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VPS9D1 Gene

protein-coding   GIFtS: 38
GCID: GC16M089774

VPS9 Domain Containing 1

(Previous name: chromosome 16 open reading frame 7)
(Previous symbol: C16orf7)
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
VPS9 Domain Containing 11 2     VPS9 Domain-Containing Protein 12
C16orf71 2 3     ATPBL3
Chromosome 16 Open Reading Frame 71     Protein ATP-BL3
ATP-BL2     

External Ids:    HGNC: 135261   Entrez Gene: 96052   Ensembl: ENSG000000753997   UniProtKB: Q9Y2B53   

Export aliases for VPS9D1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for VPS9D1 Gene:
VPS9D1 (VPS9 domain containing 1) is a protein-coding gene. Diseases associated with VPS9D1 include fanconi's anemia. GO annotations related to this gene include transporter activity and GTPase activator activity.

Gene Wiki entry for VPS9D1 (C16orf7) 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000016.10  NT_010498.16  NC_018927.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for VPS9D1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for VPS9D1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VPS9D1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16q24   Ensembl cytogenetic band:  16q24.3   HGNC cytogenetic band: 16q24.3

VPS9D1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VPS9D1 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M089774:  view genomic region     (about GC identifiers)

Start:
89,773,541 bp from pter      End:
89,787,394 bp from pter
Size:
13,854 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: VP9D1_HUMAN, Q9Y2B5 (See protein sequence)
Recommended Name: VPS9 domain-containing protein 1  
Size: 631 amino acids; 68956 Da
Sequence caution: Sequence=BAA76711.1; Type=Frameshift; Positions=Several;
Alternative splicing: 2 isoforms:  Q9Y2B5-1   Q9Y2B5-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VPS9D1: NX_Q9Y2B5

Explore proteomics data for VPS9D1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See VPS9D1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_004904.2  
    ENSEMBL proteins: 
     ENSP00000454244   ENSP00000374037   ENSP00000455792   ENSP00000454889  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR003123 VPS9

    Graphical View of Domain Structure for InterPro Entry Q9Y2B5

    ProtoNet protein and cluster: Q9Y2B5

    1 Blocks protein domain: IPB002197 FIS bacterial regulatory protein HTH signature

    UniProtKB/Swiss-Prot: VP9D1_HUMAN, Q9Y2B5
    Similarity: Contains 1 VPS9 domain


    VPS9D1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005096GTPase activator activity IEA--
    GO:0005215transporter activity TAS10231027
         
    VPS9D1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for VPS9D1:
     Increased gamma-H2AX phosphory 

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005737cytoplasm ----

    VPS9D1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for VPS9D1
    Interactions:

        Search GeneGlobe Interaction Network for VPS9D1

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    4 Interacting proteins for VPS9D1 (Q9Y2B52, 3 ENSP000003740374) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    GRB2P629933I2D: score=2 
    YWHAEP622583I2D: score=1 
    --Q9WMX22MINT-7049712
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015986ATP synthesis coupled proton transport TAS10231027

    VPS9D1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for VPS9D1 (VP9D1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for VPS9D1 gene: 
    NM_004913.2  

    Unigene Cluster for VPS9D1:

    VPS9 domain containing 1
    Hs.164410  [show with all ESTs]
    Unigene Representative Sequence: AB018551
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000561976(uc002fol.1) ENST00000389386(uc002fom.1) ENST00000565023
    ENST00000568691 ENST00000565452 ENST00000567379 ENST00000563798
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat VPS9D1

    Additional mRNA sequence: 

    AB018551.1 BC052626.1 

    3 DOTS entries:

    DT.107289  DT.99988900  DT.91970750 

    Selected AceView cDNA sequences (see all 62):

    AW161387 CB216092 BQ881114 BM920493 AL583484 BU197274 CR621709 BC052626 
    BU172610 BM975994 BM046317 BQ017220 AW140136 CA415895 AI829940 BQ957810 
    CA433700 CA428853 BM548008 BM048126 BQ007786 AW195459 BG832087 BU633452 

    GeneLoc Exon Structure


    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    VPS9D1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    VPS9D1 Expression
    About this image

    VPS9D1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VPS9D1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.164410

    UniProtKB/Swiss-Prot: VP9D1_HUMAN, Q9Y2B5
    Tissue specificity: Ubiquitous

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VPS9D1

    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for VPS9D1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vps9d11 , 5 RIKEN cDNA 1300018I17 gene5
    VPS9 domain containing 11
    81.34(n)1
    84.05(a)1
      8 (72.09 cM)5
    723251  NM_028200.11  NP_082476.11 
     1232423565 
    chicken
    (Gallus gallus)
    Aves C11H16ORF71 chromosome 11 open reading frame, human C16orf7 68.5(n)
    65.98(a)
      415839  XM_414200.4  XP_414200.4 
    lizard
    (Anolis carolinensis)
    Reptilia VPS9D16
    VPS9 domain containing 1
    64(a)
    1 ↔ 1
    GL344093.1(17504-37321)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.294002 Xenopus laevis transcribed sequence with weak similarity more 75.71(n)    CB592138.1 
    zebrafish
    (Danio rerio)
    Actinopterygii idibd51272 idibd5127 79.19(n)   338112  BM037370.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for VPS9D1 (see all 105)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1842878521,2
    --89773146(+) CCACGC/TCCGGC 1 -- int10--------
    rs7457101,2
    F,H--89773160(+) CTTCTG/ATGCAC 1 -- int14Minor allele frequency- A:0.00NS EA 416
    rs1176864661,2
    F--89773317(+) TCCAAG/CAGGGT 1 -- int11Minor allele frequency- C:0.01NA 120
    rs750885141,2
    C--89773352(+) CACAG-/CCCCAA 1 -- int10--------
    rs1889783541,2
    --89773376(+) CTATGC/TAGAGG 1 -- int10--------
    rs740338371,2
    C--89773386(+) GGTCTC/TGGAGG 1 -- int13Minor allele frequency- T:0.12WA EA 240
    rs8911071,2
    C,F,H--89773676(-) CCCTTG/ACTCAC 1 -- ut3121Minor allele frequency- A:0.02NS EA NA WA CSA 1469
    rs1140828461,2
    C,F--89773783(+) CAGCCG/AGCCCT 1 -- ut311Minor allele frequency- A:0.01WA 118
    rs756770821,2
    C--89773795(+) GTTCCG/TGACCC 1 -- ut310--------
    rs37516941,2
    C,F,H--89773886(-) GAGCCG/AGCCAG 1 -- ut3115Minor allele frequency- A:0.10EA NS NA WA 3150

    HapMap Linkage Disequilibrium report for VPS9D1 (89773541 - 89787394 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for VPS9D1: --
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing VPS9D1
    DNA2.0 Custom Variant and Variant Library Synthesis for VPS9D1

    (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.)
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    1 disease for VPS9D1:    
    About MalaCards
    fanconi's anemia


    VPS9D1 for disorders           About GeneDecksing


    Export disorders for VPS9D1 gene to outside databases

    (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)
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    PubMed articles for VPS9D1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with VPS9D1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and mapping of putative b subunit of human ATPase (ATP-BL) from human leukocytes. (PubMed id 10231027)1, 2, 3 Sugimoto J.... Isobe M. (DNA Res. 1999)
    2. TLR8-dependent TNF-(alpha) overexpression in Fanconi anemia group C cells. (PubMed id 19850743)1 Vanderwerf S.M....Bagby G.C. (Blood 2009)
    3. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    4. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. (PubMed id 16368877)1 Choy K.W....Pang C.P. (Physiol. Genomics 2006)
    5. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (Nature 2004)
    6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 9605 HGNC: 13526 AceView: C16orf7 Ensembl:ENSG00000075399 euGenes: HUgn9605
    ECgene: VPS9D1 H-InvDB: VPS9D1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for VPS9D1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for VPS9D1 gene:
    Search GeneIP for patents involving VPS9D1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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