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

SEMA6B Gene

protein-coding   GIFtS: 49
GCID: GC19M004542

sema domain, transmembrane domain (TM), and cytoplasmic...


(Previous symbol: SEMAN)
 Explore 3 diseases affiliated with
SEMA6B via our new
 Human Malady Compendium 
Biological research products
for SEMA6B
    

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

Aliases
Sema Domain, Transmembrane Domain (TM), And Cytoplasmic Domain, (Semaphorin)
6B1 2
     Semaphorin Z2
SEMAN1 2 3     Semaphorin-6B1
SEM-SEMA-Y1 2     Semaphorin-6Ba1
SEMA-VIB1 2     SEMAZ3
SemaZ1     Semaphorin-Z3
Semaphorin VIB2     Sema Z3

External Ids:    HGNC: 107391   Entrez Gene: 105012   Ensembl: ENSG000001676807   OMIM: 6088735   UniProtKB: Q9H3T33   

Export aliases for SEMA6B gene to outside databases

Previous GC identifers: GC19M004634 GC19M004482 GC19M004493 GC19M004304


(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 SEMA6B:
This gene encodes a member of the semaphorin family, a group of proteins characterized by the presence of a conserved
semaphorin (sema) domain. Whereas some semaphorins are transmembrane proteins, others are secreted. Semaphorins play a
major role in axon guidance. The protein encoded by this gene may be involved in both peripheral and central nervous
system development. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: SEM6B_HUMAN, Q9H3T3
Function: May play a role in both peripheral and central nervous system development (By similarity)




(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_000019.9  NC_018930.1  NT_011255.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SEMA6B gene promoter:
         c-Fos   AP-1   JunB   Fra-1   FosB   MZF-1   Egr-2   JunD   c-Jun   MRF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSEMA6B promoter sequence
   Search SABiosciences Chromatin IP Primers for SEMA6B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SEMA6B


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

Entrez Gene cytogenetic band: 19p13.3   Ensembl cytogenetic band:  19p13.3   HGNC cytogenetic band: 19p13.3

SEMA6B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SEMA6B gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M004542:  view genomic region     (about GC identifiers)

Start:
4,542,600 bp from pter      End:
4,559,820 bp from pter
Size:
17,221 bases      Orientation:
minus 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: SEM6B_HUMAN, Q9H3T3 (See protein sequence)
Recommended Name: Semaphorin-6B precursor  
Size: 888 amino acids; 95285 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein
Sequence caution: Sequence=AAF87661.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;
Secondary accessions: A5PKU4 Q9NRK9

Explore the universe of human proteins at neXtProt for SEMA6B: NX_Q9H3T3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H3T3

  • SEMA6B Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_115484.2  
    ENSEMBL proteins: 
     ENSP00000467290   ENSP00000465722   ENSP00000465184   ENSP00000301293  

    Human Recombinant Protein Products: 
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for SEMA6B

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016021integral to membrane IEA--


    SEMA6B for ontologies           About GeneDecksing



    SEMA6B Antibody Products: 
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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    SEMA6B for domains           About GeneDecksing

    5/6 InterPro domains/families (see all 6):
     IPR003659 Plexin-like
     IPR002165 Plexin_repeat
     IPR016201 Plexin-like_fold
     IPR027231 Semaphorin
     IPR015943 WD40/YVTN_repeat-like_dom

    Graphical View of Domain Structure for InterPro Entry Q9H3T3

    ProtoNet protein and cluster: Q9H3T3

    1 Blocks protein family: IPB001627 Semaphorin/CD100 antigen

    UniProtKB/Swiss-Prot: SEM6B_HUMAN, Q9H3T3
    Similarity: Belongs to the semaphorin family
    Similarity: Contains 1 Sema domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: SEM6B_HUMAN, Q9H3T3
    Function: May play a role in both peripheral and central nervous system development (By similarity)

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SEMA6B
    8/22 QIAGEN miScript miRNA Assays for microRNAs that regulate SEMA6B (see all 22):
    hsa-miR-30c hsa-miR-185* hsa-miR-30d hsa-miR-520a-5p hsa-miR-218 hsa-miR-3150a-3p hsa-miR-30a hsa-miR-1184
    SwitchGear 3'UTR luciferase reporter plasmidSEMA6B 3' UTR sequence
    Inhib. RNA
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    Clone
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004872receptor activity IEA--
    GO:0030215semaphorin receptor binding ----


    SEMA6B for ontologies           About GeneDecksing


    Animal Models:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Sema6b):
     nervous system 

    SEMA6B for phenotypes           About GeneDecksing


    (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

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Axon guidance
    Axon guidance1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for SEMA6B):
        Axon guidance


    SEMA6B for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SEMA6B

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007399nervous system development IEA--
    GO:0030154cell differentiation IEA--


    SEMA6B 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

    SEMA6B for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SEMA6B
    1 Novoseek chemical compound relationship for SEMA6B gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoic acid 43.1 3 16525649 (3)

    Search CenterWatch for drugs/clinical trials and news about SEMA6B / SEM6B 

    (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, 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 SEMA6B gene (3 alternative transcripts): 
    NM_032108.3  NM_020241.2  NM_133327.1  

    Unigene Cluster for SEMA6B:

    Sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B
    Hs.465642  [show with all ESTs]
    Unigene Representative Sequence: BC142617
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000586582 ENST00000586965 ENST00000589889 ENST00000301293(uc010dud.2 uc010xih.1)


    miRNA
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    8/22 QIAGEN miScript miRNA Assays for microRNAs that regulate SEMA6B (see all 22):
    hsa-miR-30c hsa-miR-185* hsa-miR-30d hsa-miR-520a-5p hsa-miR-218 hsa-miR-3150a-3p hsa-miR-30a hsa-miR-1184
    SwitchGear 3'UTR luciferase reporter plasmidSEMA6B 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for SEMA6B (see all 7)
    OriGene shRNA RFP: SEMA6B
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    Clone
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SEMA6B
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SEMA6B

    Additional cDNA sequence: 

    AB022433.1 AB209278.1 AF216389.1 AF293363.1 AK300037.1 AY358939.1 BC142617.1 FR839673.1 

    2 DOTS entries:

    DT.95368944  DT.100742029 

    24/47 AceView cDNA sequences (see all 47):

    BQ184207 T08532 BQ637712 NM_032108 CR591947 R87331 AF216389 BE302795 
    AI825934 BF973615 AW054434 NM_133327 NM_020241 BQ185898 AB022433 CA430435 
    CA433483 AY358939 CB268087 AI936745 AF293363 BE250246 BG475468 AI870375 

    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

    SEMA6B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CCACGTGGCT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    SEMA6B expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 3 LifeMap Cells 
    NameCategory
    PureStem™ endothelial progenitor 30-MV2-12 (Embryonic Progenitor Cell)Blood, Endothelium
    PureStem™ endothelial Progenitor 30-SM2-3 (Embryonic Progenitor Cell)Blood, Endothelium
    PureStem™ endothelial progenitor 30-SM2-1 (Embryonic Progenitor Cell)Endothelium
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SEMA6B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SEMA6B

    SOURCE GeneReport for Unigene cluster: Hs.465642
        SABiosciences Custom PCR Arrays for SEMA6B
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SEMA6B

    (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 SEMA6B gene from 5/17 species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves SEMA6B1 sema domain, transmembrane domain (TM), and cytoplasmic more 72.42(n)
    71.38(a)
      428330  XM_425890.3  XP_425890.3 
    lizard
    (Anolis carolinensis)
    Reptilia SEMA6B6
    --
    --
    75(a)
    13(a)
    1 ↔ 1
    possible ortholog
    GL344270.1(1200-16598)
    GL343757.1(650-4500)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1001488831 semaphorin 6bb 62.67(n)
    62.67(a)
      100148883  XM_002663110.1  XP_002663156.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Sema-1a3 axon guidance 39(a)
    (best of 3)
        --
    worm
    (Caenorhabditis elegans)
    Secernentea mab-203 Expression: ray cell precursors, ventral
    nerve more
    29(a)   I(1644872-1651256)   --


    ENSEMBL Gene Tree for SEMA6B (if available)
    TreeFam Gene Tree for SEMA6B (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SEMA6B gene
    SEMA6D2  SEMA6C2  SEMA7A2  SEMA6A2  SEMA5A2  SEMA5B2  
    7 SIMAP similar genes for SEMA6B using alignment to 3 protein entries:     SEM6B_HUMAN (see all proteins):
    SEMA6A    SEMA6D    SEMA6C    SEMA4A    SEMA3A    SEMA3C
    SEMA5B

    SEMA6B 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

    10/374 NCBI SNPs in SEMA6B are shown (see all 374    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2014243791,2
    --4542116(+) CTCAA-/AAAAAG
            
    AAAAA
    1 -- ds50010--------
    rs349314551,2
    C--4542226(+) TTTTTT/-GAGAC 1 -- ds50011Minor allele frequency- -:0.50NA 2
    rs1411655221,2
    --4542254(+) ACAGCG/TTCTCG 1 -- ds50010--------
    rs1884517861,2
    --4542299(+) CTCAGC/TTCACT 1 -- ds50010--------
    rs1386778901,2
    --4542353(+) CGGCCC/GAGTAG 1 -- ds50010--------
    rs1488637991,2
    --4542417(+) AGAGAC/TGGGGT 1 -- ds50010--------
    rs1912432081,2
    --4542496(+) AGTGCC/TGGGAT 1 -- ds50010--------
    rs1435078551,2
    --4542715(+) TCAGAA/GGGGGG 1 -- ut310--------
    rs1490720271,2
    C,--4542915(+) AGAGT-/GGGGGG 1 -- ut310--------
    rs782376911,2
    C,--4543048(+) GCACGC/TGTGGC 1 -- ut311Minor allele frequency- T:0.01WA 118

    HapMap Linkage Disequilibrium report for SEMA6B (4542600 - 4559820 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SEMA6B: --

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SEMA6B
    DNA2.0 Custom Variant and Variant Library Synthesis for SEMA6B

    (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

    SEMA6B for disorders           About GeneDecksing

    OMIM gene information: 608873    OMIM disorders: --

    3 diseases for SEMA6B:    About MalaCards
    periodontitis    breast cancer    glioblastoma


    Export disorders for SEMA6B 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 SEMA6B gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with SEMA6B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human semaphorin 6b [(HSA)SEMA6B], a novel human class 6 semaphorin gene: alternative splicing and all-trans-retinoic acid-dependent downregulation in glioblastoma cell lines. (PubMed id 11350127)1, 2, 9 Correa R.G....Simpson A.J.G. (2001)
    2. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PubMed id 15340161)1, 2 Zhang Z. and Henzel W.J. (2004)
    3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
    4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    5. The human semaphorin 6B gene is down regulated by PPARs. (PubMed id 15177567)1 Collet P....Dauca M. (2004)
    6. 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)
    7. 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)
    8. 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)
    9. A novel transmembrane semaphorin can bind c-src. (PubMed id 9361278)3 Eckhardt F....Fishman M.C. (1997)
    10. Effects of PPAR and RXR ligands in semaphorin 6B gene expression of human MCF-7 breast cancer cells. (PubMed id 16525649)9 Murad H....Dauca M. (2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 10501 HGNC: 10739 AceView: SEMA6B Ensembl:ENSG00000167680 euGenes: HUgn10501
    ECgene: SEMA6B Kegg: 10501 H-InvDB: SEMA6B

    (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 SEMA6B 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 SEMA6B gene:
    Search GeneIP for patents involving SEMA6B

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



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