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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VPS9D1 Gene

protein-coding   GIFtS: 39
GCID: GC16M089774

VPS9 Domain Containing 1

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

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for VPS9D1 Gene: 
VPS9D1 (VPS9 domain containing 1) is a protein-coding gene. Diseases associated with VPS9D1 include fanconi's anemia, and 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NT_010542.15  NC_018927.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for VPS9D1
         Other transcription factors

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

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y2B5

  • VPS9D1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    VPS9D1 Protein Expression
    REFSEQ proteins: NP_004904.2  
    ENSEMBL proteins: 
     ENSP00000454244   ENSP00000374037   ENSP00000455792   ENSP00000454889  

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    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--

    VPS9D1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    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 

    Animal Models:
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks 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 (GO ID links to tree view):    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 HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for VPS9D1 (VP9D1)

    Search CenterWatch for drugs/clinical trials and news about 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,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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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    Inhib. RNA
    Products:
         
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      QIAGEN 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 

    24/62 AceView cDNA sequences (see all 62):

    BC052626 BM920493 BU197274 BU172610 CR621709 CB216092 BQ881114 AL583484 
    AW161387 BQ007786 AL521070 BG832087 NM_004913 AI458261 BU944134 CA440187 
    AA335874 AW140136 CD370920 AI829940 CA941381 AI417599 CA415895 BM553919 

    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™, 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

    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


    See VPS9D1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VPS9D1

    SOURCE GeneReport for Unigene cluster: Hs.164410

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

        SABiosciences Custom PCR Arrays for VPS9D1
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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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for VPS9D1 gene from 5/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vps9d15
    Vsp9d11
    RIKEN cDNA 1300018I17 gene5
    VSP9 domain containing 11
    81.82(n)1
    84.21(a)1
      8 (72.09 cM)5
    723251  NM_028200.11  NP_082476.11 
     1232423565 
    chicken
    (Gallus gallus)
    Aves VPS9D11 VPS9 domain containing 1 69.99(n)
    66.94(a)
      415839  XM_414200.3  XP_414200.3 
    lizard
    (Anolis carolinensis)
    Reptilia C16ORF76
    Uncharacterized protein
    63(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)
    About This Section
      --

    (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) 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

    10/105 SNPs in VPS9D1 are shown (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: --
    SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    2 diseases for VPS9D1:    About MalaCards
    fanconi's anemia    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)
    About This Section

    PubMed articles for VPS9D1 gene integrated from 9 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. (1999)
    2. TLR8-dependent TNF-(alpha) overexpression in Fanconi anemia group C cells. (PubMed id 19850743)1 Vanderwerf S.M....Bagby G.C. (2009)
    3. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (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. (2006)
    5. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (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. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 9605 HGNC: 13526 AceView: C16orf7 Ensembl:ENSG00000075399 euGenes: HUgn9605
    ECgene: VPS9D1 H-InvDB: VPS9D1

    (According to HUGE)
    About This Section
      --

    (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
    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.)
    About This Section
    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, 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, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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