP_001128659.1  arf-GAP domain and FG repeat-containing protein 1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC105286, AK097451, BQ016135, DB456989
    Consensus CDS
    CCDS46533.1
    UniProtKB/Swiss-Prot
    P52594
    Related
    ENSP00000387282.2, ENST00000409979.6
    Conserved Domains (2) summary
    smart00105
    Location:14135
    ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF
    COG5347
    Location:8319
    COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
  2. NM_001135188.1NP_001128660.1  arf-GAP domain and FG repeat-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001128660.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 3), compared to isoform 1.
    Source sequence(s)
    AC105286, BC096272, BQ016135, DB456989
    Consensus CDS
    CCDS46534.1
    UniProtKB/Swiss-Prot
    P52594
    Related
    ENSP00000387218.1, ENST00000409171.5
    Conserved Domains (2) summary
    smart00105
    Location:14135
    ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF
    COG5347
    Location:8306
    COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
  3. NM_001135189.1NP_001128661.1  arf-GAP domain and FG repeat-containing protein 1 isoform 4

    See identical proteins and their annotated locations for NP_001128661.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate in-frame exons and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 4), compared to isoform 1.
    Source sequence(s)
    AC105286, BC096274, BQ016135, DB456989
    Consensus CDS
    CCDS46535.1
    UniProtKB/Swiss-Prot
    P52594
    Related
    ENSP00000362775.3, ENST00000373671.7
    Conserved Domains (1) summary
    smart00105
    Location:14135
    ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF
  4. NM_004504.4NP_004495.2  arf-GAP domain and FG repeat-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_004495.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC105286, BC096273, BQ016135, DB456989
    Consensus CDS
    CCDS2467.1
    UniProtKB/Swiss-Prot
    P52594
    UniProtKB/TrEMBL
    A0A0S2Z444
    Related
    ENSP00000312059.7, ENST00000310078.12
    Conserved Domains (2) summary
    smart00105
    Location:14135
    ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF
    COG5347
    Location:8306
    COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    227472169..227561222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006712480.3XP_006712543.1  arf-GAP domain and FG repeat-containing protein 1 isoform X4

    UniProtKB/TrEMBL
    A0A0S2Z3Y3
    Conserved Domains (2) summary
    smart00105
    Location:14135
    ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF
    COG5347
    Location:8306
    COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
  2. XM_006712478.4XP_006712541.1  arf-GAP domain and FG repeat-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A0S2Z462
    Conserved Domains (2) summary
    smart00105
    Location:14135
    ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF
    COG5347
    Location:8319
    COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
  3. XM_006712479.4XP_006712542.1  arf-GAP domain and FG repeat-containing protein 1 isoform X2

    Conserved Domains (3) summary
    smart00105
    Location:14135
    ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF
    COG5347
    Location:8319
    COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
    pfam09214
    Location:399580
    Prd1-P2; Bacteriophage Prd1, adsorption protein P2
  4. XM_005246516.4XP_005246573.1  arf-GAP domain and FG repeat-containing protein 1 isoform X3

    UniProtKB/TrEMBL
    A0A0S2Z3Z1
    Related
    ENSP00000387154.1, ENST00000409315.5
    Conserved Domains (2) summary
    smart00105
    Location:14135
    ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF
    COG5347
    Location:8319
    COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
  5. XM_006712481.3XP_006712544.1  arf-GAP domain and FG repeat-containing protein 1 isoform X5

  6. XM_017003954.1XP_016859443.1  arf-GAP domain and FG repeat-containing protein 1 isoform X6

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