Human Gene VPS33B (ENST00000535906.1) from GENCODE V44
  Description: Homo sapiens VPS33B late endosome and lysosome associated (VPS33B), transcript variant 3, mRNA. (from RefSeq NM_001289149)
RefSeq Summary (NM_001289148): Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene is a member of the Sec-1 domain family, and encodes the human ortholog of rat Vps33b which is homologous to the yeast class C Vps33 protein. The mammalian class C vacuolar protein sorting proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Mutations in this gene are associated with arthrogryposis-renal dysfunction-cholestasis syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014].
Gencode Transcript: ENST00000535906.1
Gencode Gene: ENSG00000184056.15
Transcript (Including UTRs)
   Position: hg38 chr15:90,998,675-91,022,596 Size: 23,922 Total Exon Count: 22 Strand: -
Coding Region
   Position: hg38 chr15:90,998,975-91,022,249 Size: 23,275 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:90,998,675-91,022,596)mRNA (may differ from genome)Protein (590 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F5H008_HUMAN
DESCRIPTION: SubName: Full=Vacuolar protein sorting-associated protein 33B;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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: VPS33B
Diseases sorted by gene-association score: arthrogryposis, renal dysfunction, and cholestasis 1* (1320), vps33b-related arthrogryposis, renal dysfunction, and cholestasis syndrome* (100), cholestasis (25), neurogenic arthrogryposis multiplex congenita (14), bile duct disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.48 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 375.73 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 -151.50347-0.437 Picture PostScript Text
3' UTR -84.50300-0.282 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

ModBase Predicted Comparative 3D Structure on F5H008
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0006904 vesicle docking involved in exocytosis
GO:0016192 vesicle-mediated transport


-  Descriptions from all associated GenBank mRNAs
  AL357472 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 41400.
BC016445 - Homo sapiens vacuolar protein sorting 33 homolog B (yeast), mRNA (cDNA clone MGC:17462 IMAGE:3449387), complete cds.
AF201694 - Homo sapiens vacuolar protein sorting 33B (VPS33B) mRNA, complete cds.
AF308803 - Homo sapiens vacuolar protein sorting protein 33B (VPS33B) mRNA, complete cds.
AK074863 - Homo sapiens cDNA FLJ90382 fis, clone NT2RP2005069, highly similar to Vacuolar protein sorting 33B.
AK293688 - Homo sapiens cDNA FLJ55636 complete cds, highly similar to Vacuolar protein sorting 33B.
AK027754 - Homo sapiens cDNA FLJ14848 fis, clone PLACE1000492, highly similar to Rat vacuolar protein sorting homolog r-vps33b mRNA.
AK300608 - Homo sapiens cDNA FLJ56248 complete cds, highly similar to Vacuolar protein sorting 33B.
AK315721 - Homo sapiens cDNA, FLJ96823.
KJ898617 - Synthetic construct Homo sapiens clone ccsbBroadEn_08011 VPS33B gene, encodes complete protein.
KU178590 - Homo sapiens vacuolar protein sorting 33-like protein B isoform 1 (VPS33B) mRNA, partial cds.
KU178591 - Homo sapiens vacuolar protein sorting 33-like protein B isoform 2 (VPS33B) mRNA, complete cds, alternatively spliced.
KU178592 - Homo sapiens vacuolar protein sorting 33-like protein B isoform 3 (VPS33B) mRNA, complete cds, alternatively spliced.
DQ594794 - Homo sapiens piRNA piR-60906, complete sequence.
CU677627 - Synthetic construct Homo sapiens gateway clone IMAGE:100019948 5' read VPS33B mRNA.
AK308480 - Homo sapiens cDNA, FLJ98521.
JD122646 - Sequence 103670 from Patent EP1572962.
JD113504 - Sequence 94528 from Patent EP1572962.
JD271689 - Sequence 252713 from Patent EP1572962.
JD100940 - Sequence 81964 from Patent EP1572962.
JD222959 - Sequence 203983 from Patent EP1572962.
JD057838 - Sequence 38862 from Patent EP1572962.
JD220688 - Sequence 201712 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: F5H008, F5H008_HUMAN, NM_001289149, uc010uqu.1, uc010uqu.2, uc010uqu.3
UCSC ID: ENST00000535906.1
RefSeq Accession: NM_001289148
Protein: F5H008 CCDS: CCDS10369.1, CCDS73783.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.