Human Gene ARF1 (uc001hrr.3) Description and Page Index
  Description: Homo sapiens ADP-ribosylation factor 1 (ARF1), transcript variant 3, mRNA.
RefSeq Summary (NM_001024226): ADP-ribosylation factor 1 (ARF1) is a member of the human ARF gene family. The family members encode small guanine nucleotide-binding proteins that stimulate the ADP-ribosyltransferase activity of cholera toxin and play a role in vesicular trafficking as activators of phospholipase D. The gene products, including 6 ARF proteins and 11 ARF-like proteins, constitute a family of the RAS superfamily. The ARF proteins are categorized as class I (ARF1, ARF2 and ARF3), class II (ARF4 and ARF5) and class III (ARF6), and members of each class share a common gene organization. The ARF1 protein is localized to the Golgi apparatus and has a central role in intra-Golgi transport. Multiple alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr1:228,270,361-228,286,913 Size: 16,553 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr1:228,284,816-228,285,714 Size: 899 Coding Exon Count: 4 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:228,270,361-228,286,913)mRNA (may differ from genome)Protein (181 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: ARF1_HUMAN
DESCRIPTION: RecName: Full=ADP-ribosylation factor 1;
FUNCTION: GTP-binding protein that functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP- ribosyltransferase. Involved in protein trafficking among different compartments. Modulates vesicle budding and uncoating within the Golgi complex. Deactivation induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, suggesting a crucial role in protein trafficking. In its GTP-bound form, its triggers the association with coat proteins with the Golgi membrane. The hydrolysis of ARF1-bound GTP, which is mediated by ARFGAPs proteins, is required for dissociation of coat proteins from Golgi membranes and vesicles.
SUBUNIT: Interacts with PRKCABP, GGA1 and PIP5K1B (By similarity). Interacts with ARFGAP1, which hydrolyzes GTP and thus, regulates its function. Interacts with ASAP2, HERC1 and ARHGAP21. Interacts with PI4KB in the Golgi complex. Interacts with NCS1/FREQ in the Golgi and at the plasma membrane. This interaction at the plasma membrane requires a myristoylated NCS1/FREQ. Interacts with TMED2 and TMED10. Interacts with PLEKHA3. Interacts with PLEKHA8; the interaction, together with phosphatidylinositol 4-phosphate binding, is required for the FAPP2-mediated glucosylceramide transfer activity.
INTERACTION: Q99418:CYTH2; NbExp=4; IntAct=EBI-447171, EBI-448974;
SUBCELLULAR LOCATION: Golgi apparatus. Cytoplasm, perinuclear region.
SIMILARITY: Belongs to the small GTPase superfamily. Arf family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ARF1
CDC HuGE Published Literature: ARF1

-  MalaCards Disease Associations
  MalaCards Gene Search: ARF1
Diseases sorted by gene-association score: cholera (54), robinow syndrome, autosomal dominant 2 (12), rheumatic myocarditis (11), legionellosis (7), creutzfeldt-jakob disease (6)

-  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: 164.77 RPKM in Pituitary
Total median expression: 5779.70 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 -117.50228-0.515 Picture PostScript Text
3' UTR -413.291199-0.345 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

1HUR
- X-ray MuPIT

1RE0
- X-ray

1U81
- NMR MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
3O47 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P84077
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005057 signal transducer activity, downstream of receptor
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0019904 protein domain specific binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0002090 regulation of receptor internalization
GO:0006661 phosphatidylinositol biosynthetic process
GO:0006878 cellular copper ion homeostasis
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0034315 regulation of Arp2/3 complex-mediated actin nucleation
GO:0035722 interleukin-12-mediated signaling pathway
GO:0050690 regulation of defense response to virus by virus
GO:0060292 long term synaptic depression
GO:0097061 dendritic spine organization
GO:0098586 cellular response to virus

Cellular Component:
GO:0000139 Golgi membrane
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030054 cell junction
GO:0031252 cell leading edge
GO:0032991 macromolecular complex
GO:0043005 neuron projection
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK000620 - Homo sapiens cDNA FLJ20613 fis, clone KAT05486, highly similar to M36340 Human ADP-ribosylation factor 1.
LF385528 - JP 2014500723-A/193031: Polycomb-Associated Non-Coding RNAs.
BC011358 - Homo sapiens ADP-ribosylation factor 1, mRNA (cDNA clone MGC:9347 IMAGE:3463523), complete cds.
AK293553 - Homo sapiens cDNA FLJ61099 complete cds, highly similar to ADP-ribosylation factor 1.
AK297792 - Homo sapiens cDNA FLJ51902 complete cds, highly similar to ADP-ribosylation factor 1.
AK057875 - Homo sapiens cDNA FLJ25146 fis, clone CBR07332, highly similar to ADP-RIBOSYLATION FACTOR 1.
AF052179 - Homo sapiens clone 24537 ADP-ribosylation factor 1 mRNA, complete cds.
M36340 - Human ADP-ribosylation factor 1 (ARF1) mRNA, complete cds.
AK130737 - Homo sapiens cDNA FLJ27227 fis, clone SYN05501, highly similar to ADP-ribosylation factor 1.
AF055002 - Homo sapiens clone 24614 ADP-ribosylation factor 1 mRNA, complete cds.
M84326 - Human ADP-ribosylation factor 1 mRNA, complete cds.
AK057838 - Homo sapiens cDNA FLJ25109 fis, clone CBR01561, highly similar to ADP-RIBOSYLATION FACTOR 1.
BC010429 - Homo sapiens ADP-ribosylation factor 1, mRNA (cDNA clone MGC:15747 IMAGE:3356859), complete cds.
JD159804 - Sequence 140828 from Patent EP1572962.
AK296020 - Homo sapiens cDNA FLJ51215 complete cds, highly similar to ADP-ribosylation factor 1.
BC009247 - Homo sapiens ADP-ribosylation factor 1, mRNA (cDNA clone MGC:3958 IMAGE:2963635), complete cds.
KJ890700 - Synthetic construct Homo sapiens clone ccsbBroadEn_00094 ARF1 gene, encodes complete protein.
AB385094 - Synthetic construct DNA, clone: pF1KB5398, Homo sapiens ARF1 gene for ADP-ribosylation factor 1, complete cds, without stop codon, in Flexi system.
AM393462 - Synthetic construct Homo sapiens clone IMAGE:100002742 for hypothetical protein (ARF1 gene).
AM393595 - Synthetic construct Homo sapiens clone IMAGE:100002743 for hypothetical protein (ARF1 gene).
AM393261 - Synthetic construct Homo sapiens clone IMAGE:100002992 for hypothetical protein (ARF1 gene).
AM393712 - Synthetic construct Homo sapiens clone IMAGE:100002993 for hypothetical protein (ARF1 gene).
BT007393 - Homo sapiens ADP-ribosylation factor 1 mRNA, complete cds.
AF493881 - Homo sapiens ADP-ribosylation factor protein 1 (ARF1) mRNA, complete cds.
LF209085 - JP 2014500723-A/16588: Polycomb-Associated Non-Coding RNAs.
LF325964 - JP 2014500723-A/133467: Polycomb-Associated Non-Coding RNAs.
DQ579447 - Homo sapiens piRNA piR-47559, complete sequence.
LF325962 - JP 2014500723-A/133465: Polycomb-Associated Non-Coding RNAs.
LF325960 - JP 2014500723-A/133463: Polycomb-Associated Non-Coding RNAs.
BC010415 - Homo sapiens ADP-ribosylation factor 1, mRNA (cDNA clone IMAGE:4024984), partial cds.
JD254480 - Sequence 235504 from Patent EP1572962.
JD454310 - Sequence 435334 from Patent EP1572962.
JD545467 - Sequence 526491 from Patent EP1572962.
LF325958 - JP 2014500723-A/133461: Polycomb-Associated Non-Coding RNAs.
JD241847 - Sequence 222871 from Patent EP1572962.
JD099874 - Sequence 80898 from Patent EP1572962.
JD322829 - Sequence 303853 from Patent EP1572962.
LF325957 - JP 2014500723-A/133460: Polycomb-Associated Non-Coding RNAs.
JD114236 - Sequence 95260 from Patent EP1572962.
JD097232 - Sequence 78256 from Patent EP1572962.
JD052622 - Sequence 33646 from Patent EP1572962.
JD389770 - Sequence 370794 from Patent EP1572962.
JD458187 - Sequence 439211 from Patent EP1572962.
JD252153 - Sequence 233177 from Patent EP1572962.
JD484615 - Sequence 465639 from Patent EP1572962.
JD458375 - Sequence 439399 from Patent EP1572962.
JD335910 - Sequence 316934 from Patent EP1572962.
JD399353 - Sequence 380377 from Patent EP1572962.
JD283867 - Sequence 264891 from Patent EP1572962.
LF325956 - JP 2014500723-A/133459: Polycomb-Associated Non-Coding RNAs.
JD093567 - Sequence 74591 from Patent EP1572962.
LF325955 - JP 2014500723-A/133458: Polycomb-Associated Non-Coding RNAs.
JD428754 - Sequence 409778 from Patent EP1572962.
MA621105 - JP 2018138019-A/193031: Polycomb-Associated Non-Coding RNAs.
MA561541 - JP 2018138019-A/133467: Polycomb-Associated Non-Coding RNAs.
MA561539 - JP 2018138019-A/133465: Polycomb-Associated Non-Coding RNAs.
MA561537 - JP 2018138019-A/133463: Polycomb-Associated Non-Coding RNAs.
MA561535 - JP 2018138019-A/133461: Polycomb-Associated Non-Coding RNAs.
MA561534 - JP 2018138019-A/133460: Polycomb-Associated Non-Coding RNAs.
MA561533 - JP 2018138019-A/133459: Polycomb-Associated Non-Coding RNAs.
MA561532 - JP 2018138019-A/133458: Polycomb-Associated Non-Coding RNAs.
MA444662 - JP 2018138019-A/16588: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05110 - Vibrio cholerae infection

BioCarta from NCI Cancer Genome Anatomy Project
h_ptdinsPathway - Phosphoinositides and their downstream targets.
h_arapPathway - ADP-Ribosylation Factor

Reactome (by CSHL, EBI, and GO)

Protein P84077 (Reactome details) participates in the following event(s):

R-HSA-8870499 PLEKHA3,8 bind PI4P, ARF1
R-HSA-200879 Formation of a Nef:ARF1:CD4 complex
R-HSA-421833 Vamp And trans-Golgi Network AP-1 Binding Coupled With Cargo Capture
R-HSA-432712 Vamp And trans-Golgi Network AP-1 Binding Coupled With Cargo Capture On Lysosome Vesicle Destined Golgi Membrane
R-HSA-350769 trans-Golgi Network Coat Activation
R-HSA-8847875 ARF1:GTP binds Golgin TRIP11
R-HSA-8847880 CYTH proteins bind ARF1:GTP
R-HSA-421831 trans-Golgi Network Coat Assembly
R-HSA-432706 trans-Golgi Network Lysosome Vesicle Destined Membrane Coat Assembly
R-HSA-8951498 Dissociation of Arf1:GDP, AP-1 Clathrin coated nonameric complex
R-HSA-8847883 CYTH proteins stimulate ARF1 GTPase activity
R-HSA-1676152 PI4KB binds to ARF1/3:GTP at the Golgi membrane
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-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-1675883 PI is phosphorylated to PI4P by PI4KB at the Golgi membrane
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-1660499 Synthesis of PIPs at the plasma membrane
R-HSA-167590 Nef Mediated CD4 Down-regulation
R-HSA-8950505 Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-432720 Lysosome Vesicle Biogenesis
R-HSA-2132295 MHC class II antigen presentation
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-6811438 Intra-Golgi traffic
R-HSA-1483255 PI Metabolism
R-HSA-164938 Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters
R-HSA-9020591 Interleukin-12 signaling
R-HSA-1280218 Adaptive Immune System
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-1660514 Synthesis of PIPs at the Golgi membrane
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-1483257 Phospholipid metabolism
R-HSA-6807878 COPI-mediated anterograde transport
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-164952 The role of Nef in HIV-1 replication and disease pathogenesis
R-HSA-447115 Interleukin-12 family signaling
R-HSA-168256 Immune System
R-HSA-199991 Membrane Trafficking
R-HSA-556833 Metabolism of lipids
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-162909 Host Interactions of HIV factors
R-HSA-449147 Signaling by Interleukins
R-HSA-5653656 Vesicle-mediated transport
R-HSA-1430728 Metabolism
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-162906 HIV Infection
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-5663205 Infectious disease
R-HSA-597592 Post-translational protein modification
R-HSA-1643685 Disease
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ARF1_HUMAN, NM_001024226, NP_001649, P10947, P32889, P84077
UCSC ID: uc001hrr.3
RefSeq Accession: NM_001024226
Protein: P84077 (aka ARF1_HUMAN)
CCDS: CCDS1565.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001024226.1
exon count: 5CDS single in 3' UTR: no RNA size: 1986
ORF size: 546CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1292.00frame shift in genome: no % Coverage: 99.35
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.