Human Gene AGFG1 (ENST00000310078.13_6) from GENCODE V47lift37
  Description: ArfGAP with FG repeats 1, transcript variant 2 (from RefSeq NM_004504.5)
Gencode Transcript: ENST00000310078.13_6
Gencode Gene: ENSG00000173744.18_16
Transcript (Including UTRs)
   Position: hg19 chr2:228,336,872-228,425,933 Size: 89,062 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr2:228,337,138-228,419,211 Size: 82,074 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:228,336,872-228,425,933)mRNA (may differ from genome)Protein (562 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: AGFG1_HUMAN
DESCRIPTION: RecName: Full=Arf-GAP domain and FG repeat-containing protein 1; AltName: Full=HIV-1 Rev-binding protein; AltName: Full=Nucleoporin-like protein RIP; AltName: Full=Rev-interacting protein; AltName: Full=Rev/Rex activation domain-binding protein;
FUNCTION: Required for vesicle docking or fusion during acrosome biogenesis (By similarity). May play a role in RNA trafficking or localization. In case of infection by HIV-1, acts as a cofactor for viral Rev and promotes movement of Rev-responsive element- containing RNAs from the nuclear periphery to the cytoplasm. This step is essential for HIV-1 replication.
SUBUNIT: Interacts with EPS15R and EPS15. Interacts with FCHO1.
INTERACTION: P51809:VAMP7; NbExp=7; IntAct=EBI-996560, EBI-1052205;
SUBCELLULAR LOCATION: Nucleus. Cytoplasmic vesicle.
TISSUE SPECIFICITY: Ubiquitously expressed.
DOMAIN: Contains FG repeats. The FG repeat region is required for acting as a cofactor of HIV-1 Rev.
PTM: O-glycosylated (By similarity).
SIMILARITY: Contains 1 Arf-GAP domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: AGFG1
Diseases sorted by gene-association score: choroideremia (12), hiv-1 (5), griscelli syndrome (4), warburg micro syndrome 4 (2), hypotrichosis 3 (2), progressive bulbar palsy (2), testis seminoma (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.62 RPKM in Testis
Total median expression: 408.39 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -164.60266-0.619 Picture PostScript Text
3' UTR -1607.506722-0.239 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001164 - ArfGAP

Pfam Domains:
PF01412 - Putative GTPase activating protein for Arf

SCOP Domains:
57863 - ArfGap/RecO-like zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2D9L - NMR MuPIT 2OLM - X-ray MuPIT 2VX8 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P52594
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0001675 acrosome assembly
GO:0006406 mRNA export from nucleus
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0007289 spermatid nucleus differentiation
GO:0030154 cell differentiation
GO:0043547 positive regulation of GTPase activity
GO:0045109 intermediate filament organization
GO:0051028 mRNA transport
GO:0061024 membrane organization

Cellular Component:
GO:0005634 nucleus
GO:0005643 nuclear pore
GO:0005829 cytosol
GO:0031410 cytoplasmic vesicle
GO:0042995 cell projection
GO:0043025 neuronal cell body
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  HZ409693 - JP 2015528002-A/2290: CHIRAL CONTROL.
LG053027 - KR 1020150036642-A/2293: CHIRAL CONTROL.
AK097451 - Homo sapiens cDNA FLJ40132 fis, clone TESTI2012155, highly similar to NUCLEOPORIN-LIKE PROTEIN RIP.
JD317388 - Sequence 298412 from Patent EP1572962.
JD538149 - Sequence 519173 from Patent EP1572962.
BC030592 - Homo sapiens ArfGAP with FG repeats 1, mRNA (cDNA clone MGC:26523 IMAGE:4836885), complete cds.
X89478 - H.sapiens mRNA for nucleoporin-like protein.
BC096272 - Homo sapiens ArfGAP with FG repeats 1, mRNA (cDNA clone MGC:116938 IMAGE:40006445), complete cds.
BC096273 - Homo sapiens ArfGAP with FG repeats 1, mRNA (cDNA clone MGC:116939 IMAGE:40006446), complete cds.
BC096274 - Homo sapiens ArfGAP with FG repeats 1, mRNA (cDNA clone MGC:116940 IMAGE:40006448), complete cds.
BC096275 - Homo sapiens ArfGAP with FG repeats 1, mRNA (cDNA clone MGC:116941 IMAGE:40006449), complete cds.
AB527534 - Synthetic construct DNA, clone: pF1KB5974, Homo sapiens AGFG1 gene for ArfGAP with FG repeats-containing protein 1, without stop codon, in Flexi system.
KJ905214 - Synthetic construct Homo sapiens clone ccsbBroadEn_14670 AGFG1 gene, encodes complete protein.
CU688928 - Synthetic construct Homo sapiens gateway clone IMAGE:100020392 5' read HRB mRNA.
KJ905783 - Synthetic construct Homo sapiens clone ccsbBroadEn_15453 AGFG1 gene, encodes complete protein.
KU178123 - Homo sapiens ArfGAP with FG repeats 1 isoform 1 (AGFG1) mRNA, partial cds.
KU178124 - Homo sapiens ArfGAP with FG repeats 1 isoform 2 (AGFG1) mRNA, partial cds, alternatively spliced.
KU178125 - Homo sapiens ArfGAP with FG repeats 1 isoform 3 (AGFG1) mRNA, partial cds, alternatively spliced.
KU178126 - Homo sapiens ArfGAP with FG repeats 1 isoform 4 (AGFG1) mRNA, partial cds, alternatively spliced.
AK295030 - Homo sapiens cDNA FLJ57927 complete cds, highly similar to Nucleoporin-like protein RIP.
JD296502 - Sequence 277526 from Patent EP1572962.
JD239199 - Sequence 220223 from Patent EP1572962.
JD061383 - Sequence 42407 from Patent EP1572962.
JD292672 - Sequence 273696 from Patent EP1572962.
JD447756 - Sequence 428780 from Patent EP1572962.
JD085265 - Sequence 66289 from Patent EP1572962.
JD326933 - Sequence 307957 from Patent EP1572962.
BX648387 - Homo sapiens mRNA; cDNA DKFZp686I15205 (from clone DKFZp686I15205).
BC039332 - Homo sapiens hypothetical protein LOC285086, mRNA (cDNA clone IMAGE:5267907).
BC045581 - Homo sapiens hypothetical protein LOC285086, mRNA (cDNA clone IMAGE:4838790).
JD436179 - Sequence 417203 from Patent EP1572962.
JD393831 - Sequence 374855 from Patent EP1572962.
JD498071 - Sequence 479095 from Patent EP1572962.
JD300577 - Sequence 281601 from Patent EP1572962.
JD098628 - Sequence 79652 from Patent EP1572962.
JD087365 - Sequence 68389 from Patent EP1572962.
JD250474 - Sequence 231498 from Patent EP1572962.
JD083730 - Sequence 64754 from Patent EP1572962.
JD543596 - Sequence 524620 from Patent EP1572962.
JD244899 - Sequence 225923 from Patent EP1572962.
JD403811 - Sequence 384835 from Patent EP1572962.
JD096832 - Sequence 77856 from Patent EP1572962.
JD112768 - Sequence 93792 from Patent EP1572962.
JD276855 - Sequence 257879 from Patent EP1572962.
JD453286 - Sequence 434310 from Patent EP1572962.
MB407784 - WO 2019159884-A/1274: Kit, device, and method for detection of dementia.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P52594 (Reactome details) participates in the following event(s):

R-HSA-8863718 AGFG1 binds VAMP7
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: AGFG1_HUMAN, B3KUL1, E9PHX7, ENST00000310078.1, ENST00000310078.10, ENST00000310078.11, ENST00000310078.12, ENST00000310078.2, ENST00000310078.3, ENST00000310078.4, ENST00000310078.5, ENST00000310078.6, ENST00000310078.7, ENST00000310078.8, ENST00000310078.9, HRB, NM_004504, P52594, Q15277, Q4VAS0, Q4VAS1, Q4VAS3, Q53QT8, Q53R11, RAB, RIP, uc317ori.1, uc317ori.2
UCSC ID: ENST00000310078.13_6
RefSeq Accession: NM_004504.5
Protein: P52594 (aka AGFG1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.