Human Gene ARF4 (ENST00000303436.11_7) from GENCODE V47lift37
  Description: ADP ribosylation factor 4 (from RefSeq NM_001660.4)
Gencode Transcript: ENST00000303436.11_7
Gencode Gene: ENSG00000168374.11_13
Transcript (Including UTRs)
   Position: hg19 chr3:57,557,090-57,583,071 Size: 25,982 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr3:57,557,939-57,582,867 Size: 24,929 Coding Exon Count: 6 

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 (chr3:57,557,090-57,583,071)mRNA (may differ from genome)Protein (180 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ARF4_HUMAN
DESCRIPTION: RecName: Full=ADP-ribosylation factor 4;
FUNCTION: GTP-binding protein that functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP- ribosyltransferase. Involved in protein trafficking; may modulate vesicle budding and uncoating within the Golgi apparatus.
INTERACTION: Q96PM5:RCHY1; NbExp=3; IntAct=EBI-1237085, EBI-947779;
SUBCELLULAR LOCATION: Golgi apparatus.
SIMILARITY: Belongs to the small GTPase superfamily. Arf family.
CAUTION: Was originally thought to be ARF2.

-  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: ARF4
Diseases sorted by gene-association score: cholera (37)

-  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: 127.66 RPKM in Cells - Cultured fibroblasts
Total median expression: 2331.72 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 -56.30204-0.276 Picture PostScript Text
3' UTR -179.80849-0.212 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
IPR005225 - Small_GTP-bd_dom
IPR024156 - Small_GTPase_ARF
IPR006689 - Small_GTPase_ARF/SAR

Pfam Domains:
PF00025 - ADP-ribosylation factor family
PF00071 - Ras family
PF01926 - 50S ribosome-binding GTPase
PF04670 - Gtr1/RagA G protein conserved region
PF08477 - Ras of Complex, Roc, domain of DAPkinase
PF09439 - Signal recognition particle receptor beta subunit

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1Z6X - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P18085
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 orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003924 GTPase activity
GO:0005086 ARF guanyl-nucleotide exchange factor activity
GO:0005154 epidermal growth factor receptor binding
GO:0005515 protein binding
GO:0005525 GTP binding

Biological Process:
GO:0006471 protein ADP-ribosylation
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0006890 retrograde vesicle-mediated transport, Golgi to ER
GO:0007173 epidermal growth factor receptor signaling pathway
GO:0007420 brain development
GO:0007612 learning
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0016477 cell migration
GO:0031584 activation of phospholipase D activity
GO:0043066 negative regulation of apoptotic process
GO:0045176 apical protein localization
GO:0045197 establishment or maintenance of epithelial cell apical/basal polarity
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048678 response to axon injury
GO:0060996 dendritic spine development
GO:0061512 protein localization to cilium
GO:2000377 regulation of reactive oxygen species metabolic process

Cellular Component:
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0032587 ruffle membrane
GO:0043197 dendritic spine
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  M36341 - Human ADP-ribosylation factor 4 (ARF4) mRNA, complete cds.
AH005719 - Homo sapiens clone J2-3 ADP-ribosylation factor 2 mRNA, partial 5'UTR sequence.
BC003364 - Homo sapiens ADP-ribosylation factor 4, mRNA (cDNA clone MGC:5322 IMAGE:2900495), complete cds.
LF384973 - JP 2014500723-A/192476: Polycomb-Associated Non-Coding RNAs.
BC022866 - Homo sapiens ADP-ribosylation factor 4, mRNA (cDNA clone MGC:23747 IMAGE:4105832), complete cds.
BC016325 - Homo sapiens ADP-ribosylation factor 4, mRNA (cDNA clone MGC:23710 IMAGE:4093061), complete cds.
JD305868 - Sequence 286892 from Patent EP1572962.
LF333551 - JP 2014500723-A/141054: Polycomb-Associated Non-Coding RNAs.
JD188534 - Sequence 169558 from Patent EP1572962.
LF333550 - JP 2014500723-A/141053: Polycomb-Associated Non-Coding RNAs.
JD303425 - Sequence 284449 from Patent EP1572962.
JD394204 - Sequence 375228 from Patent EP1572962.
JD359091 - Sequence 340115 from Patent EP1572962.
JD083827 - Sequence 64851 from Patent EP1572962.
LF333549 - JP 2014500723-A/141052: Polycomb-Associated Non-Coding RNAs.
BC008753 - Homo sapiens ADP-ribosylation factor 4, mRNA (cDNA clone MGC:1097 IMAGE:3346199), complete cds.
LF333548 - JP 2014500723-A/141051: Polycomb-Associated Non-Coding RNAs.
LF333547 - JP 2014500723-A/141050: Polycomb-Associated Non-Coding RNAs.
AF493883 - Homo sapiens ADP-ribosylation factor protein 4 (ARF4) mRNA, complete cds.
AK313008 - Homo sapiens cDNA, FLJ93473, Homo sapiens ADP-ribosylation factor 4 (ARF4), mRNA.
EU176202 - Synthetic construct Homo sapiens clone IMAGE:100006597; FLH263976.01X; RZPDo839F02245D ADP-ribosylation factor 4 (ARF4) gene, encodes complete protein.
DQ894082 - Synthetic construct Homo sapiens clone IMAGE:100008542; FLH167536.01L; RZPDo839B1289D ADP-ribosylation factor 4 (ARF4) gene, encodes complete protein.
AB463400 - Synthetic construct DNA, clone: pF1KB8245, Homo sapiens ARF4 gene for ADP-ribosylation factor 4, without stop codon, in Flexi system.
LF333545 - JP 2014500723-A/141048: Polycomb-Associated Non-Coding RNAs.
LF333542 - JP 2014500723-A/141045: Polycomb-Associated Non-Coding RNAs.
JD056201 - Sequence 37225 from Patent EP1572962.
JD430058 - Sequence 411082 from Patent EP1572962.
JD552558 - Sequence 533582 from Patent EP1572962.
JD563671 - Sequence 544695 from Patent EP1572962.
LF333540 - JP 2014500723-A/141043: Polycomb-Associated Non-Coding RNAs.
JD528828 - Sequence 509852 from Patent EP1572962.
JD398085 - Sequence 379109 from Patent EP1572962.
JD329960 - Sequence 310984 from Patent EP1572962.
JD290781 - Sequence 271805 from Patent EP1572962.
JD077274 - Sequence 58298 from Patent EP1572962.
JD528698 - Sequence 509722 from Patent EP1572962.
MA620550 - JP 2018138019-A/192476: Polycomb-Associated Non-Coding RNAs.
MA569128 - JP 2018138019-A/141054: Polycomb-Associated Non-Coding RNAs.
MA569127 - JP 2018138019-A/141053: Polycomb-Associated Non-Coding RNAs.
MA569126 - JP 2018138019-A/141052: Polycomb-Associated Non-Coding RNAs.
MA569125 - JP 2018138019-A/141051: Polycomb-Associated Non-Coding RNAs.
MA569124 - JP 2018138019-A/141050: Polycomb-Associated Non-Coding RNAs.
MA569122 - JP 2018138019-A/141048: Polycomb-Associated Non-Coding RNAs.
MA569119 - JP 2018138019-A/141045: Polycomb-Associated Non-Coding RNAs.
MA569117 - JP 2018138019-A/141043: Polycomb-Associated Non-Coding RNAs.

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

Protein P18085 (Reactome details) participates in the following event(s):

R-HSA-5620914 ARF4:GTP binds VxPx-motifs of membrane proteins
R-HSA-5623508 GBF1 stimulates nucleotide exchange on ARF4
R-HSA-5623513 ASAP1 stimulates GTPase activity of ARF4
R-HSA-5620918 ASAP1 dimer binds membrane proteins
R-HSA-6807866 GBF1 recruits ARF:GDP to the ERGIC
R-HSA-6811411 GBF1 recruits ARF:GDP to the Golgi
R-HSA-6807877 ARFGAPs stimulate ARF GTPase activity
R-HSA-6811418 ARFGAPs stimulate ARF GTPase activity at the Golgi membrane
R-HSA-5620921 ASAP1 recruits RAB11FIP3 and RAB11 to the ciliary targeting complex
R-HSA-6807868 GBF1 stimulates ARF nucleotide exchange
R-HSA-6811414 GBF1 stimulates nucleotide exchange on ARF
R-HSA-6807872 Active ARF recruits coatomer
R-HSA-6811412 Active ARF recruits coatomer to the Golgi
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-5620916 VxPx cargo-targeting to cilium
R-HSA-5620920 Cargo trafficking to the periciliary membrane
R-HSA-6807878 COPI-mediated anterograde transport
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-5617833 Cilium Assembly
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-1852241 Organelle biogenesis and maintenance
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: ARF2, ARF4_HUMAN, B2R7J7, ENST00000303436.1, ENST00000303436.10, ENST00000303436.2, ENST00000303436.3, ENST00000303436.4, ENST00000303436.5, ENST00000303436.6, ENST00000303436.7, ENST00000303436.8, ENST00000303436.9, NM_001660, P18085, P21371, uc317nfx.1, uc317nfx.2
UCSC ID: ENST00000303436.11_7
RefSeq Accession: NM_001660.4
Protein: P18085 (aka ARF4_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.