VPS33B Gene
protein-coding GIFtS: 54
GCID: GC15M091541
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|
vacuolar protein sorting 33 homolog B (yeast)(Previous name: vacuolar protein sorting 33B (yeast homolog) )
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Aliases
for VPS33B gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Vacuolar Protein Sorting 33 Homolog B (Yeast)1 2 | | HVPS33B1 | | FLJ148481 | | Vacuolar Protein Sorting 33B (Yeast Homolog)1 | | Vacuolar Protein Sorting 33B2 | | Vacuolar Protein Sorting-Associated Protein 33B2 |
Export aliases for VPS33B gene to outside databasesPrevious GC identifers: GC15P087731 GC15M084982 GC15M089129 GC15M089271 GC15M089342 GC15M067652 |
Summaries
for VPS33B gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for VPS33B:
Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinctorganelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved invesicle transport to vacuoles. This gene is a member of the Sec-1 domain family, and encodes the human ortholog of ratVps33b which is homologous to the yeast class C Vps33 protein. The mammalian class C Vps proteins are predominantlyassociated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps inthe endosome/lysosome pathway. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: VP33B_HUMAN, Q9H267Function: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membranedocking/fusion reactions of late endosomes/lysosomes. Mediates phagolysosomal fusion in macrophages
Gene Wiki entry for VPS33B
|
Genomic Views
for VPS33B gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000015.9 NC_018926.1 NT_010274.17
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the VPS33B gene promoter:
ER-alpha HFH-3 AML1a Olf-1 Lmo2 POU3F2 (N-Oct-5b) Nkx2-5 c-Ets-1 E47 FOXI1
Other transcription factors
Search SABiosciences Chromatin IP Primers for VPS33B
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VPS33B |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 15q26.1 Ensembl cytogenetic band: 15q26.1 HGNC cytogenetic band: 15q26.1VPS33B Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 15 GeneLoc Exon Structure GeneLoc location for GC15M091541: view genomic region
(about GC identifiers)
Start:
|
91,541,646 bp from pter |
End:
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91,565,833 bp from pter |
Size:
|
24,188 bases |
Orientation:
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minus strand |
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Proteins
for VPS33B gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: VP33B_HUMAN, Q9H267 (See
protein sequence)Recommended Name: Vacuolar protein sorting-associated protein 33B Size: 617 amino acids; 70585 Da
Subunit: Interacts with RAB11A and VIPAS39. Interacts with M.tuberculosis PtpA
Subcellular location: Late endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane;Peripheral membrane protein; Cytoplasmic side. Note=Cytoplasmic, peripheral membrane protein associated with lateendosomes/lysosomes. Colocalizes with M.tuberculosis PtpA in the cytosol of tuberculosis-infected macrophages andassociates with phagosomes. Colocalizes in clusters with VIPAS39 at cytoplasmic organelles
Caution: According to PubMed:18474358, it is autophosphorylated. However, it is not related with protein kinases,suggesting it is phosphorylated by another protein
Secondary accessions: Q96K14 Q9NRP6 Q9NSF3Explore the universe of human proteins at neXtProt for VPS33B: NX_Q9H267
Post-translational modifications:
Phosphorylated on tyrosine residues. Dephosphorylation by M.tuberculosis PtpA is necessary to induce the reduction ofhost phagolysosome fusion in M.tuberculosis-infected macrophages1
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9H267
VPS33B Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_061138.3
ENSEMBL proteins: ENSP00000327650 ENSP00000460413 ENSP00000444053 ENSP00000446267
Human Recombinant Protein Products:
Gene Ontology (GO): 5/8 cellular component terms (GO ID links to tree view) (see all 8): About this table
VPS33B for ontologies About GeneDecksing
VPS33B Antibody Products:
Assay Products for VPS33B: |
Protein
Domains /
Families
for VPS33B gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
VPS33B for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9H267ProtoNet protein and cluster: Q9H267 1 Blocks protein family: IPB001619 Sec1-like protein
UniProtKB/Swiss-Prot: VP33B_HUMAN, Q9H267Similarity: Belongs to the STXBP/unc-18/SEC1 family |
Function
for VPS33B gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Function Summary:
UniProtKB/Swiss-Prot: VP33B_HUMAN, Q9H267Function: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membranedocking/fusion reactions of late endosomes/lysosomes. Mediates phagolysosomal fusion in macrophages
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for VPS33B (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VPS33B |
Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005515 | protein binding |
IPI | -- |
VPS33B for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for VPS33B:
|
Pathways & Interactions
for VPS33B gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VPS33B
STRING Interaction
Network Preview (showing 5 interactants - click image to see 10)
5/748 Interacting proteins for VPS33B (Q9H2671, 2, 3 ENSP000003276504) via UniProtKB, MINT, STRING, and/or I2D (see all 748)About this table
Gene Ontology (GO): 5/7 biological process terms (GO ID links to tree view) (see all 7): About this table
VPS33B for ontologies About GeneDecksing
|
Drugs & Compounds
for VPS33B gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for VPS33B
Search CenterWatch for drugs/clinical trials and news about VPS33B / VP33B
|
Transcripts
for VPS33B gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for VPS33B gene: NM_018668.3 Unigene Cluster for VPS33B: Vacuolar protein sorting 33 homolog B (yeast) Hs.459366 [show with all ESTs]Unigene Representative Sequence: NM_0186689 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000333371(uc002bqp.1 uc002bqq.1 uc010uqu.1) ENST00000557470
ENST00000574755 ENST00000535906 ENST00000554660 ENST00000556096 ENST00000554264
ENST00000557358 ENST00000535843
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for VPS33B (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for VPS33B (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
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Additional cDNA sequence: AF201694.1 AF308803.1 AK027754.1 AK074863.1 AK293688.1 AK300608.1 AK308480.1 AK315721.1 AL357472.1 BC016445.1 16 DOTS entries: DT.441610 DT.100694312 DT.100776662 DT.121031376 DT.101967521 DT.75103845 DT.121031325 DT.97842704 DT.100776664 DT.121031276 DT.121031348 DT.92433072 DT.100774402 DT.121031283 DT.91669040 DT.121031395 24/146 AceView cDNA sequences (see all 146): AW139485 NM_018668 AA482390 BM808670 BQ642641 BQ014188 BE223017 CF132227 AI271343 AI690749 BQ066026 AL357472 AK074863 AA626231 BX281265 BM014183 CA429118 AI631066 BM828487 BP357794 BM713195 CR604260 BM988158 AA452072
GeneLoc Exon Structure
5 Alternative Splicing Database (ASD) splice patterns (SP) for VPS33B About this scheme
| ExUns: | 1a | · | 1b | · | 1c | · | 1d | ^ | 2 | ^ | 3a | · | 3b | ^ | 4 | ^ | 5a | · | 5b | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 |
|---|
|
| SP1: | | | | | | | | | | | - | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP3: | | | | | | | | | | | - | | - | | | | | | | | | | | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | - | | - | | - | | | | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for VPS33B
|
Expression
for VPS33B gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| VPS33B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CTGCTAAGAT
About this image
See VPS33B Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for VPS33B
SOURCE GeneReport for Unigene cluster: Hs.459366
UniProtKB/Swiss-Prot: VP33B_HUMAN, Q9H267Tissue specificity: Ubiquitous; highly expressed in testis and low expression in the lung
SABiosciences Custom PCR Arrays for VPS33B
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for VPS33B
Browse OriGene validated miRNA SYBR primer pairs
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Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VPS33B |
Orthologs
for VPS33B gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of animals.
Orthologs for VPS33B gene from 6/21 species (see all 21) About this table
ENSEMBL Gene Tree for VPS33B (if available)
TreeFam Gene Tree for VPS33B (if available) |
Paralogs
for VPS33B gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for VPS33B gene
- VPS33A2 ENSG000002568612
1 SIMAP similar gene for VPS33B using alignment to 4 protein entries: VP33B_HUMAN (see all proteins):VPS33A
VPS33B for paralogs About GeneDecksing
1 Pseudogenes.org Pseudogene for VPS33B
PGOHUM00000260482
|
Genomic Variants
for VPS33B gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 15 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for VPS33B (91541646 - 91565833 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for VPS33B
2 CNVs: 4910 4909
Human Gene Mutation Database (HGMD): VPS33B
| SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing VPS33B |
|
Disorders
/ Diseases
for VPS33B gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
VPS33B for disorders About GeneDecksing
OMIM gene information: 608552
OMIM disorders: 208085
UniProtKB/Swiss-Prot: VP33B_HUMAN, Q9H267
Defects in VPS33B are the cause of arthrogryposis-renal dysfunction-cholestasis syndrome type 1 (ARCS1)[MIM:208085]. ARCS1 is an autosomal recessive multisystem disorder, characterized by neurogenic arthrogryposismultiplex congenita, renal tubular dysfunction and neonatal cholestasis with bile duct hypoplasia and low gammaglutamyl transpeptidase activity. Platelet dysfunction is common
7  diseases for VPS33B: About MalaCardsarthrogryposis renal dysfunction cholestasis syndrome arthrogryposis arc syndrome cholestasis
ichthyosis tuberculosis mycobacterium tuberculosis
2 diseases from the University of Copenhagen DISEASES database for VPS33B:ARC syndrome Cholestasis Human Genome Epidemiology (HuGE) Navigator: VPS33B (2 documents)
Export disorders for VPS33B gene to outside databases
|
Publications
for VPS33B gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for VPS33B gene, integrated from 9 sources (see all 29):
(articles sorted by number of sources associating them with VPS33B) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Mycobacterium tuberculosis virulence is mediated by PtpA dephosphorylation of human vacuolar protein sorting 33B. (PubMed id 18474358)1, 2, 9 Bach H....Av-Gay Y. (2008)
- Mutations in VPS33B, encoding a regulator of SNARE-dependent membrane fusion, cause arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome. (PubMed id 15052268)1, 2 Gissen P.... Maher E.R. (2004)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- Molecular cloning and characterization of human VPS18, VPS11, VPS16, and VPS33. (PubMed id 11250079)1, 2 Huizing M.... Kraemer H. (2001)
- Cloning, mapping and expression analysis of VPS33B, the human orthologue of rat Vps33b. (PubMed id 10894945)1, 2 Carim-Todd L.... Escarceller M. (2000)
- Mammalian homologues of yeast vacuolar protein sorting (vps) genes implicated in Golgi-to-lysosome trafficking. (PubMed id 8996080)1, 3 Pevsner J.... Scheller R.H. (1996)
- Comparative evolutionary analysis of VPS33 homologues: genetic and functional insights. (PubMed id 15790593)1, 9 Gissen P....Maher E.R. (2005)
- A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
- Functional dissection of lysine deacetylases reveals t hat HDAC1 and p300 regulate AMPK. (PubMed id 22318606)1 Lin Y.Y....Boeke J.D. (2012)
|
External Searches for VPS33B gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing VPS33B gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing VPS33B gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing VPS33B gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for VPS33B | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for VPS33B gene:
Search GeneIP for patents involving VPS33B
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for VPS33B gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VPS33B |
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