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VWA5B2 Gene

protein-coding   GIFtS: 39
GCID: GC03P183948

Von Willebrand Factor A Domain Containing 5B2

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(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
Von Willebrand Factor A Domain Containing 5B21 2
Von Willebrand Factor A Domain-Containing Protein 5B22

External Ids:    HGNC: 251441   Entrez Gene: 901132   Ensembl: ENSG000001451987   UniProtKB: Q8N3983   

Export aliases for VWA5B2 gene to outside databases

Previous GC identifers: GC03P185436 GC03P181354


(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 VWA5B2 Gene:
VWA5B2 (von Willebrand factor A domain containing 5B2) is a protein-coding gene. An important paralog of this gene is PARP4.


(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 at NCBI GenBank:
NC_000003.11  NT_005612.17  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the VWA5B2 gene promoter:
         GR   Egr-2   Tal-1   GR-beta   Pax-2   Pax-2a   GR-alpha   LCR-F1   E47   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for VWA5B2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VWA5B2


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

Entrez Gene cytogenetic band: 3q27.1   Ensembl cytogenetic band:  3q27.1   HGNC cytogenetic band: 3q27.1

VWA5B2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VWA5B2 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P183948:  view genomic region     (about GC identifiers)

Start:
183,948,217 bp from pter      End:
183,960,117 bp from pter
Size:
11,901 bases      Orientation:
plus 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: VW5B2_HUMAN, Q8N398 (See protein sequence)
Recommended Name: von Willebrand factor A domain-containing protein 5B2  
Size: 1253 amino acids; 132764 Da
Secondary accessions: B9EGN7
Alternative splicing: 2 isoforms:  Q8N398-1   Q8N398-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VWA5B2: NX_Q8N398

Explore proteomics data for VWA5B2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See VWA5B2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_612354.1  
    ENSEMBL proteins: 
     ENSP00000398688   ENSP00000273794  

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    antibodies-online kits for VWA5B2 (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR013694 VIT
     IPR002035 VWF_A

    Graphical View of Domain Structure for InterPro Entry Q8N398

    ProtoNet protein and cluster: Q8N398

    UniProtKB/Swiss-Prot: VW5B2_HUMAN, Q8N398
    Similarity: Contains 1 VIT domain
    Similarity: Contains 1 VWFA domain


    Find genes that share domains with VWA5B2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for VWA5B2

    miRNA
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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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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    plasma membrane3
    cytosol2
    golgi apparatus1

    (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 VWA5B2
    Interactions:

        Search GeneGlobe Interaction Network for VWA5B2

    1 Interacting protein for VWA5B2 (Q8N3983) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    XRN1Q8IZH23I2D: score=1 
    About this table

    (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 VWA5B2 (VW5B2)



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for VWA5B2 gene: 
    NM_138345.1  

    Unigene Cluster for VWA5B2:

    Von Willebrand factor A domain containing 5B2
    Hs.584997  [show with all ESTs]
    Unigene Representative Sequence: BC136609
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000426955(uc011bra.2 uc011brb.2) ENST00000497229(uc003fnc.3)
    ENST00000273794 ENST00000461141(uc003fnd.3) ENST00000474580 ENST00000493493

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    Selected qRT-PCR Assays for microRNAs that regulate VWA5B2 (see all 15):
    hsa-miR-448 hsa-miR-34c-5p hsa-miR-137 hsa-miR-92a hsa-miR-449b hsa-miR-367 hsa-miR-25 hsa-miR-4306
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      QuantiFast Probe-based Assays in human, mouse, rat VWA5B2

    Additional mRNA sequence: 

    AK293885.1 AL834499.1 BC001200.1 BC136609.1 

    4 DOTS entries:

    DT.75164324  DT.91925596  DT.120894216  DT.40232021 

    1 AceView cDNA sequence:

    BV189600 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for VWA5B2    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14
    SP1:        -                                                                       -                                 
    SP2:                                                                                                                  
    SP3:                                                                                                                  
    SP4:                                                                                                                  


    ECgene alternative splicing isoforms for VWA5B2

    (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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    VWA5B2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACTACCTGCC
    VWA5B2 Expression
    About this image


    VWA5B2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Pancreas (Endocrine System)    fully expand to see all 4 entries
             Endocrine Progenitor Cells Ventral Pancreatic Bud
     
     Adrenal Gland (Endocrine System)
    VWA5B2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VWA5B2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.584997
        Custom PCR Arrays for VWA5B2
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    In Situ
    Assay Products:
     

     
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    (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 VWA5B2 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vwa5b21 , 5 von Willebrand factor A domain containing 5B21, 5 84.29(n)1
    83.88(a)1
      16 (12.47 cM)5
    3286431  NM_001144953.11  NP_001138425.11 
     205894715 
    chicken
    (Gallus gallus)
    Aves VWA5B21 von Willebrand factor A domain containing 5B2 60.45(n)
    51.89(a)
      424951  XM_422758.4  XP_422758.4 
    lizard
    (Anolis carolinensis)
    Reptilia VWA5B26
    von Willebrand factor A domain containing 5B2
    44(a)
    1 ↔ 1
    GL343245.1(640997-721112)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia vwa5b21 von Willebrand factor A domain containing 5B2 49.05(n)
    42.65(a)
      100488101  XM_002935141.2  XP_002935187.2 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1018824271 von Willebrand factor A domain-containing protein 5B1-like 50.48(n)
    42.73(a)
      101882427  XM_005171437.1  XP_005171494.1 


    ENSEMBL Gene Tree for VWA5B2 (if available)
    TreeFam Gene Tree for VWA5B2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for VWA5B2 gene
    PARP42  VWA5B12  VWA5A2  

    Find genes that share paralogs with VWA5B2           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for VWA5B2
    PGOHUM00000247746


    (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 VWA5B2 (see all 195)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1138784851,2
    F--183946318(+) CCATCC/TCCAGC 1 -- us2k12Minor allele frequency- T:0.04CSA WA 120
    rs1416420711,2
    --183946324(+) CCAGCG/TCTCCT 1 -- us2k10--------
    rs1470732321,2
    --183946519(+) GCCAAA/TAACAA 1 -- us2k10--------
    rs67675411,2
    C,F--183946524(+) TAACAA/GGGGGC 1 -- us2k11Minor allele frequency- G:0.14WA 118
    rs1911134431,2
    --183946615(+) CCATAA/GGAAGG 1 -- us2k10--------
    rs1164958131,2
    F--183946782(+) TCGCTG/ACAGTG 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs1166198731,2
    C,F--183946833(+) CTGCAT/GGAACT 1 -- us2k11Minor allele frequency- G:0.03NA 120
    rs7065851,2
    C,F--183946956(+) GGGGGG/TTTCGC 1 -- us2k13Minor allele frequency- T:0.15NA WA EA 240
    rs1163677941,2
    F--183946993(+) GCGATG/AGGAAG 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs98262431,2
    C--183947164(+) TCCGTG/TCGGCG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for VWA5B2 (183948217 - 183960117 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for VWA5B2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv878060CNV Loss21882294
    dgv5354n71CNV Loss21882294
    nsv829812CNV Loss17160897
    nsv528639CNV Loss19592680
    nsv878057CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
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    (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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      --

    (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 VWA5B2 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with VWA5B2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A protein interaction framework for human mRNA degradation. (PubMed id 15231747)1, 3 Lehner B. and Sanderson C.M. (Genome Res. 2004)
    2. A mega-analysis of genome-wide association studies for major depressive disorder. (PubMed id 22472876)1  ....Sullivan P.F. (Mol. Psychiatry 2013)
    3. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    4. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (Nature 2006)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 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: 90113 HGNC: 25144 AceView: LOC90113.1 Ensembl:ENSG00000145198 euGenes: HUgn90113
    ECgene: VWA5B2 H-InvDB: VWA5B2

    (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 VWA5B2 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 VWA5B2 gene:
    Search GeneIP for patents involving VWA5B2

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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