Human Gene VPS33A (ENST00000267199.9_8) from GENCODE V47lift37
  Description: VPS33A core subunit of CORVET and HOPS complexes, transcript variant 1 (from RefSeq NM_022916.6)
Gencode Transcript: ENST00000267199.9_8
Gencode Gene: ENSG00000139719.12_14
Transcript (Including UTRs)
   Position: hg19 chr12:122,714,111-122,751,041 Size: 36,931 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr12:122,716,793-122,750,955 Size: 34,163 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:122,714,111-122,751,041)mRNA (may differ from genome)Protein (596 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VP33A_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 33A; Short=hVPS33A;
FUNCTION: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane docking/fusion reactions of late endosomes/lysosomes (By similarity).
SUBUNIT: Large heterooligomeric complex together with VPS11, VPS16 and VPS18. Interacts with STX7 (By similarity). Interacts with VIPAS39.
SUBCELLULAR LOCATION: Late endosome membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Lysosome membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Note=Cytoplasmic, peripheral membrane protein associated with late endosomes/lysosomes (By similarity).
SIMILARITY: Belongs to the STXBP/unc-18/SEC1 family.
SEQUENCE CAUTION: Sequence=BAB15570.1; Type=Frameshift; Positions=140;

-  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: VPS33A
Diseases sorted by gene-association score: mucopolysaccharidosis-plus syndrome* (1233), charcot-marie-tooth disease, axonal, type 2l (12), hermansky-pudlak syndrome 5 (8), arthrogryposis, renal dysfunction, and cholestasis 1 (6), dysostosis (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C023514 2,6-dinitrotoluene
  • C518576 2-methylbutyric acid 4-((1,3)dioxan-5-ylmethoxyimino)-8-(2-(4-hydroxy-6-oxo-tetrahydropyran-2-yl)ethyl -7-methyl-6-oxo-1,2,3,4,6,7,8,8a-octahydronaphthyl)heptanoate
  • D000082 Acetaminophen
  • D016604 Aflatoxin B1
  • D000643 Ammonium Chloride
  • D001564 Benzo(a)pyrene
  • D002794 Choline
  • D004997 Ethinyl Estradiol
  • D005492 Folic Acid
          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: 2.65 RPKM in Testis
Total median expression: 45.40 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 -29.9086-0.348 Picture PostScript Text
3' UTR -882.202682-0.329 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
IPR001619 - Sec1-like

Pfam Domains:
PF00995 - Sec1 family

SCOP Domains:
56815 - Sec1/munc18-like (SM) proteins

ModBase Predicted Comparative 3D Structure on Q96AX1
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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

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

Biological Process:
GO:0006904 vesicle docking involved in exocytosis
GO:0006914 autophagy
GO:0008333 endosome to lysosome transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0030220 platelet formation
GO:0032400 melanosome localization
GO:0032418 lysosome localization
GO:0035751 regulation of lysosomal lumen pH
GO:0048070 regulation of developmental pigmentation
GO:0097352 autophagosome maturation

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005776 autophagosome
GO:0016020 membrane
GO:0030136 clathrin-coated vesicle
GO:0030897 HOPS complex
GO:0031410 cytoplasmic vesicle
GO:0031902 late endosome membrane
GO:0048471 perinuclear region of cytoplasm
GO:0030123 AP-3 adaptor complex
GO:0071439 clathrin complex


-  Descriptions from all associated GenBank mRNAs
  AL833244 - Homo sapiens mRNA; cDNA DKFZp761B1220 (from clone DKFZp761B1220).
JD212997 - Sequence 194021 from Patent EP1572962.
JD542893 - Sequence 523917 from Patent EP1572962.
JD560935 - Sequence 541959 from Patent EP1572962.
AK026048 - Homo sapiens cDNA: FLJ22395 fis, clone HRC07889.
BC016617 - Homo sapiens vacuolar protein sorting 33 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:9362 IMAGE:3855313), complete cds.
AF439857 - Homo sapiens vacuolar sorting protein 33A (VPS33A) mRNA, complete cds.
AK026840 - Homo sapiens cDNA: FLJ23187 fis, clone LNG11989.
LP895273 - Sequence 137 from Patent EP3253886.
JD216363 - Sequence 197387 from Patent EP1572962.
JD261257 - Sequence 242281 from Patent EP1572962.
JD189502 - Sequence 170526 from Patent EP1572962.
JD107302 - Sequence 88326 from Patent EP1572962.
JD505546 - Sequence 486570 from Patent EP1572962.
JD375853 - Sequence 356877 from Patent EP1572962.
JD415330 - Sequence 396354 from Patent EP1572962.
JD397347 - Sequence 378371 from Patent EP1572962.
JD476874 - Sequence 457898 from Patent EP1572962.
JD256615 - Sequence 237639 from Patent EP1572962.
JD278167 - Sequence 259191 from Patent EP1572962.
JD415327 - Sequence 396351 from Patent EP1572962.
JD267435 - Sequence 248459 from Patent EP1572962.
JD335035 - Sequence 316059 from Patent EP1572962.
JD242972 - Sequence 223996 from Patent EP1572962.
JD321738 - Sequence 302762 from Patent EP1572962.
JD095250 - Sequence 76274 from Patent EP1572962.
JD182707 - Sequence 163731 from Patent EP1572962.
JD463067 - Sequence 444091 from Patent EP1572962.
JD131580 - Sequence 112604 from Patent EP1572962.
JD413213 - Sequence 394237 from Patent EP1572962.
JD524465 - Sequence 505489 from Patent EP1572962.
JD274908 - Sequence 255932 from Patent EP1572962.
JD152942 - Sequence 133966 from Patent EP1572962.
JD198303 - Sequence 179327 from Patent EP1572962.
JD491967 - Sequence 472991 from Patent EP1572962.
JD281386 - Sequence 262410 from Patent EP1572962.
JD491966 - Sequence 472990 from Patent EP1572962.
JD281385 - Sequence 262409 from Patent EP1572962.
JD160731 - Sequence 141755 from Patent EP1572962.
JD152941 - Sequence 133965 from Patent EP1572962.
JD061434 - Sequence 42458 from Patent EP1572962.
JD174896 - Sequence 155920 from Patent EP1572962.
EU176253 - Synthetic construct Homo sapiens clone IMAGE:100006367; FLH169611.01X; RZPDo839B09250D vacuolar protein sorting 33 homolog A (S. cerevisiae) (VPS33A) gene, encodes complete protein.
AK315545 - Homo sapiens cDNA, FLJ96613, highly similar to Homo sapiens vacuolar protein sorting 33A (yeast) (VPS33A), mRNA.
KJ899496 - Synthetic construct Homo sapiens clone ccsbBroadEn_08890 VPS33A gene, encodes complete protein.
AB527663 - Synthetic construct DNA, clone: pF1KB6151, Homo sapiens VPS33A gene for vacuolar protein sorting 33 homolog A, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000267199.1, ENST00000267199.2, ENST00000267199.3, ENST00000267199.4, ENST00000267199.5, ENST00000267199.6, ENST00000267199.7, ENST00000267199.8, NM_022916, Q547V4, Q96AX1, Q9H5Q0, uc317ijt.1, uc317ijt.2, VP33A_HUMAN
UCSC ID: ENST00000267199.9_8
RefSeq Accession: NM_022916.6
Protein: Q96AX1 (aka VP33A_HUMAN or VP3A_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.