Human Gene ARFRP1 (uc031rup.1)
  Description: Homo sapiens ADP-ribosylation factor related protein 1 (ARFRP1), transcript variant 7, mRNA.
RefSeq Summary (NM_001267548): The protein encoded by this gene is a membrane-associated GTP-ase which localizes to the plasma membrane and is related to the ADP-ribosylation factor (ARF) and ARF-like (ARL) proteins. This gene plays a role in membrane trafficking between the trans-Golgi network and endosomes. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, May 2012].
Transcript (Including UTRs)
   Position: hg19 chr20:62,329,995-62,339,205 Size: 9,211 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr20:62,331,795-62,338,443 Size: 6,649 Coding Exon Count: 7 

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 (chr20:62,329,995-62,339,205)mRNA (may differ from genome)Protein (201 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ARFRP_HUMAN
DESCRIPTION: RecName: Full=ADP-ribosylation factor-related protein 1; Short=ARF-related protein 1; Short=ARP;
FUNCTION: Possibly involved in plasma membrane-related signaling events.
SUBUNIT: Interacts with SYS1.
SUBCELLULAR LOCATION: Golgi apparatus.
TISSUE SPECIFICITY: Found in most tissues.
SIMILARITY: Belongs to the small GTPase superfamily. Arf family.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ARFRP1
CDC HuGE Published Literature: ARFRP1
Positive Disease Associations: Body Height
Related Studies:
  1. Body Height
    , , . [PubMed 0]

-  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: 17.88 RPKM in Spleen
Total median expression: 585.78 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 -18.0050-0.360 Picture PostScript Text
3' UTR -925.001800-0.514 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
IPR001806 - Small_GTPase
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

ModBase Predicted Comparative 3D Structure on Q13795
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:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding

Biological Process:
GO:0007165 signal transduction
GO:0007369 gastrulation
GO:0034067 protein localization to Golgi apparatus
GO:0042147 retrograde transport, endosome to Golgi
GO:0043001 Golgi to plasma membrane protein transport

Cellular Component:
GO:0005622 intracellular
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0016020 membrane
GO:0032588 trans-Golgi network membrane


-  Descriptions from all associated GenBank mRNAs
  AK095962 - Homo sapiens cDNA FLJ38643 fis, clone HHDPC2005513, highly similar to ARF-related protein 1.
X91504 - H.sapiens mRNA for ARP1 protein.
BC021023 - Homo sapiens ADP-ribosylation factor related protein 1, mRNA (cDNA clone IMAGE:2989010).
BC010068 - Homo sapiens cDNA clone IMAGE:4123760, **** WARNING: chimeric clone ****.
AL833084 - Homo sapiens mRNA; cDNA DKFZp451K0719 (from clone DKFZp451K0719).
BC092480 - Homo sapiens ADP-ribosylation factor related protein 1, mRNA (cDNA clone MGC:104649 IMAGE:30531333), complete cds.
GQ900918 - Homo sapiens clone HEL-T-30 epididymis secretory sperm binding protein mRNA, complete cds.
JD109264 - Sequence 90288 from Patent EP1572962.
JD385312 - Sequence 366336 from Patent EP1572962.
JD122372 - Sequence 103396 from Patent EP1572962.
JD457739 - Sequence 438763 from Patent EP1572962.
JD546520 - Sequence 527544 from Patent EP1572962.
JD281494 - Sequence 262518 from Patent EP1572962.
JD399667 - Sequence 380691 from Patent EP1572962.
JD527977 - Sequence 509001 from Patent EP1572962.
JD077725 - Sequence 58749 from Patent EP1572962.
JD468456 - Sequence 449480 from Patent EP1572962.
JD408040 - Sequence 389064 from Patent EP1572962.
JD393135 - Sequence 374159 from Patent EP1572962.
JD321202 - Sequence 302226 from Patent EP1572962.
JD468451 - Sequence 449475 from Patent EP1572962.
JD479694 - Sequence 460718 from Patent EP1572962.
JD149763 - Sequence 130787 from Patent EP1572962.
JD172366 - Sequence 153390 from Patent EP1572962.
JD395235 - Sequence 376259 from Patent EP1572962.
JD388629 - Sequence 369653 from Patent EP1572962.
JD187177 - Sequence 168201 from Patent EP1572962.
BC093967 - Homo sapiens ADP-ribosylation factor related protein 1, mRNA (cDNA clone MGC:121002 IMAGE:7939812), complete cds.
BC143447 - Homo sapiens ADP-ribosylation factor related protein 1, mRNA (cDNA clone MGC:176972 IMAGE:9051955), complete cds.
BC143448 - Homo sapiens ADP-ribosylation factor related protein 1, mRNA (cDNA clone MGC:176973 IMAGE:9051956), complete cds.
BC143467 - Homo sapiens ADP-ribosylation factor related protein 1, mRNA (cDNA clone MGC:176992 IMAGE:9051975), complete cds.
BC143472 - Homo sapiens cDNA clone IMAGE:9051980, containing frame-shift errors.
BC143477 - Homo sapiens cDNA clone IMAGE:9051985.
BT019624 - Homo sapiens ADP-ribosylation factor related protein 1 mRNA, complete cds.
BT019663 - Homo sapiens ADP-ribosylation factor related protein 1 mRNA, complete cds.
KJ898168 - Synthetic construct Homo sapiens clone ccsbBroadEn_07562 ARFRP1 gene, encodes complete protein.
CR456752 - Homo sapiens full open reading frame cDNA clone RZPDo834A094D for gene ARFRP1, ADP-ribosylation factor related protein 1; complete cds, incl. stopcodon.

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

Protein Q13795 (Reactome details) participates in the following event(s):

R-HSA-6814090 NatC acetylates ARFFRP1
R-HSA-6814088 SYS1 binds AcM-ARFRP1
R-HSA-6814086 ARFRP1 recruits ARL1 to the TGN
R-HSA-6814091 ARL1 recruits TGN Golgin homodimers
R-HSA-6811431 RAB6:GTP binds the GARP and COG complexes, t-SNAREs and endosome-derived vesicles
R-HSA-6811440 Retrograde transport at the Trans-Golgi-Network
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ARFRP_HUMAN, ARP1, B7ZKX7, E1P5J9, NM_001267548, NP_001254475, Q13795, Q6IBQ0, uc002yga.3
UCSC ID: uc031rup.1
RefSeq Accession: NM_001267548
Protein: Q13795 (aka ARFRP_HUMAN)
CCDS: CCDS13533.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001267548.1
exon count: 8CDS single in 3' UTR: no RNA size: 2472
ORF size: 606CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1412.00frame 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.