Human Gene ARFGAP3 (uc003bdd.2)
  Description: Homo sapiens ADP-ribosylation factor GTPase activating protein 3 (ARFGAP3), transcript variant 1, mRNA.
RefSeq Summary (NM_014570): 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].
Transcript (Including UTRs)
   Position: hg19 chr22:43,192,532-43,253,408 Size: 60,877 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr22:43,193,594-43,253,188 Size: 59,595 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:43,192,532-43,253,408)mRNA (may differ from genome)Protein (516 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ARFG3_HUMAN
DESCRIPTION: RecName: Full=ADP-ribosylation factor GTPase-activating protein 3; Short=ARF GAP 3;
FUNCTION: GTPase-activating protein (GAP) for ADP ribosylation factor 1 (ARF1). Hydrolysis of ARF1-bound GTP may lead to dissociation of coatomer from Golgi-derived membranes to allow fusion with target membranes.
ENZYME REGULATION: GAP activity stimulated by phosphatidylinositol 4,5-bisphosphate (PIP2).
SUBCELLULAR LOCATION: Cytoplasm. Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side. Note=Also found on peripheral punctate structures likely to be endoplasmic reticulum- Golgi intermediate compartment.
TISSUE SPECIFICITY: Widely expressed. Highest expression in endocrine glands (pancreas, pituitary gland, salivary gland, and prostate) and testis with a much higher expression in the testis than in the ovary.
DEVELOPMENTAL STAGE: Expressed at higher level in adult thymus, brain and lung, than in corresponding fetal tissues. Expressed at lower level in spleen, heart, kidney and liver during development.
SIMILARITY: Contains 1 Arf-GAP domain.
CAUTION: Was originally (PubMed:10704287) termed ARFGAP1.
SEQUENCE CAUTION: Sequence=BAA92076.1; Type=Erroneous initiation; Sequence=BAB14236.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

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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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ARFGAP3
CDC HuGE Published Literature: ARFGAP3

-  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: 57.49 RPKM in Adrenal Gland
Total median expression: 1016.35 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 -129.60220-0.589 Picture PostScript Text
3' UTR -289.091062-0.272 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 - Pyk2-associated protein beta ARF-GAP domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2CRW - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9NP61
FrontTopSide
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 orthologGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
   FlyBaseWormBase 
   Protein SequenceProtein Sequence 
   AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0008565 protein transporter activity
GO:0046872 metal ion binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER
GO:0009306 protein secretion
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0043547 positive regulation of GTPase activity

Cellular Component:
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK022768 - Homo sapiens cDNA FLJ12706 fis, clone NT2RP1000902, weakly similar to HYPOTHETICAL 127.4 KD PROTEIN F07F6.4 IN CHROMOSOME III.
LF385064 - JP 2014500723-A/192567: Polycomb-Associated Non-Coding RNAs.
AL137598 - Homo sapiens mRNA; cDNA DKFZp434D1411 (from clone DKFZp434D1411); partial cds.
BC005122 - Homo sapiens ADP-ribosylation factor GTPase activating protein 3, mRNA (cDNA clone MGC:10272 IMAGE:3938853), complete cds.
AF111847 - Homo sapiens ARFGAP1 protein (ARFGAP1) mRNA, complete cds.
AK127525 - Homo sapiens cDNA FLJ45618 fis, clone BRTHA3027171.
AK002083 - Homo sapiens cDNA FLJ11221 fis, clone PLACE1008132.
JD082849 - Sequence 63873 from Patent EP1572962.
JD088056 - Sequence 69080 from Patent EP1572962.
JD311442 - Sequence 292466 from Patent EP1572962.
JD050243 - Sequence 31267 from Patent EP1572962.
JD039262 - Sequence 20286 from Patent EP1572962.
AL159143 - Novel human gene mapping to chomosome 22.
JD525266 - Sequence 506290 from Patent EP1572962.
AK300531 - Homo sapiens cDNA FLJ54156 complete cds, highly similar to ADP-ribosylation factor GTPase-activating protein 3.
JD254530 - Sequence 235554 from Patent EP1572962.
JD296749 - Sequence 277773 from Patent EP1572962.
JD093660 - Sequence 74684 from Patent EP1572962.
JD184332 - Sequence 165356 from Patent EP1572962.
JD196357 - Sequence 177381 from Patent EP1572962.
AK297635 - Homo sapiens cDNA FLJ55728 complete cds, highly similar to ADP-ribosylation factor GTPase-activating protein 3.
AK307967 - Homo sapiens cDNA, FLJ97915.
JD352617 - Sequence 333641 from Patent EP1572962.
JD284262 - Sequence 265286 from Patent EP1572962.
JD562686 - Sequence 543710 from Patent EP1572962.
JD440253 - Sequence 421277 from Patent EP1572962.
CR456382 - Homo sapiens ARFGAP1 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.ARFGAP1).
CU012940 - Homo sapiens ARFGAP3, mRNA (cDNA clone IMAGE:100000104), complete cds, with stop codon, in Gateway system.
AK315720 - Homo sapiens cDNA, FLJ96822.
DQ893007 - Synthetic construct clone IMAGE:100005637; FLH191622.01X; RZPDo839F0377D ADP-ribosylation factor GTPase activating protein 3 (ARFGAP3) gene, encodes complete protein.
KJ898618 - Synthetic construct Homo sapiens clone ccsbBroadEn_08012 ARFGAP3 gene, encodes complete protein.
DQ896253 - Synthetic construct Homo sapiens clone IMAGE:100010713; FLH191618.01L; RZPDo839F0367D ADP-ribosylation factor GTPase activating protein 3 (ARFGAP3) gene, encodes complete protein.
CU013228 - Homo sapiens ARFGAP3, mRNA (cDNA clone IMAGE:100000008), complete cds, without stop codon, in Gateway system.
LF337481 - JP 2014500723-A/144984: Polycomb-Associated Non-Coding RNAs.
LF337482 - JP 2014500723-A/144985: Polycomb-Associated Non-Coding RNAs.
LF337491 - JP 2014500723-A/144994: Polycomb-Associated Non-Coding RNAs.
CU674999 - Synthetic construct Homo sapiens gateway clone IMAGE:100020330 5' read ARFGAP3 mRNA.
BC041383 - Homo sapiens ADP-ribosylation factor GTPase activating protein 3, mRNA (cDNA clone IMAGE:5275602), with apparent retained intron.
JD117749 - Sequence 98773 from Patent EP1572962.
JD216366 - Sequence 197390 from Patent EP1572962.
MA620641 - JP 2018138019-A/192567: Polycomb-Associated Non-Coding RNAs.
MA573058 - JP 2018138019-A/144984: Polycomb-Associated Non-Coding RNAs.
MA573059 - JP 2018138019-A/144985: Polycomb-Associated Non-Coding RNAs.
MA573068 - JP 2018138019-A/144994: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04144 - Endocytosis

BioCarta from NCI Cancer Genome Anatomy Project
h_arapPathway - ADP-Ribosylation Factor

Reactome (by CSHL, EBI, and GO)

Protein Q9NP61 (Reactome details) participates in the following event(s):

R-HSA-6807875 ARFGAP, cargo, v-SNAREs and p24 proteins bind nascent COPI complex
R-HSA-6811417 ARFGAP, cargo, vSNARES and p24 proteins bind COPI vesicles at Golgi
R-HSA-6807877 ARFGAPs stimulate ARF GTPase activity
R-HSA-6811418 ARFGAPs stimulate ARF GTPase activity at the Golgi membrane
R-HSA-6807878 COPI-mediated anterograde transport
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ARFG3_HUMAN, ARFGAP1, NM_014570, NP_055385, Q9BSC6, Q9H9J0, Q9NP61, Q9NT10, Q9NUP5, Q9Y4V3, Q9Y4V4
UCSC ID: uc003bdd.2
RefSeq Accession: NM_014570
Protein: Q9NP61 (aka ARFG3_HUMAN or ARG3_HUMAN)
CCDS: CCDS14042.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014570.4
exon count: 16CDS single in 3' UTR: no RNA size: 2851
ORF size: 1551CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3302.00frame shift in genome: no % Coverage: 99.37
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.