Human Gene GAPVD1 (uc004bps.3)
  Description: Homo sapiens GTPase activating protein and VPS9 domains 1 (GAPVD1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:128,061,169-128,127,290 Size: 66,122 Total Exon Count: 24 Strand: +
Coding Region
   Position: hg19 chr9:128,061,201-128,125,025 Size: 63,825 Coding Exon Count: 24 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:128,061,169-128,127,290)mRNA (may differ from genome)Protein (1433 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  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): GAPVD1
CDC HuGE Published Literature: GAPVD1
Positive Disease Associations: Potassium
Related Studies:
  1. Potassium
    , , . [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: 8.44 RPKM in Testis
Total median expression: 233.93 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 -0.6032-0.019 Picture PostScript Text
3' UTR -594.332265-0.262 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
  Pfam Domains:
PF00616 - GTPase-activator protein for Ras-like GTPase
PF02204 - Vacuolar sorting protein 9 (VPS9) domain

SCOP Domains:
48350 - GTPase activation domain, GAP
109993 - VPS9 domain (Pfam 02204)

ModBase Predicted Comparative 3D Structure on Q14C86-3
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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 orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
    WormBase 
    Protein Sequence 
    Alignment 

-  Descriptions from all associated GenBank mRNAs
  AK294542 - Homo sapiens cDNA FLJ52111 complete cds, highly similar to Homo sapiens GTPase activating protein and VPS9 domains 1 (GAPVD1), mRNA.
AK296381 - Homo sapiens cDNA FLJ61592 partial cds, highly similar to Homo sapiens GTPase activating protein and VPS9 domains 1 (GAPVD1), mRNA.
BC110990 - Homo sapiens cDNA clone IMAGE:5203707, containing frame-shift errors.
AK056493 - Homo sapiens cDNA FLJ31931 fis, clone NT2RP7006188, weakly similar to GTPASE-ACTIVATING PROTEIN.
LF383691 - JP 2014500723-A/191194: Polycomb-Associated Non-Coding RNAs.
AB040954 - Homo sapiens KIAA1521 mRNA for KIAA1521 protein.
BC114937 - Homo sapiens GTPase activating protein and VPS9 domains 1, mRNA (cDNA clone MGC:138847 IMAGE:40083103), complete cds.
BC114962 - Homo sapiens GTPase activating protein and VPS9 domains 1, mRNA (cDNA clone MGC:138848 IMAGE:40083104), complete cds.
MA619268 - JP 2018138019-A/191194: Polycomb-Associated Non-Coding RNAs.
BC010027 - Homo sapiens GTPase activating protein and VPS9 domains 1, mRNA (cDNA clone IMAGE:3355777).
AB384614 - Synthetic construct DNA, clone: pF1KA1521, Homo sapiens GAPVD1 gene for GTPase activating protein and VPS9 domains 1, complete cds, without stop codon, in Flexi system.
DQ233254 - Homo sapiens Rab5-activating protein 6 mRNA, complete cds.
BC021119 - Homo sapiens GTPase activating protein and VPS9 domains 1, mRNA (cDNA clone IMAGE:4866709), complete cds.
JD285252 - Sequence 266276 from Patent EP1572962.
AK000126 - Homo sapiens cDNA FLJ20119 fis, clone COL05853.
LF346955 - JP 2014500723-A/154458: Polycomb-Associated Non-Coding RNAs.
AK027049 - Homo sapiens cDNA: FLJ23396 fis, clone HEP17895.
LF346952 - JP 2014500723-A/154455: Polycomb-Associated Non-Coding RNAs.
LF346950 - JP 2014500723-A/154453: Polycomb-Associated Non-Coding RNAs.
AK023841 - Homo sapiens cDNA FLJ13779 fis, clone PLACE4000445, highly similar to Homo sapiens GTPase activating protein and VPS9 domains 1 (GAPVD1), mRNA.
LF346949 - JP 2014500723-A/154452: Polycomb-Associated Non-Coding RNAs.
LF346948 - JP 2014500723-A/154451: Polycomb-Associated Non-Coding RNAs.
AL080196 - Homo sapiens mRNA; cDNA DKFZp434C212 (from clone DKFZp434C212).
LF346947 - JP 2014500723-A/154450: Polycomb-Associated Non-Coding RNAs.
LF346946 - JP 2014500723-A/154449: Polycomb-Associated Non-Coding RNAs.
BC013635 - Homo sapiens GTPase activating protein and VPS9 domains 1, mRNA (cDNA clone IMAGE:3451647), partial cds.
AK096224 - Homo sapiens cDNA FLJ38905 fis, clone NT2NE2002162, highly similar to Homo sapiens GTPase activating protein and VPS9 domains 1 (GAPVD1), mRNA.
AL834325 - Homo sapiens mRNA; cDNA DKFZp434J231 (from clone DKFZp434J231).
AK021533 - Homo sapiens cDNA FLJ11471 fis, clone HEMBA1001675, highly similar to Mus musculus GTPase activating protein and VPS9 domains 1 (Gapvd1), mRNA.
LF346941 - JP 2014500723-A/154444: Polycomb-Associated Non-Coding RNAs.
LF346940 - JP 2014500723-A/154443: Polycomb-Associated Non-Coding RNAs.
JD456609 - Sequence 437633 from Patent EP1572962.
JD039945 - Sequence 20969 from Patent EP1572962.
JD331156 - Sequence 312180 from Patent EP1572962.
JD432200 - Sequence 413224 from Patent EP1572962.
LF346939 - JP 2014500723-A/154442: Polycomb-Associated Non-Coding RNAs.
LF346938 - JP 2014500723-A/154441: Polycomb-Associated Non-Coding RNAs.
JD203233 - Sequence 184257 from Patent EP1572962.
JD047243 - Sequence 28267 from Patent EP1572962.
JD536926 - Sequence 517950 from Patent EP1572962.
JD305979 - Sequence 287003 from Patent EP1572962.
JD403603 - Sequence 384627 from Patent EP1572962.
JD214432 - Sequence 195456 from Patent EP1572962.
JD483176 - Sequence 464200 from Patent EP1572962.
LF346937 - JP 2014500723-A/154440: Polycomb-Associated Non-Coding RNAs.
JD566818 - Sequence 547842 from Patent EP1572962.
JD066491 - Sequence 47515 from Patent EP1572962.
JD212968 - Sequence 193992 from Patent EP1572962.
JD415668 - Sequence 396692 from Patent EP1572962.
JD268303 - Sequence 249327 from Patent EP1572962.
JD203768 - Sequence 184792 from Patent EP1572962.
JD364060 - Sequence 345084 from Patent EP1572962.
JD242577 - Sequence 223601 from Patent EP1572962.
JD242576 - Sequence 223600 from Patent EP1572962.
JD374853 - Sequence 355877 from Patent EP1572962.
JD296882 - Sequence 277906 from Patent EP1572962.
JD432338 - Sequence 413362 from Patent EP1572962.
JD560673 - Sequence 541697 from Patent EP1572962.
JD397026 - Sequence 378050 from Patent EP1572962.
JD120512 - Sequence 101536 from Patent EP1572962.
JD311607 - Sequence 292631 from Patent EP1572962.
JD504424 - Sequence 485448 from Patent EP1572962.
JD553172 - Sequence 534196 from Patent EP1572962.
JD340624 - Sequence 321648 from Patent EP1572962.
JD347583 - Sequence 328607 from Patent EP1572962.
JD183142 - Sequence 164166 from Patent EP1572962.
JD313409 - Sequence 294433 from Patent EP1572962.
JD332688 - Sequence 313712 from Patent EP1572962.
JD357682 - Sequence 338706 from Patent EP1572962.
LF346936 - JP 2014500723-A/154439: Polycomb-Associated Non-Coding RNAs.
JD090739 - Sequence 71763 from Patent EP1572962.
MA582532 - JP 2018138019-A/154458: Polycomb-Associated Non-Coding RNAs.
MA582529 - JP 2018138019-A/154455: Polycomb-Associated Non-Coding RNAs.
MA582527 - JP 2018138019-A/154453: Polycomb-Associated Non-Coding RNAs.
MA582526 - JP 2018138019-A/154452: Polycomb-Associated Non-Coding RNAs.
MA582525 - JP 2018138019-A/154451: Polycomb-Associated Non-Coding RNAs.
MA582524 - JP 2018138019-A/154450: Polycomb-Associated Non-Coding RNAs.
MA582523 - JP 2018138019-A/154449: Polycomb-Associated Non-Coding RNAs.
MA582518 - JP 2018138019-A/154444: Polycomb-Associated Non-Coding RNAs.
MA582517 - JP 2018138019-A/154443: Polycomb-Associated Non-Coding RNAs.
MA582516 - JP 2018138019-A/154442: Polycomb-Associated Non-Coding RNAs.
MA582515 - JP 2018138019-A/154441: Polycomb-Associated Non-Coding RNAs.
MA582514 - JP 2018138019-A/154440: Polycomb-Associated Non-Coding RNAs.
MA582513 - JP 2018138019-A/154439: Polycomb-Associated Non-Coding RNAs.

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

Protein Q14C86 (Reactome details) participates in the following event(s):

R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8875320 RAB5 GEFs exchange GTP for GDP on RAB5
R-HSA-8877311 RAB31 GEFs exchange GTP for GDP on RAB31
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-199991 Membrane Trafficking
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-5653656 Vesicle-mediated transport
R-HSA-9007101 Rab regulation of trafficking

-  Other Names for This Gene
  Alternate Gene Symbols: BC114962, GAPEX5, KIAA1521, NM_015635, NP_056450, Q14C86-3, RAP6
UCSC ID: uc004bps.3
RefSeq Accession: NM_015635
Protein: Q14C86-3, splice isoform of Q14C86 CCDS: CCDS35138.1, CCDS65130.1, CCDS65131.1, CCDS65132.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC114962.1
exon count: 24CDS single in 3' UTR: no RNA size: 5758
ORF size: 4302CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 8619.00frame shift in genome: no % Coverage: 99.11
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # 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.