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

SOBP Gene

protein-coding   GIFtS: 49
GCID: GC06P107811

sine oculis binding protein homolog (Drosophila)

 Explore 9 diseases affiliated with
SOBP via our new
 Human Malady Compendium 
Biological research products
for SOBP
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Sine Oculis Binding Protein Homolog (Drosophila)1 2
JXC12 3 5
Jackson Circler Protein 12 3
MRAMS2 5
FLJ101591
Sine Oculis-Binding Protein Homolog2

External Ids:    HGNC: 292561   Entrez Gene: 550842   Ensembl: ENSG000001123207   OMIM: 6136675   UniProtKB: A7XYQ13   

Export aliases for SOBP gene to outside databases

Previous GC identifers: GC06P107920 GC06P105382


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

Entrez Gene summary for SOBP:
The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea.
Defects in this gene have also been linked to intellectual disability. (provided by RefSeq, Mar 2011)

UniProtKB/Swiss-Prot: SOBP_HUMAN, A7XYQ1
Function: Implicated in development of the cochlea (By similarity)

Gene Wiki entry for SOBP (Sobp)


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_025741.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SOBP gene promoter:
         HFH-3   Pbx1a   Pax-2   Pax-2a   CREB   AREB6   FOXI1   SRY   deltaCREB   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSOBP promoter sequence
   Search SABiosciences Chromatin IP Primers for SOBP

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SOBP


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

Entrez Gene cytogenetic band: 6q21   Ensembl cytogenetic band:  6q21   HGNC cytogenetic band: 6q21

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

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P107811:  view genomic region     (about GC identifiers)

Start:
107,811,162 bp from pter      End:
107,982,513 bp from pter
Size:
171,352 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: SOBP_HUMAN, A7XYQ1 (See protein sequence)
Recommended Name: Sine oculis-binding protein homolog  
Size: 873 amino acids; 92658 Da
Subunit: Interacts (via SIM domains) with SUMO1 and SUMO2
Sequence caution: Sequence=AAH91526.2; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=BAC03537.1;
Type=Miscellaneous discrepancy; Note=Intron retention;
Secondary accessions: B0QZ12 Q5BJD4 Q8N2B2

Explore the universe of human proteins at neXtProt for SOBP: NX_A7XYQ1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_A7XYQ1

  • SOBP Protein expression data from MOPED and PaxDb:    About this image 
    SOBP Protein Expression
    REFSEQ proteins: NP_060483.3  
    ENSEMBL proteins: 
     ENSP00000318900  

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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    SOBP for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR026092 RAI2/SOBP

    Graphical View of Domain Structure for InterPro Entry A7XYQ1

    ProtoNet protein and cluster: A7XYQ1

    UniProtKB/Swiss-Prot: SOBP_HUMAN, A7XYQ1
    Similarity: Belongs to the SOBP family
    Similarity: Contains 2 FCS-type zinc fingers


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, 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, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SOBP_HUMAN, A7XYQ1
    Function: Implicated in development of the cochlea (By similarity)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032184SUMO polymer binding IDA--
    GO:0046872metal ion binding IEA--
         
    SOBP for ontologies           About GeneDecksing


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Sobp):
     behavior/neurological  hearing/vestibular/ear 

    SOBP for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for SOBP 

    miRNA
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    hsa-miR-3607-3p hsa-miR-4254 hsa-miR-106a hsa-miR-15a hsa-miR-200a hsa-miR-30d hsa-miR-219-5p hsa-miR-519a
    SwitchGear 3'UTR luciferase reporter plasmidSOBP 3' UTR sequence
    Inhib. RNA
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOBP


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SOBP

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    3 Interacting proteins for SOBP (A7XYQ12, 3 ENSP000003189004) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CTBP1Q133632, 3, ENSP000002909214MINT-8253902 I2D: score=2 STRING: ENSP00000290921
    CELF3Q5SZQ83, ENSP000002905834I2D: score=3 STRING: ENSP00000290583
    --Q9BTF33I2D: score=1 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007605sensory perception of sound IEA--
    GO:0007626locomotory behavior IEA--
    GO:0042472inner ear morphogenesis IEA--

    SOBP for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 SOBP
    Search CenterWatch for drugs/clinical trials and news about SOBP 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SOBP gene: 
    NM_018013.3  

    Unigene Cluster for SOBP:

    Sine oculis binding protein homolog (Drosophila)
    Hs.445244  [show with all ESTs]
    Unigene Representative Sequence: NM_018013
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000317357(uc003prw.1 uc003prx.3) ENST00000477448 ENST00000494935


    miRNA
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    8/93 QIAGEN miScript miRNA Assays for microRNAs that regulate SOBP (see all 93):
    hsa-miR-3607-3p hsa-miR-4254 hsa-miR-106a hsa-miR-15a hsa-miR-200a hsa-miR-30d hsa-miR-219-5p hsa-miR-519a
    SwitchGear 3'UTR luciferase reporter plasmidSOBP 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AK001021.1 AK021973.1 AK090879.1 BC091526.1 BC109391.1 BC113966.1 DQ507800.1 

    13 DOTS entries:

    DT.100669778  DT.442502  DT.121342917  DT.121342962  DT.99932764  DT.100016937  DT.121343071  DT.91888651 
    DT.92432923  DT.75151183  DT.121342912  DT.92415113  DT.99976486 

    24/178 AceView cDNA sequences (see all 178):

    AI964012 CA776408 AI472873 BE550849 Z45812 AA704793 BF195668 Z43938 
    F03111 BF222381 F05158 F04375 Z45513 AA884687 BE219860 BE348321 
    BU740687 AI668889 F03187 BE551663 F04680 AA708910 BM669736 AW590516 

    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

    SOBP expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TAATCTTGAA
    SOBP Expression
    About this image

    SOBP expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    SomiteLumbar Vertebral BodySomite
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 3 LifeMap Cells 
    NameCategory
    PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)Lateral Plate Mesoderm, Neural Crest
    PureStem™ progenitor E44 (Embryonic Progenitor Cell)
    PureStem™ progenitor EN7 (Embryonic Progenitor Cell)

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

    SOURCE GeneReport for Unigene cluster: Hs.445244
        SABiosciences Custom PCR Arrays for SOBP
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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for SOBP gene from 4/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves SOBP1 sine oculis binding protein homolog (Drosophila) 82.08(n)
    87.29(a)
      421775  NM_001110177.1  NP_001103647.1 
    lizard
    (Anolis carolinensis)
    Reptilia SOBP6
    --
    82(a)
    1 ↔ 1
    1(189797941-189980111)
    zebrafish
    (Danio rerio)
    Actinopterygii sobpa1 sine oculis binding protein homolog (Drosophila) a 59.33(n)
    60.41(a)
      573683  NM_001098618.1  NP_001092088.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Sobp6
    Sine oculis-binding protein
    21(a)
    1 → many
    2R(7714668-7727035)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SOBP gene
    RAI22  
    1 SIMAP similar gene for SOBP using alignment to 2 protein entries:     SOBP_HUMAN (see all proteins):
    FLJ10159

    SOBP for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/2596 NCBI SNPs in SOBP are shown (see all 2596    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1112495841,2
    --105380546(+) GTTTTA/TAAGTT 1 -- us2k12Minor allele frequency- T:0.00CSA 2
    rs121539941,2
    H--105380572(+) CAAAAT/CGATGC 1 -- us2k14Minor allele frequency- C:0.00NS EA 416
    rs1126569291,2
    --105381347(+) CAGGGC/TATAAG 1 -- us2k12Minor allele frequency- T:0.21CSA WA 120
    rs1155746871,2
    C,F--105382400(+) GCACTA/GTCCTT 1 -- ut512Minor allele frequency- G:0.11WA NA 238
    rs772826481,2
    --105382852(+) TCCTCC/TTCCAG 1 -- int10--------
    rs735149761,2
    C,F--105382878(+) CAACTC/GGAGGG 1 -- int13Minor allele frequency- G:0.15WA 122
    rs9224861,2
    C,F,A,H--105383026(-) GGAAAG/ACCTCT 1 -- int119Minor allele frequency- A:0.09NA EA MN NS WA 2648
    rs750478851,2
    C,F--105383411(+) TGCAGG/AGCGCC 1 -- int11Minor allele frequency- A:0.07NA 120
    rs21271401,2
    F--105384523(-) ACAACG/ACGAGC 1 -- int11Minor allele frequency- A:0.04NA 120
    rs104568571,2
    --105384878(+) AAATAA/CCCCTA 1 -- int10--------

    HapMap Linkage Disequilibrium report for SOBP (107811162 - 107982513 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SOBP: --
    Human Gene Mutation Database (HGMD): SOBP

    SABiosciences Cancer Mutation 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.)
    About This Section

    SOBP for disorders           About GeneDecksing

    OMIM gene information: 613667   
    OMIM disorders: 613671  
    UniProtKB/Swiss-Prot: SOBP_HUMAN, A7XYQ1
  • Defects in SOBP are the cause of mental retardation-anterior maxillary protrusion-strabismus (MRAMS)
  • [MIM:613671]. A syndrome characterized by severe mental retardation, strabismus and dysmorphic features such as
    anterior maxillary protrusion with vertical maxillary excess, open bite and prominent crowded teeth. Some patients may
    lack dysmorphic features and manifest temporal lobe epilepsy and psychosis. Esotropia and amblyopia are present in
    some individuals

    9 diseases for SOBP:    About MalaCards
    mental retardation, anterior maxillary protrusion, and strabismus    intellectual disability    strabismus    postcholecystectomy syndrome
    biliary dyskinesia    hypopharynx cancer    esotropia    amblyopia
    albinism

    2 diseases from the University of Copenhagen DISEASES database for SOBP:
    Postcholecystectomy syndrome     Biliary dyskinesia
    Human Genome Epidemiology (HuGE) Navigator: SOBP (1 document)

    Export disorders for SOBP 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 SOBP gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with SOBP)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system. (PubMed id 21035105)1, 2 Birk E....Basel-Vanagaite L. (2010)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. PolySUMO-binding proteins identified through a string search. (PubMed id 23086935)2 Sun H. and Hunter T. (2012)
    4. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    6. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (2005)
    7. 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. (2004)
    8. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)2 Mungall A.J.... Beck S. (2003)
    9. 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)
    10. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

    (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: 55084 HGNC: 29256 AceView: FLJ10159 Ensembl:ENSG00000112320 euGenes: HUgn55084
    ECgene: SOBP H-InvDB: SOBP

    (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 SOBP 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 SOBP gene:
    Search GeneIP for patents involving SOBP

    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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, 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)
    About This Section

     
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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013 , 14 May 2013

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    von Willebrand factor
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