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

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; AllianceGenome:HGNC:5175
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: mouse all
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Genomic context

Location:: 2q36.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (227472156..227561217)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (227954843..228043867)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (228336872..228425933)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Circular RNA circ-AGFG1 contributes to esophageal squamous cell carcinoma progression and glutamine catabolism by targeting microRNA-497-5p/solute carrier family 1 member 5 axis.
Title: Circular RNA circ-AGFG1 contributes to esophageal squamous cell carcinoma progression and glutamine catabolism by targeting microRNA-497-5p/solute carrier family 1 member 5 axis.
CircAGFG1 aggravates the progression of cervical cancer by downregulating p53.
Title: CircAGFG1 aggravates the progression of cervical cancer by downregulating p53.
Analyses indicated that circAGFG1 acts as a sponge for miR-203 to repress the effect of miR-203 on its target, ZNF281. In conclusion, study suggests that circAGFG1 promotes NSCLC growth and metastasis though a circAGFG1/miR-203/ZNF281 axis.
Title: CircAGFG1 sponges miR-203 to promote EMT and metastasis of non-small-cell lung cancer by upregulating ZNF281 expression.
CircAGFG1 promoted RAF1 expression by sponging miR-370-3p and further activated RAF/MEK/ERK pathway to regulate cervical cancer progression.
Title: CircAGFG1 promotes cervical cancer progression via miR-370-3p/RAF1 signaling.
human miR-186, 210 and 222 directly regulate the human genes Dicer1, HRB and HIV-EP2, thus may be filling key roles during HIV-1 replication and miRNA biogenesis.
Title: HIV-1 infection increases microRNAs that inhibit Dicer1, HRB and HIV-EP2, thereby reducing viral replication.
Necroptotic RIP1 phosphorylation and ubiquitination seem to be tightly coordinated: inhibition or absence of RIP1 kinase activity blocks necroptotic RIP1 ubiquitination, whereas mutation of RIP1 necroptosis-associated ubiquitination site (K115R) dampens RIP1 kinase activity during necroptotic signaling.
Title: Coordinated ubiquitination and phosphorylation of RIP1 regulates necroptotic cell death.
HRB knock-down affected CD4 downregulation induced by Nef but not by HIV-1 Vpu.
Title: The human immunodeficiency virus (HIV) Rev-binding protein (HRB) is a co-factor for HIV-1 Nef-mediated CD4 downregulation.
Selenite caused CYLD upregulation via LEF1 and cIAP downregulation, both of which contribute to the degradation of ubiquitin chains on RIP1 and subsequent caspase-8 activation and colorectal tumor cell apoptosis.
Title: The LEF1/CYLD axis and cIAPs regulate RIP1 deubiquitination and trigger apoptosis in selenite-treated colorectal cancer cells.
The top primary GWAS association of Airway hyperresponsiveness was in rs6731443 (P-value 2.5E-06) located within the AGFG1 genes.
Title: ITGB5 and AGFG1 variants are associated with severity of airway responsiveness.
Association ofalpha-synuclein with Rab attachment receptor protein and soluble sensitive factor attachment receptors (SNAREs) highlights a key role for membrane transport defects in alpha-synuclein-mediated pathology.
Title: Rabs, SNAREs and α-synuclein--membrane trafficking defects in synucleinopathies.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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
ITGB5 and AGFG1 variants are associated with severity of airway responsiveness. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-14347 (e-PCR)
- UniSTS:20480

WI-4486 (e-PCR)
- UniSTS:59500

HRB__6586 (e-PCR)
- UniSTS:463989

WI-15569 (e-PCR)
- UniSTS:64378

SHGC-58449 (e-PCR)
- UniSTS:94340

NoName (e-PCR)
- UniSTS:482720

HRB (e-PCR)
- UniSTS:266403

RH36613 (e-PCR)
- UniSTS:18106

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables GTPase activator activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	TAS Traceable Author Statement 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 acrosome assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in intermediate filament organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA export from nucleus	TAS Traceable Author Statement more info	PubMed
involved_in spermatid nucleus differentiation	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytoplasmic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
part_of nuclear pore	TAS Traceable Author Statement more info	PubMed

General protein information

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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)

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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)

NM_001135187.2 → NP_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)

AC097662, AC105286, AK097451, BQ016135, DB456989

Consensus CDS

CCDS46533.1

UniProtKB/TrEMBL

A0A0S2Z3Z1

Related

ENSP00000387282.2, ENST00000409979.6

Conserved Domains (2) summary

smart00105
Location:14 → 135

ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF

COG5347
Location:8 → 319

COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
NM_001135188.2 → NP_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)

AC097662, AC105286, BC096272, BQ016135, DB456989

Consensus CDS

CCDS46534.1

UniProtKB/TrEMBL

A0A0S2Z3Y3

Related

ENSP00000387218.1, ENST00000409171.5

Conserved Domains (2) summary

smart00105
Location:14 → 135

ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF

COG5347
Location:8 → 306

COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
NM_001135189.2 → NP_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)

AC097662, AC105286, BC096274, BQ016135, DB456989

Consensus CDS

CCDS46535.1

UniProtKB/TrEMBL

A0A0S2Z3Y3

Related

ENSP00000362775.3, ENST00000373671.7

Conserved Domains (1) summary

smart00105
Location:14 → 135

ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF
NM_004504.5 → NP_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)

AC097662, AC105286, BC096273, BQ016135, DB456989

Consensus CDS

CCDS2467.1

UniProtKB/Swiss-Prot

B3KUL1, E9PHX7, P52594, Q15277, Q4VAS0, Q4VAS1, Q4VAS3, Q53QT8, Q53R11

UniProtKB/TrEMBL

A0A0S2Z3Y3, A0A0S2Z444

Related

ENSP00000312059.7, ENST00000310078.13

Conserved Domains (2) summary

smart00105
Location:14 → 135

ArfGap; Putative GTP-ase activating proteins for the small GTPase, ARF

COG5347
Location:8 → 306

COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]