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SBSPON Gene

protein-coding   GIFtS: 39
GCID: GC08M073977

Somatomedin B And Thrombospondin, Type 1 Domain Containing

(Previous name: chromosome 8 open reading frame 84)
(Previous symbol: C8orf84)
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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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Somatomedin B And Thrombospondin, Type 1 Domain Containing1 2     RPESP2 3
C8orf841 2 3     Chromosome 8 Open Reading Frame 841
RPE Spondin1 2     rpe-spondin1
RPE-spondin2 3     Somatomedin-B And Thrombospondin Type-1 Domain-Containing Protein2

External Ids:    HGNC: 303621   Entrez Gene: 1578692   Ensembl: ENSG000001647647   UniProtKB: Q8IVN83   
ORGUL members:         

Export aliases for SBSPON 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 SBSPON Gene:
SBSPON (somatomedin B and thrombospondin, type 1 domain containing) is a protein-coding gene. GO annotations related to this gene include scavenger receptor activity and polysaccharide binding.


(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_000008.10  NT_008183.20  NC_018919.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SBSPON
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSBSPON promoter sequence
   Search Chromatin IP Primers for SBSPON

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


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

Entrez Gene cytogenetic band: 8q21.11   Ensembl cytogenetic band:  8q21.11   HGNC cytogenetic band: 8q21.11

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

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M073977:  view genomic region     (about GC identifiers)

Start:
73,976,775 bp from pter      End:
74,036,323 bp from pter
Size:
59,549 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, 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: SBSPO_HUMAN, Q8IVN8 (See protein sequence)
Recommended Name: Somatomedin-B and thrombospondin type-1 domain-containing protein precursor  
Size: 264 amino acids; 29610 Da
Sequence caution: Sequence=AAH42877.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAK83466.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAF85659.1;
Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: A8KAA5 Q96J64

Explore the universe of human proteins at neXtProt for SBSPON: NX_Q8IVN8

Explore proteomics data for SBSPON at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn227

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

    REFSEQ proteins: NP_694957.3  
    ENSEMBL proteins: 
     ENSP00000297354  
    Reactome Protein details: Q8IVN8

    SBSPON Human Recombinant Protein Products:

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    Browse Proteins at Cloud-Clone Corp.

     
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    antibodies-online proteins for SBSPON 

     
    antibodies-online peptides for SBSPON

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    antibodies-online antibodies for SBSPON (6 products) 

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    antibodies-online kits for SBSPON (3 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:
     IPR000884 Thrombospondin_1_rpt
     IPR001212 Somatomedin_B_dom

    Graphical View of Domain Structure for InterPro Entry Q8IVN8

    ProtoNet protein and cluster: Q8IVN8

    UniProtKB/Swiss-Prot: SBSPO_HUMAN, Q8IVN8
    Similarity: Belongs to the thrombospondin family
    Similarity: Contains 1 SMB (somatomedin-B) domain
    Similarity: Contains 1 TSP type-1 domain


    Find genes that share domains with SBSPON           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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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005044scavenger receptor activity IEA--
    GO:0030247polysaccharide binding IEA--
         
    Find genes that share ontologies with SBSPON           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for SBSPON:
     Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SBSPON

    miRNA
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    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SBSPON

    Gene Editing
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    GenScript Custom all cDNA clones Services for SBSPON
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SBSPON
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SBSPON

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SBSPON


    (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 UniProtKB/Swiss-Prot
    SBSPO_HUMAN, Q8IVN8: Secreted, extracellular space, extracellular matrix

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005578proteinaceous extracellular matrix IEA--
    GO:0031012colocalizes with extracellular matrix IDA--

    Find genes that share ontologies with SBSPON           About GenesLikeMe


    (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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    Find genes that share SuperPaths with SBSPON           About GenesLikeMe

    Pathways by sourceSee SuperPaths
    Show all pathways


    1 Reactome Pathway for SBSPON
        O-glycosylation of TSR domain-containing proteins


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SBSPON
    Interactions:

        Search GeneGlobe Interaction Network for SBSPON

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006955immune response IEA--

    Find genes that share ontologies with SBSPON           About GenesLikeMe



    (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 SBSPON (SBSPO)



    (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 SBSPON gene: 
    NM_153225.3  

    Unigene Cluster for SBSPON:

    Somatomedin B and thrombospondin, type 1 domain containing
    Hs.439040  [show with all ESTs]
    Unigene Representative Sequence: NM_153225
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000297354(uc003xzf.3) ENST00000519697
    miRNA
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    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat SBSPON
      QuantiFast Probe-based Assays in human, mouse, rat SBSPON

    Additional mRNA sequence: 

    AF087977.1 AK292970.1 AL080094.1 AY040546.1 BC042877.1 

    4 DOTS entries:

    DT.211522  DT.100778889  DT.100778892  DT.100712381 

    Selected AceView cDNA sequences (see all 77):

    AI217135 BQ024333 BX089861 AF087977 H88831 AI565404 CR592835 AA939100 
    NM_153225 BQ448226 BC042877 BX324902 BQ182470 H88832 AL697631 CR616775 
    CR594707 CA413403 CB046312 BX344501 AW135859 AL545906 BG399214 AA922441 

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


    SBSPON expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Kidney (Urinary System)    fully expand to see all 2 entries
             Ureteric Bud Cells Ureteric Bud
     
     Umbilical Cord (Extraembryonic Tissues)
             Wharton's jelly-derived stem cells
     
     Intermediate Mesoderm (Gastrulation Derivatives)
             Mesonephros
     
     Bone (Muscoskeletal System)
             Zeugopod Epiphyseal End
     
     Ovary (Reproductive System)
    SBSPON Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SBSPON Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.439040

    UniProtKB/Swiss-Prot: SBSPO_HUMAN, Q8IVN8
    Tissue specificity: Detected in aorta extracellular matrix (at protein level)

        Custom PCR Arrays for SBSPON
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SBSPON

    (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 animals.

    Orthologs for SBSPON gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sbspon1 , 5 predicted gene 1065
    somatomedin B and thrombospondin, type 1 domain containing1
    87.63(n)1
    89.39(a)1
      1 (4.89 cM)5
    2268661  NM_001033288.31  NP_001028460.11 
     158538625 
    chicken
    (Gallus gallus)
    Aves C2H8ORF841 chromosome 2 open reading frame, human C8orf84 70.83(n)
    65.62(a)
      420181  XM_004939912.1  XP_004939969.1 
    lizard
    (Anolis carolinensis)
    Reptilia SBSPON6
    somatomedin B and thrombospondin, type 1 domain co...
    64(a)
    1 ↔ 1
    4(33393157-33407503)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia sbspon1 somatomedin B and thrombospondin, type 1 domain containing 65.64(n)
    63.85(a)
      100489582  XM_004915167.1  XP_004915224.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1001512181 somatomedin-B and thrombospondin type-1 domain-containing more 62.23(n)
    60.52(a)
      100151218  XM_001920112.2  XP_001920147.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG423396
    --
    19(a)
    1 ↔ 1
    X(10861755-10933934)
    worm
    (Caenorhabditis elegans)
    Secernentea CELE_R17.31 CELE_R17.3 42.74(n)
    32.26(a)
      176513  NM_066986.3  NP_499387.1 


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

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

    Find genes that share paralogs with SBSPON           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for SBSPON
    PGOHUM00000259647


    (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 SBSPON (see all 640)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs667603821,2
    C--73976308(+) TATGG-/TCTTT 
            
    TCTTT
    1 -- int12Minor allele frequency- TCTTT:0.25NA CSA 4
    rs2013517421,2
    C--73976311(+) GGTCTG/TTTCTT 1 -- int10--------
    rs1884936971,2
    --73976446(+) ACCCCA/GTATTA 1 -- int10--------
    rs788653081,2
    C,F--73976472(+) TTATTC/ATGGTT 1 -- int11Minor allele frequency- A:0.09WA 118
    rs746672871,2
    C,F--73976501(+) ATTTGC/GTTTCA 1 -- int14Minor allele frequency- G:0.14NA CSA EA 244
    rs582080701,2
    C--73976509(+) TCAATC/AGTAAA 1 -- int12Minor allele frequency- A:0.11WA 120
    rs1930826981,2
    C--73976518(+) AAAAAA/CATTAT 1 -- int10--------
    rs1502621501,2
    C--73976681(+) CTCACA/GGTGCT 1 -- int10--------
    rs1389453261,2
    --73976712(+) CTCAGA/GAGGCC 1 -- int10--------
    rs613283281,2
    C,F--73976876(+) ACTTTA/TAATTA 1 -- ut312Minor allele frequency- T:0.11WA 120

    HapMap Linkage Disequilibrium report for SBSPON (73976775 - 74036323 bp)

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

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

    1. Expressed sequence tag analysis of human RPE/choroid for the NEIBank project: over 6000 non-redundant transcripts, novel genes and splice variants. (PubMed id 12107410)1, 2, 3 Wistow G.... Peterson K. (Mol. Vis. 2002)
    2. Proteomics characterization of extracellular space components in the human aorta. (PubMed id 20551380)1, 2 Didangelos A.... Mayr M. (Mol. Cell. Proteomics 2010)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. (PubMed id 22412388)1 Kenny E.E....Peter I. (PLoS Genet. 2012)
    5. Genetic variants near PDGFRA are associated with corneal curvature in Australians. (PubMed id 22969067)1 Mishra A....Mackey D.A. (amp 2012)
    6. DNA sequence and analysis of human chromosome 8. (PubMed id 16421571)2 Nusbaum C....Lander E.S. (Nature 2006)
    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. (Genome Res. 2004)
    8. 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)
    9. Identifying differentially expressed genes in the mammalian retina and the retinal pigment epithelium by suppression subtractive hybridization. (PubMed id 15218245)9 Schulz H.L....Weber B.H.F. (Cytogenet. Genome Res. 2004)

    (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: 157869 HGNC: 30362 AceView: RPESP Ensembl:ENSG00000164764 euGenes: HUgn157869
    ECgene: SBSPON H-InvDB: SBSPON

    (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 SBSPON 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 SBSPON gene:
    Search GeneIP for patents involving SBSPON

    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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     Browse OriGene Antibodies   OriGene RNAi products in human, mouse, rat for SBSPON  
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     Block miRNA regulation of human, mouse, rat SBSPON using miScript Target Protectors SeqTarget long-range PCR primers for resequencing SBSPON
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     Browse ESI BIO Cell Lines and PureStem Progenitors for SBSPON
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     antibodies-online antibodies for SBSPON (6 products)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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