Aliases &
Descriptions
for VPS16 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase)
About This Section
|
| Aliases & Descriptions |
|---|
| vacuolar protein sorting 16 homolog (S. cerevisiae)1 2 | | hVPS162 3 | | vacuolar protein sorting protein 162 | | vacuolar protein sorting-associated protein 16 homolog2 |
Export aliases for VPS16 gene to outside databasesPrevious GC identifers: GC20U990060 GC20P002817 GC20P002818 GC20P002821 |
Summaries
for VPS16 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for VPS16:
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 encodes the human homolog of yeast class C Vps16 protein. The mammalian classC Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, maymediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding differentisoforms have been found for this gene. (provided by RefSeq)
UniProtKB/Swiss-Prot: VPS16_HUMAN, Q9H269Function: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membranedocking/fusion reactions of late endosomes/lysosomes
|
Genomic Views
for VPS16 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 60),
Regulatory elements and Epigenetics data according to
Qiagen and/or
SABiosciences)
About This Section
|
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the VPS16 gene promoter:
NF-1 SREBP-1c SREBP-1b SREBP-1a POU2F1 AP-4 c-Myc Max c-Rel Tal-1beta
Other transcription factors
Search SABiosciences Chromatin IP Primers for VPS16
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for VPS16  |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 20p13 Ensembl cytogenetic band: 20p13 HGNC cytogenetic band: 20p13VPS16 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc gene densities for chromosome 20 GeneLoc Exon Structure GeneLoc location for GC20P002769: view genomic region
(about GC identifiers)
Start:
|
2,769,563 bp from pter |
End:
|
2,796,285 bp from pter |
Size:
|
26,723 bases |
Orientation:
|
plus strand |
1 alternative location:
| Chr20+ 2,821,349-2,847,378 |
|
Proteins
for VPS16 gene
(According to
1UniProtKB,
neXtProt,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological, and/or
ProSpec,
Biochemical Assays by
Millipore,
Sigma-Aldrich,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Dec 2010 and
Entrez Gene,
Antibodies by
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals, and/or
Epitomics)
About This Section
|
UniProtKB/Swiss-Prot: VPS16_HUMAN, Q9H269 (See
protein sequence)Recommended Name: Vacuolar protein sorting-associated protein 16 homolog Size: 839 amino acids; 94694 Da
Subunit: Large hetero-oligomeric complex together with VPS11, VPS18 and VPS33A. Interacts with STX7
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
Secondary accessions: Q5JUB1 Q8WU31 Q96EE7 Q96N92 Q9H1Q4 Q9H1Q5Alternative splicing: 2 isoforms: Q9H269-1 Q9H269-2 Explore the universe of human proteins at neXtProt for VPS16: NX_Q9H269
Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins (2 alternative transcripts):
NP_072097.2 NP_536338.1
ENSEMBL proteins: ENSP00000399724 ENSP00000369836 ENSP00000417031 ENSP00000369810 ENSP00000409840 ENSP00000369808
Human Recombinant Proteins
5/11 Gene Ontology (GO) cellular component terms (GO ID links to tree view) (see all 11): About this table
VPS16 for ontologies About GeneDecksing
Antibodies for VPS16:
Assays for VPS16: |
Protein
Domains/
Families
for VPS16 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
VPS16 for domains About GeneDecksing
3 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9H269ProtoNet protein and cluster: Q9H269 1 Blocks protein family: IPB006926 Vps16
UniProtKB/Swiss-Prot: VPS16_HUMAN, Q9H269Similarity: Belongs to the VPS16 family |
Gene Function
for VPS16 gene
(According to UniProtKB,
IUBMB,and/or
Genatlas, Animal models from MGI Dec 24 2010,
shRNA from
OriGene,
Sigma-Aldrich,
RNAi from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Clones from Millipore,
Sigma-Aldrich,
OriGene,
GenScript,
Sino Biological,
Cell Lines from GenScript,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene.)
About This Section
|
UniProtKB/Swiss-Prot: VPS16_HUMAN, Q9H269Function: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membranedocking/fusion reactions of late endosomes/lysosomes
2 Gene Ontology (GO) molecular function terms (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005515 | protein binding |
IPI | -- | | GO:0051015 | actin filament binding |
IEA | -- |
About this table
VPS16 for ontologies About GeneDecksing
|
Pathways & Interactions
for VPS16 gene
(Pathways according to
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
PCR Arrays from
SABiosciences,
Proteins Network according to
SABiosciences,
Sigma-Aldrich,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene).
About This Section
|
SABiosciences Custom Pathway-Focused PCR Arrays for VPS16
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VPS16
2 Interacting proteins for VPS16 (Q9H2691) via UniProtKB, MINT, and/or STRINGAbout this table
1 Gene Ontology (GO) biological process term (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0006886 | intracellular protein transport |
IEA | -- |
About this table
VPS16 for ontologies About GeneDecksing
|
Drugs & Compounds
for VPS16 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
|
 Browse Tocris compounds for VPS16
|
Transcripts
for VPS16 gene(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Tagged/untagged cDNA clones from
OriGene,
Sigma-Aldrich,
GenScript,
Primers from
OriGene and/or
SABiosciences)
About This Section
|
REFSEQ mRNAs for VPS16 gene (2 alternative transcripts): NM_022575.2 NM_080413.1 24/232 AceView cDNA sequences (see all 232): BG701461 AW627753 NM_080414 BC073959 CA454999 BU730199 AU131514 AL045069 CN479639 AI282429 AL530956 BU150610 CD631486 BM693073 BX384233 BC021291 NM_022575 AL834401 AI568221 BG470488 BQ070914 BQ954225 CR626842 AI554931
 highest scoring ESTs for VPS16:BF850547 BI049024 AI874233 AA017123 AA455181 AA492377 AA573078 AA580425 AA661625 AA688317
GeneLoc Exon Structure
9 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000458279 ENST00000380469(uc002whf.2 uc002whi.2) ENST00000453689
ENST00000380445(uc002whd.2 uc002whe.2 uc002whh.2) ENST00000417508
ENST00000487461 ENST00000466415 ENST00000481812 ENST00000380443(uc002whg.2)
|
Expression
for VPS16 gene
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 228 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Primers from
OriGene and/or
SABiosciences
)
About This Section
| VPS16 expression in normal and diseased human tissues
1 / 2 / 3 3 probe-sets matching VPS16 gene
Affymetrix
probe-set |
Array |
GeneAnnot data |
GeneNote data |
GeneTide data |
| # genes |
Sensitivity |
Specificity |
Correlation |
Length |
Gb_Accession |
Consensus |
Uniqueness |
Score |
Rank |
| 44684_at2, 3
|
U95-B |
1 |
0.75 |
1.00 |
1.00 |
1.00 |
AI874233 |
0.60 |
0.75 |
0.68 |
1 |
| 203459_s_at2, 3
|
U133-A |
1 |
1.00 |
1.00 |
-- |
-- |
NM_022575 |
0.40 |
0.50 |
0.45 |
1 |
| 203459_s_at2
|
U133Plus2 |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
About this table
VPS16 for expression About GeneDecksing
Data from
Genenote
(Publications) and GNF BioGPS
About these images
About these images
CGAP SAGE TAG: --
UniProtKB/Swiss-Prot: VPS16_HUMAN, Q9H269Tissue specificity: Ubiquitous
SABiosciences Custom PCR Arrays for VPS16
|
Orthologs
for VPS16 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Dec 24 2010,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for VPS16 gene from 5/16 species (see all 16)
About this table Species with no ortholog for VPS16
ENSEMBL Gene Tree for VPS16 (if available) |
Paralogs
for VPS16 gene(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
| -- |
Genomic Variants
for VPS16 gene(SNPs according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Chr 20 pos | Sequence | Recs | AA
Chg | Type | More | Recs | Allele
freq | Pop | Total
sample | More |
|---|
About this tableHapMap Linkage Disequilibrium images for VPS16 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for VPS16
1 CNV: 35915 | | QIAGEN SeqTarget long-range PCR primers for resequencing VPS16 |
|
Disorders & Mutations
for VPS16 gene
(in which this Gene is Involved, According to
OMIM, UniProtKB,
PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
LSDB, HGMD, GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
VPS16 for disorders About GeneDecksing
OMIM: 608550
Export disorders and mutations for VPS16 gene to outside databases
|
Medical News
for VPS16 gene(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications
for VPS16 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6UniProtKB/TrEMBL, and/or
7Novoseek)
About This Section
|
10/12 PubMed articles for VPS16 gene, integrated from 7 sources (see all 12):
(articles sorted by number of sources associating them with VPS16)- Molecular characterization of mammalian homologues of class c Vps proteins that interact with syntaxin-7. (PubMed id 11382755)1, 2, 7 Kim B.Y....Akazawa C. (2001)
- 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)
- The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (2001)
- Molecular cloning and characterization of human VPS18, VPS11, VPS16, and VPS33. (PubMed id 11250079)1, 2 Huizing M.... Kraemer H. (2001)
- SPE-39 family proteins interact with the HOPS complex and function in lysosomal delivery. (PubMed id 19109425)1 Zhu G.D....L'hernault S.W. (2009)
- Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking. (PubMed id 18552835)1 Liang C....Jung J.U. (2008)
- The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
- Integral and associated lysosomal membrane proteins. (PubMed id 17897319)2 Schroeder B.... Hasilik A. (2007)
- Ubiquitylation and degradation of serum-inducible kin ase by hVPS18, a RING-H2 type ubiquitin ligase. (PubMed id 16203730)1 Yogosawa S....Akazawa C. (2005)
|
External Searches for VPS16 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing VPS16 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing VPS16 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing VPS16 gene(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
|
About This Section
| Patent Information for VPS16 gene:
Search GeneIP for patents involving VPS16
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for VPS16 gene(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or
Enzo Life Sciences)
About This Section
|
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 |  |  |  | |
| |  | Search Tocris compounds for VPS16 |
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 | | | ELISAs and CLIAs for VPS16 |
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