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Aliases for VPS9D1 Gene

Aliases for VPS9D1 Gene

  • VPS9 Domain Containing 1 2 3 5
  • C16orf7 3 4
  • Chromosome 16 Open Reading Frame 7 2
  • VPS9 Domain-Containing Protein 1 3
  • Protein ATP-BL 4
  • ATP-BL 3
  • ATPBL 4

External Ids for VPS9D1 Gene

Previous HGNC Symbols for VPS9D1 Gene

  • C16orf7

Previous GeneCards Identifiers for VPS9D1 Gene

  • GC16M089774

Summaries for VPS9D1 Gene

GeneCards Summary for VPS9D1 Gene

VPS9D1 (VPS9 Domain Containing 1) is a Protein Coding gene. GO annotations related to this gene include GTPase activator activity and transporter activity.

Gene Wiki entry for VPS9D1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS9D1 Gene

Genomics for VPS9D1 Gene

Regulatory Elements for VPS9D1 Gene

Enhancers for VPS9D1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16G089717 1.4 ENCODE dbSUPER 19.9 +0.2 219 7.5 HNRNPUL1 PKNOX1 MLX CREB3L1 ARNT AGO1 ZFP64 ARID4B SIN3A DMAP1 CDK10 VPS9D1 DBNDD1 VPS9D1-AS1 TUBB3 FANCA MC1R AFG3L1P LOC101927863 GALNS
GH16G089832 1.9 FANTOM5 Ensembl ENCODE dbSUPER 11.8 -114.5 -114527 6.6 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 BRCA1 ZNF48 YY1 ZNF121 CDK10 SPIRE2 TUBB3 VPS9D1 ZNF276 FANCA RPL13 ACSF3 MC1R LOC105371419
GH16G089842 1.5 Ensembl ENCODE dbSUPER 11.8 -121.8 -121831 1.5 SIN3A ARID4B ZNF2 ZNF48 ZNF121 GLIS2 GATA2 FOS ZNF263 NFYC SPATA2L SPIRE2 CDK10 FANCA ZNF276 VPS9D1 LOC105371419
GH16G089760 1.3 Ensembl ENCODE 12.9 -40.3 -40315 2.3 FOXA2 ARNT AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 FANCA CDK10 SPIRE2 VPS9D1 ZNF276 SPATA2L DBNDD1 PIR55781
GH16G089763 1.2 Ensembl ENCODE 12.9 -43.4 -43400 2.9 HDGF PKNOX1 FOXA2 MLX WRNIP1 ARID4B SLC30A9 ZNF143 ZNF207 SP5 FANCA CDK10 SPIRE2 VPS9D1 ZNF276 SPATA2L GAS8 PIR55781
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VPS9D1 on UCSC Golden Path with GeneCards custom track

Promoters for VPS9D1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000089773 -328 2401 HNRNPUL1 PKNOX1 MLX ARNT CREB3L1 AGO1 ZFP64 ARID4B SIN3A DMAP1

Genomic Location for VPS9D1 Gene

Chromosome:
16
Start:
89,707,133 bp from pter
End:
89,721,272 bp from pter
Size:
14,140 bases
Orientation:
Minus strand

Genomic View for VPS9D1 Gene

Genes around VPS9D1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS9D1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS9D1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS9D1 Gene

Proteins for VPS9D1 Gene

  • Protein details for VPS9D1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2B5-VP9D1_HUMAN
    Recommended name:
    VPS9 domain-containing protein 1
    Protein Accession:
    Q9Y2B5

    Protein attributes for VPS9D1 Gene

    Size:
    631 amino acids
    Molecular mass:
    68956 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA76711.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS9D1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS9D1 Gene

Post-translational modifications for VPS9D1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for VPS9D1 Gene

Domains & Families for VPS9D1 Gene

Gene Families for VPS9D1 Gene

Protein Domains for VPS9D1 Gene

Suggested Antigen Peptide Sequences for VPS9D1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with VPS9D1: view

No data available for UniProtKB/Swiss-Prot for VPS9D1 Gene

Function for VPS9D1 Gene

Gene Ontology (GO) - Molecular Function for VPS9D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA --
GO:0005215 transporter activity TAS 10231027
genes like me logo Genes that share ontologies with VPS9D1: view
genes like me logo Genes that share phenotypes with VPS9D1: view

Animal Model Products

CRISPR Products

miRNA for VPS9D1 Gene

miRTarBase miRNAs that target VPS9D1

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS9D1 Gene

Localization for VPS9D1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VPS9D1 gene
Compartment Confidence
nucleus 3
cytosol 3
mitochondrion 1
endosome 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for VPS9D1 Gene

Pathways & Interactions for VPS9D1 Gene

SuperPathways for VPS9D1 Gene

No Data Available

Interacting Proteins for VPS9D1 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000374037%0d%0a9606.ENSP00000269305%0d%0a9606.ENSP00000417281%0d%0a
Selected Interacting proteins: Q9Y2B5-VP9D1_HUMAN ENSP00000374037 for VPS9D1 Gene via IID STRING

Gene Ontology (GO) - Biological Process for VPS9D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015986 ATP synthesis coupled proton transport TAS 10231027
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with VPS9D1: view

No data available for Pathways by source and SIGNOR curated interactions for VPS9D1 Gene

Drugs & Compounds for VPS9D1 Gene

No Compound Related Data Available

Transcripts for VPS9D1 Gene

Unigene Clusters for VPS9D1 Gene

VPS9 domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS9D1 Gene

No ASD Table

Relevant External Links for VPS9D1 Gene

GeneLoc Exon Structure for
VPS9D1
ECgene alternative splicing isoforms for
VPS9D1

Expression for VPS9D1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS9D1 Gene

mRNA differential expression in normal tissues according to GTEx for VPS9D1 Gene

This gene is overexpressed in Whole Blood (x7.3).

Protein differential expression in normal tissues from HIPED for VPS9D1 Gene

This gene is overexpressed in Fetal Brain (31.4), Frontal cortex (26.7), and Retina (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for VPS9D1 Gene



Protein tissue co-expression partners for VPS9D1 Gene

NURSA nuclear receptor signaling pathways regulating expression of VPS9D1 Gene:

VPS9D1

SOURCE GeneReport for Unigene cluster for VPS9D1 Gene:

Hs.164410

mRNA Expression by UniProt/SwissProt for VPS9D1 Gene:

Q9Y2B5-VP9D1_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for VPS9D1 Gene

  • Blood(4.1)
genes like me logo Genes that share expression patterns with VPS9D1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS9D1 Gene

Orthologs for VPS9D1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for VPS9D1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS9D1 34 35
  • 92.25 (n)
cow
(Bos Taurus)
Mammalia VPS9D1 34 35
  • 83.64 (n)
dog
(Canis familiaris)
Mammalia VPS9D1 34 35
  • 82.78 (n)
mouse
(Mus musculus)
Mammalia Vps9d1 34 16 35
  • 81.34 (n)
rat
(Rattus norvegicus)
Mammalia Vps9d1 34
  • 80.96 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS9D1 35
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS9D1 35
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves C11H16ORF7 34
  • 68.5 (n)
VPS9D1 35
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS9D1 35
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps9d1 34
  • 58.08 (n)
Str.15453 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.29400 34
zebrafish
(Danio rerio)
Actinopterygii vps9d1 34 35
  • 60 (n)
idibd5127 34
Species where no ortholog for VPS9D1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for VPS9D1 Gene

ENSEMBL:
Gene Tree for VPS9D1 (if available)
TreeFam:
Gene Tree for VPS9D1 (if available)

Paralogs for VPS9D1 Gene

No data available for Paralogs for VPS9D1 Gene

Variants for VPS9D1 Gene

Sequence variations from dbSNP and Humsavar for VPS9D1 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs1000156031 -- 89,722,405(+) CGAGC(C/T)GCTTG intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs1000230947 -- 89,722,210(+) AAACC(A/G)CGGCG intron-variant, upstream-variant-2KB
rs1000364012 -- 89,718,607(+) AGAAG(G/T)ATACA intron-variant, downstream-variant-500B, upstream-variant-2KB, utr-variant-5-prime
rs1000392219 -- 89,709,819(+) AAAAG(A/G)GTTCC nc-transcript-variant, reference, missense
rs1000797349 -- 89,718,309(+) TGAGG(C/T)TCCAC intron-variant, downstream-variant-500B, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for VPS9D1 Gene

Variant ID Type Subtype PubMed ID
esv2762221 CNV gain+loss 21179565
nsv1057351 CNV loss 25217958
nsv1931 CNV insertion 18451855
nsv428331 CNV gain+loss 18775914
nsv457623 CNV gain 19166990
nsv482951 CNV loss 15286789
nsv509639 CNV insertion 20534489
nsv516241 CNV loss 19592680
nsv573743 CNV gain 21841781
nsv833330 CNV loss 17160897
nsv952079 CNV deletion 24416366

Variation tolerance for VPS9D1 Gene

Residual Variation Intolerance Score: 58.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.07; 50.73% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS9D1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS9D1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS9D1 Gene

Disorders for VPS9D1 Gene

Relevant External Links for VPS9D1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS9D1

No disorders were found for VPS9D1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS9D1 Gene

Publications for VPS9D1 Gene

  1. Isolation and mapping of putative b subunit of human ATPase (ATP-BL) from human leukocytes. (PMID: 10231027) Sugimoto J. … Isobe M. (DNA Res. 1999) 2 3 4 64
  2. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3 64
  3. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L. … Andersson-Svahn H. (Mol. Cell Proteomics 2008) 3 64
  4. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. (PMID: 16368877) Choy K.W. … Pang C.P. (Physiol. Genomics 2006) 3 64
  5. The sequence and analysis of duplication-rich human chromosome 16. (PMID: 15616553) Martin J. … Pennacchio L.A. (Nature 2004) 4 64

Products for VPS9D1 Gene

Sources for VPS9D1 Gene

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