Mouse Gene Vps33a (ENSMUST00000031388.12) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus VPS33A CORVET/HOPS core subunit (Vps33a), transcript variant 1, mRNA. (from RefSeq NM_029929)
Gencode Transcript: ENSMUST00000031388.12
Gencode Gene: ENSMUSG00000029434.12
Transcript (Including UTRs)
   Position: mm10 chr5:123,528,659-123,573,038 Size: 44,380 Total Exon Count: 13 Strand: -
Coding Region
   Position: mm10 chr5:123,531,040-123,572,981 Size: 41,942 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:123,528,659-123,573,038)mRNA (may differ from genome)Protein (598 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: VP33A_MOUSE
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 33A;
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. Interacts with VIPAS39 (By similarity).
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).
DISEASE: Note=Defects in Vps33a are the cause of the buff mutant which exhibits hypopigmentation in the coat and eyes, due to reduced size and number of melanosomes in their cells. In addition, mice are prone to prolonged bleeding, due to a platelet- storage pool defect.
SIMILARITY: Belongs to the STXBP/unc-18/SEC1 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
  • 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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.4057-0.358 Picture PostScript Text
3' UTR -780.302381-0.328 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
IPR023144 - Phe_NH3-lyase_shielding_dom
IPR001619 - Sec1-like

Pfam Domains:
PF00995 - Sec1 family

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

ModBase Predicted Comparative 3D Structure on Q9D2N9
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details    Gene Details
Gene Sorter    Gene Sorter
GenBankRGDEnsemblEnsemblWormBaseSGD
Protein SequenceProtein Sequence Protein SequenceProtein Sequence 
AlignmentAlignment AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0044877 macromolecular complex 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:0043473 pigmentation
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:0033263 CORVET complex
GO:0048471 perinuclear region of cytoplasm
GO:0030123 AP-3 adaptor complex
GO:0071439 clathrin complex


-  Descriptions from all associated GenBank mRNAs
  BC046417 - Mus musculus vacuolar protein sorting 33A (yeast), mRNA (cDNA clone MGC:25670 IMAGE:4501207), complete cds.
AK080345 - Mus musculus 3 days neonate thymus cDNA, RIKEN full-length enriched library, clone:A630060A19 product:vacuolar protein sorting 33A (yeast), full insert sequence.
AK140553 - Mus musculus 10 days neonate cerebellum cDNA, RIKEN full-length enriched library, clone:B930026I24 product:vacuolar protein sorting 33A (yeast), full insert sequence.
AK041982 - Mus musculus 3 days neonate thymus cDNA, RIKEN full-length enriched library, clone:A630050G06 product:VACUOLAR PROTEIN SORTING HOMOLOG R-VPS33A homolog [Rattus norvegicus], full insert sequence.
AK178363 - Mus musculus cDNA, clone:Y0G0106G18, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031388, based on BLAT search.
AK188278 - Mus musculus cDNA, clone:Y0G0144K09, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031388, based on BLAT search.
AK198758 - Mus musculus cDNA, clone:Y1G0129B13, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031388, based on BLAT search.
AK150282 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830001H06 product:vacuolar protein sorting 33A (yeast), full insert sequence.
AK150550 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830011N02 product:vacuolar protein sorting 33A (yeast), full insert sequence.
AF439858 - Mus musculus vacuolar sorting protein 33a (Vps33a) mRNA, complete cds.
AK019463 - Mus musculus 18 days pregnant adult female placenta and extra embryonic tissue cDNA, RIKEN full-length enriched library, clone:3830421M04 product:VACUOLAR PROTEIN SORTING HOMOLOG R-VPS33A homolog [Rattus norvegicus], full insert sequence.
AK206082 - Mus musculus cDNA, clone:Y2G0103L05, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031388, based on BLAT search.
AK207581 - Mus musculus cDNA, clone:Y2G0108H10, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031388, based on BLAT search.
AK203866 - Mus musculus cDNA, clone:Y1G0146H12, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031388, based on BLAT search.
AK187752 - Mus musculus cDNA, clone:Y0G0142O22, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031388, based on BLAT search.
AK179865 - Mus musculus cDNA, clone:Y0G0111P07, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031388, based on BLAT search.
AK194964 - Mus musculus cDNA, clone:Y1G0116P10, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031388, based on BLAT search.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
m_compPathway - Complement Pathway
m_alternativePathway - Alternative Complement Pathway

-  Other Names for This Gene
  Alternate Gene Symbols: Bf, Buff, NM_029929, Q8BGT3, Q9D2N9, uc008znz.1, uc008znz.2, uc008znz.3, uc008znz.4, VP33A_MOUSE
UCSC ID: uc008znz.4
RefSeq Accession: NM_029929
Protein: Q9D2N9 (aka VP33A_MOUSE or VP3A_MOUSE)
CCDS: CCDS19666.1

-  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.