Human Gene VPS26A (ENST00000263559.11_5) from GENCODE V47lift37
  Description: VPS26, retromer complex component A, transcript variant 1 (from RefSeq NM_004896.5)
Gencode Transcript: ENST00000263559.11_5
Gencode Gene: ENSG00000122958.15_8
Transcript (Including UTRs)
   Position: hg19 chr10:70,883,934-70,934,168 Size: 50,235 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr10:70,884,034-70,931,025 Size: 46,992 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:70,883,934-70,934,168)mRNA (may differ from genome)Protein (327 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VP26A_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 26A; AltName: Full=Vesicle protein sorting 26A; Short=hVPS26;
FUNCTION: Essential component of the retromer complex, a complex required to retrieve lysosomal enzyme receptors (IGF2R and M6PR) from endosomes to the trans-Golgi network. Also required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA).
SUBUNIT: Component of the retromer complex composed of VPS26 (VPS26A or VPS26B), VPS29, VPS35, SNX1 and SNX2. Interacts directly with VPS35. Found in a complex with XPO7, EIF4A1, ARHGAP1, VPS26A, VPS29, VPS35 and SFN. Interacts with ECM29.
SUBCELLULAR LOCATION: Cytoplasm. Endosome membrane; Peripheral membrane protein.
INDUCTION: Down-regulated in Alzheimer disease. No polymorphism or variant is however associated with Alzheimer disease for VPS26A.
SIMILARITY: Belongs to the VPS26 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


-  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: 26.27 RPKM in Testis
Total median expression: 795.43 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 -33.10100-0.331 Picture PostScript Text
3' UTR -858.603143-0.273 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
IPR005377 - VPS26

Pfam Domains:
PF03643 - Vacuolar protein sorting-associated protein 26

SCOP Domains:
81296 - E set domains

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2FAU - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O75436
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    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008565 protein transporter activity

Biological Process:
GO:0006886 intracellular protein transport
GO:0007165 signal transduction
GO:0015031 protein transport
GO:0016055 Wnt signaling pathway
GO:0016241 regulation of macroautophagy
GO:0042147 retrograde transport, endosome to Golgi
GO:1990126 retrograde transport, endosome to plasma membrane

Cellular Component:
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005768 endosome
GO:0005769 early endosome
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030904 retromer complex
GO:0030906 retromer, cargo-selective complex
GO:0031982 vesicle
GO:0097422 tubular endosome


-  Descriptions from all associated GenBank mRNAs
  BC022505 - Homo sapiens vacuolar protein sorting 26 homolog A (S. pombe), mRNA (cDNA clone MGC:26471 IMAGE:4799288), complete cds.
BX649092 - Homo sapiens mRNA; cDNA DKFZp779H0669 (from clone DKFZp779H0669).
AK315496 - Homo sapiens cDNA, FLJ96559, Homo sapiens vacuolar protein sorting 26 (yeast) (VPS26), mRNA.
AK297142 - Homo sapiens cDNA FLJ59716 complete cds, highly similar to Vacuolar protein sorting 26A.
AF054179 - Homo sapiens H beta 58 homolog mRNA, complete cds.
AF175266 - Homo sapiens vacuolar sorting protein 26 (VPS26) mRNA, complete cds.
AK309021 - Homo sapiens cDNA, FLJ99062.
AK022992 - Homo sapiens cDNA FLJ12930 fis, clone NT2RP2004816, highly similar to H58 PROTEIN.
BX647725 - Homo sapiens mRNA; cDNA DKFZp686H24262 (from clone DKFZp686H24262).
AK290536 - Homo sapiens cDNA FLJ78510 complete cds.
EU832561 - Synthetic construct Homo sapiens clone HAIB:100067590; DKFZo004D1030 vacuolar protein sorting 26 homolog A (S. pombe) protein (VPS26A) gene, encodes complete protein.
KJ892803 - Synthetic construct Homo sapiens clone ccsbBroadEn_02197 VPS26A gene, encodes complete protein.
EU832481 - Synthetic construct Homo sapiens clone HAIB:100067510; DKFZo008D1029 vacuolar protein sorting 26 homolog A (S. pombe) protein (VPS26A) gene, encodes complete protein.
JD462313 - Sequence 443337 from Patent EP1572962.
JD443545 - Sequence 424569 from Patent EP1572962.
JD500745 - Sequence 481769 from Patent EP1572962.
BC131761 - Homo sapiens cDNA clone IMAGE:40121067.
JD248606 - Sequence 229630 from Patent EP1572962.
JD266886 - Sequence 247910 from Patent EP1572962.
JD287348 - Sequence 268372 from Patent EP1572962.
JD099104 - Sequence 80128 from Patent EP1572962.
JD226263 - Sequence 207287 from Patent EP1572962.
JD163057 - Sequence 144081 from Patent EP1572962.
JD288094 - Sequence 269118 from Patent EP1572962.
AL110166 - Homo sapiens mRNA; cDNA DKFZp586M1424 (from clone DKFZp586M1424).
JD322716 - Sequence 303740 from Patent EP1572962.
JD272744 - Sequence 253768 from Patent EP1572962.
JD188078 - Sequence 169102 from Patent EP1572962.
JD064731 - Sequence 45755 from Patent EP1572962.
JD319263 - Sequence 300287 from Patent EP1572962.
JD556339 - Sequence 537363 from Patent EP1572962.
JD441387 - Sequence 422411 from Patent EP1572962.
JD441388 - Sequence 422412 from Patent EP1572962.
JD564332 - Sequence 545356 from Patent EP1572962.
JD043109 - Sequence 24133 from Patent EP1572962.
JD329107 - Sequence 310131 from Patent EP1572962.

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

Protein O75436 (Reactome details) participates in the following event(s):

R-HSA-3247839 Retromer associates with WLS
R-HSA-3238698 WNT ligand biogenesis and trafficking
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: A8MZ56, B2RDD3, ENST00000263559.1, ENST00000263559.10, ENST00000263559.2, ENST00000263559.3, ENST00000263559.4, ENST00000263559.5, ENST00000263559.6, ENST00000263559.7, ENST00000263559.8, ENST00000263559.9, NM_004896, O75436, Q8TBH4, Q9H982, uc317hkj.1, uc317hkj.2, VP26A_HUMAN, VPS26, VPS26A
UCSC ID: ENST00000263559.11_5
RefSeq Accession: NM_004896.5
Protein: O75436 (aka VP26A_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.