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SEMA4D Gene

protein-coding   GIFtS: 69
GCID: GC09M091975

Sema Domain, Immunoglobulin Domain (Ig), Transmembrane Domain...

(Previous name: chromosome 9 open reading frame 164)
(Previous symbols: SEMAJ, C9orf164)
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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
Sema Domain, Immunoglobulin Domain (Ig), Transmembrane Domain (TM) And
Short Cytoplasmic Domain, (Semaphorin) 4D1 2
     Chromosome 9 Open Reading Frame 1641
C9orf1641 2 3     M-Sema G1
SEMAJ1 2 3     M-sema-G2
A82 3     coll-42
BB182 3     Sema Domain, Immunoglobulin Domain (Ig), Transmembrane Domain (TM) And
Short Cytoplasmic Domain, 4D2
CD1002 3     semaphorin-4D2
GR32 3     CD100 Antigen3

External Ids:    HGNC: 107321   Entrez Gene: 105072   Ensembl: ENSG000001877647   OMIM: 6018665   UniProtKB: Q928543   

Export aliases for SEMA4D gene to outside databases

Previous GC identifers: GC09U990094 GC09M083868 GC09M085576 GC09M9O0142 GC09M089221 GC09M091181 GC09M061809


(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 SEMA4D Gene:
SEMA4D (sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D) is a protein-coding gene. GO annotations related to this gene include transmembrane signaling receptor activity and receptor binding. An important paralog of this gene is SEMA3C.

UniProtKB/Swiss-Prot: SEM4D_HUMAN, Q92854
Function: Cell surface receptor for PLXN1B and PLXNB2 that plays an important role in cell-cell signaling.
Promotes reorganization of the actin cytoskeleton and plays a role in axonal growth cone guidance in the
developing central nervous system. Regulates dendrite and axon branching and morphogenesis. Promotes the
migration of cerebellar granule cells and of endothelial cells. Plays a role in the immune system; induces
B-cells to aggregate and improves their viability (in vitro). Promotes signaling via SRC and PTK2B/PYK2, which
then mediates activation of phosphatidylinositol 3-kinase and of the AKT1 signaling cascade. Interaction with
PLXNB1 mediates activation of RHOA

Gene Wiki entry for SEMA4D 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SEMA4D gene promoter:
         Elk-1   AP-1   p53   Pbx1a   MyoD   Evi-1   FOXL1   CP2   POU2F1   POU2F1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SEMA4D promoter sequence
   Search Chromatin IP Primers for SEMA4D

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SEMA4D


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

Entrez Gene cytogenetic band: 9q22.2   Ensembl cytogenetic band:  9q22.2   HGNC cytogenetic band: 9q22-q31

SEMA4D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SEMA4D gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M091975:  view genomic region     (about GC identifiers)

Start:
91,975,702 bp from pter      End:
92,113,045 bp from pter
Size:
137,344 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: SEM4D_HUMAN, Q92854 (See protein sequence)
Recommended Name: Semaphorin-4D precursor  
Size: 862 amino acids; 96150 Da
Subunit: Homodimer. Interacts with PLXNB2 (By similarity). Binds PLXNB1
Sequence caution: Sequence=AAI37516.1; Type=Miscellaneous discrepancy; Note=Cloning artifact; Sequence=AAI37519.1;
Type=Miscellaneous discrepancy; Note=Cloning artifact; Sequence=BAC04938.1; Type=Miscellaneous discrepancy;
Note=Cloning artifact; Sequence=CAI95794.1; Type=Erroneous gene model prediction;
2 PDB 3D structures from and Proteopedia for SEMA4D:
1OLZ (3D)        3OL2 (3D)    
Secondary accessions: B2RPM6 Q7Z5S4 Q8N8B0
Alternative splicing: 2 isoforms:  Q92854-1   Q92854-2   

Explore the universe of human proteins at neXtProt for SEMA4D: NX_Q92854

Explore proteomics data for SEMA4D at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn49, Asn74, Asn77, Asn139, Asn191, Asn329, Asn379, Asn419, Asn613, Asn632,
                                 Thr657, Thr663, Ser666, Thr670, Thr716, Ser722
  • Modification sites at PhosphoSitePlus

  • See SEMA4D Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001135759.1  NP_006369.3  

    ENSEMBL proteins: 
     ENSP00000344923   ENSP00000399948   ENSP00000411981   ENSP00000395222   ENSP00000446394  
     ENSP00000416523   ENSP00000405102   ENSP00000388768   ENSP00000390754   ENSP00000413352  
     ENSP00000438389   ENSP00000416747   ENSP00000405652   ENSP00000391733   ENSP00000343418  
     ENSP00000348822  
    Reactome Protein details: Q92854

    SEMA4D Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
    R&D Systems Recombinant & Natural Proteins for SEMA4D (Semaphorin 4D/CD100)
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Protein for SEMA4D
    OriGene Protein Over-expression Lysate for SEMA4D
    OriGene MassSpec for SEMA4D
    OriGene Custom Protein Services for SEMA4D
    GenScript Custom Purified and Recombinant Proteins Services for SEMA4D
    Novus Biologicals SEMA4D Protein
    Novus Biologicals SEMA4D Lysate
    Sino Biological Recombinant Protein for SEMA4D
    Sino Biological Cell Lysate for SEMA4D
    ProSpec Recombinant Protein for SEMA4D
    Cloud-Clone Corp. Proteins for SEMA4D

     
    Search eBioscience for Proteins for SEMA4D 

     
    antibodies-online proteins for SEMA4D (10 products) 

     
    antibodies-online peptides for SEMA4D

    SEMA4D Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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    Abcam antibodies for SEMA4D
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    ThermoFisher Antibodies for SEMA4D
    antibodies-online antibodies for SEMA4D (89 products) 

    SEMA4D Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for SEMA4D
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SEMA4D
    Cloud-Clone Corp. CLIAs for SEMA4D
    Search eBioscience for ELISAs for SEMA4D 
    antibodies-online kits for SEMA4D (16 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    CD: CD molecules
    IGD: Immunoglobulin superfamily / Immunoglobulin-like domain containing
    SEMA: Semaphorins

    Selected InterPro protein domains (see all 9):
     IPR002165 Plexin_repeat
     IPR013783 Ig-like_fold
     IPR027231 Semaphorin
     IPR001627 Semap_dom
     IPR007110 Ig-like_dom

    Graphical View of Domain Structure for InterPro Entry Q92854

    ProtoNet protein and cluster: Q92854

    2 Blocks protein domains:
    IPB001627 Semaphorin/CD100 antigen
    IPB003599 Immunoglobulin subtype


    UniProtKB/Swiss-Prot: SEM4D_HUMAN, Q92854
    Similarity: Belongs to the semaphorin family
    Similarity: Contains 1 Ig-like C2-type (immunoglobulin-like) domain
    Similarity: Contains 1 PSI domain
    Similarity: Contains 1 Sema domain


    Find genes that share domains with SEMA4D           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SEM4D_HUMAN, Q92854
    Function: Cell surface receptor for PLXN1B and PLXNB2 that plays an important role in cell-cell signaling.
    Promotes reorganization of the actin cytoskeleton and plays a role in axonal growth cone guidance in the
    developing central nervous system. Regulates dendrite and axon branching and morphogenesis. Promotes the
    migration of cerebellar granule cells and of endothelial cells. Plays a role in the immune system; induces
    B-cells to aggregate and improves their viability (in vitro). Promotes signaling via SRC and PTK2B/PYK2, which
    then mediates activation of phosphatidylinositol 3-kinase and of the AKT1 signaling cascade. Interaction with
    PLXNB1 mediates activation of RHOA

         Genatlas biochemistry entry for SEMA4D:
    semaphorin 4D,mostly expressed in lymphocytes and the nervous system,inducing B cell to aggregate and improving
    their viability in vitro,repellent of the nerve growth cone guidance,ligand for plexin B1 (PLXN4)

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004872receptor activity IDA15613544
    GO:0004888transmembrane signaling receptor activity IMP--
    GO:0005102receptor binding IDA11254688
    GO:0005515protein binding IPI--
    GO:0030215semaphorin receptor binding ISS--
         
    Find genes that share ontologies with SEMA4D           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SEMA4D:
     Increased G1 DNA content 

         6 MGI mutant phenotypes (inferred from 1 allele(MGI details for Sema4d):
     behavior/neurological  cardiovascular system  hematopoietic system  immune system  nervous system 
     renal/urinary system 

    Find genes that share phenotypes with SEMA4D           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Sema4dtm1Kik for SEMA4D

       genOway: Develop your customized and physiologically relevant rodent model for SEMA4D

    miRNA
    Products:
        
    miRTarBase miRNAs that target SEMA4D:
    hsa-mir-192-5p (MIRT004149), hsa-mir-484 (MIRT042320), hsa-mir-215-5p (MIRT024391), hsa-mir-1 (MIRT024017), hsa-mir-335-5p (MIRT017224), hsa-mir-25-3p (MIRT050315)

    Block miRNA regulation of human, mouse, rat SEMA4D using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SEMA4D (see all 28):
    hsa-miR-125a-5p hsa-miR-875-3p hsa-miR-137 hsa-miR-188-5p hsa-miR-4251 hsa-miR-340 hsa-miR-378b hsa-miR-877*
    SwitchGear 3'UTR luciferase reporter plasmidSEMA4D 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for SEMA4D
    Predesigned siRNA for gene silencing in human, mouse, rat SEMA4D

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for SEMA4D

    Clone
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    OriGene clones in human, mouse for SEMA4D (see all 12)
    OriGene ORF clones in mouse, rat for SEMA4D
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): SEMA4D (NM_001142287)
    Sino Biological Human cDNA Clone for SEMA4D
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SEMA4D
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SEMA4D

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for SEMA4D 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SEMA4D

    Flow Cytometry
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    eBioscience FlowRNA Probe Sets ( VA1-12606) for SEMA4D 


    (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
    SEM4D_HUMAN, Q92854: Cell membrane; Single-pass type I membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    endoplasmic reticulum3
    extracellular3
    golgi apparatus1
    mitochondrion1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615extracellular space ISS--
    GO:0005886plasma membrane TAS--
    GO:0005887integral component of plasma membrane IDA8876214
    GO:0016020membrane ----

    Find genes that share ontologies with SEMA4D           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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    SuperPaths for SEMA4D About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1Semaphorin interactions
    Sema4D in semaphorin signaling0.90
    Other semaphorin interactions0.00
    Sema4D induced cell migration and growth-cone collapse0.90
    Sema4D mediated inhibition of cell attachment and migration0.00
    Semaphorin interactions0.43
    2L1CAM interactions
    Axon guidance0.63
    Developmental Biology0.63
    3Development Slit Robo signaling
    Neurophysiological process Receptor mediated axon growth repulsion0.41
    4Semaphorin Signaling
    Semaphorin Signaling
    5Guidance Cues and Growth Cone Motility
    Guidance Cues and Growth Cone Motility


    Find genes that share SuperPaths with SEMA4D           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SEMA4D
        Guidance Cues and Growth Cone Motility
    Semaphorin Signaling

    1 GeneGo (Thomson Reuters) Pathway for SEMA4D
        Neurophysiological process Receptor-mediated axon growth repulsion


    3 Reactome Pathways for SEMA4D
        Sema4D induced cell migration and growth-cone collapse
    Other semaphorin interactions
    Sema4D mediated inhibition of cell attachment and migration


    1 Kegg Pathway  (Kegg details for SEMA4D):
        Axon guidance

        Pathway & Disease-focused RT2 Profiler PCR Array including SEMA4D: 
              Apoptosis 384HT in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SEMA4D

    STRING Interaction Network Preview (showing 5 interactants - click image to see 18)

    Selected Interacting proteins for SEMA4D (Q928542, 3 ENSP000003434184) via UniProtKB, MINT, STRING, and/or I2D (see all 18)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PTPRCP085752, 3, ENSP000003563464MINT-8312043 I2D: score=3 STRING: ENSP00000356346
    PLXNB1O431573, ENSP000002964404I2D: score=3 STRING: ENSP00000296440
    CD72P218543, ENSP000002596334I2D: score=3 STRING: ENSP00000259633
    ARHGAP35ENSP000003857204STRING: ENSP00000385720
    ARHGEF11ENSP000003571774STRING: ENSP00000357177
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 23):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IMP--
    GO:0001934positive regulation of protein phosphorylation IDA16055703
    GO:0006955immune response TAS8876214
    GO:0007155cell adhesion TAS8876214
    GO:0007275multicellular organismal development ----

    Find genes that share ontologies with SEMA4D           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 SEMA4D (SEM4D)

    3 Novoseek inferred chemical compound relationships for SEMA4D gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    phosphatidylinositol 34.4 2 12565860 (1)
    tyrosine 34.1 4 19805522 (2), 15210733 (1), 12906260 (1)
    serine 0 3 11254687 (2), 12906260 (1)



    Find genes that share compounds with SEMA4D           About GenesLikeMe



    (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 SEMA4D gene (3 alternative transcripts): 
    NM_182635.1  NM_001142287.1  NM_006378.3  

    Unigene Cluster for SEMA4D:

    Sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D
    Hs.494406  [show with all ESTs]
    Unigene Representative Sequence: AB210030
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 25):
    ENST00000339861 ENST00000492386(uc004aql.2) ENST00000420101 ENST00000475255
    ENST00000469653(uc004aqm.2) ENST00000455551 ENST00000429836 ENST00000537934
    ENST00000450295 ENST00000438547(uc004aqo.1) ENST00000422704 ENST00000486935
    ENST00000540183 ENST00000544513 ENST00000474258 ENST00000420681 ENST00000433650
    ENST00000540475
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SEMA4D (see all 28):
    hsa-miR-125a-5p hsa-miR-875-3p hsa-miR-137 hsa-miR-188-5p hsa-miR-4251 hsa-miR-340 hsa-miR-378b hsa-miR-877*
    SwitchGear 3'UTR luciferase reporter plasmidSEMA4D 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SEMA4D
    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): SEMA4D (NM_001142287)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SEMA4D
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SEMA4D
    Primer
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    OriGene qPCR primer pairs and template standards for SEMA4D
    OriGene qSTAR qPCR primer pairs in human, mouse for SEMA4D
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SEMA4D
      QuantiTect SYBR Green Assays in human, mouse, rat SEMA4D
      QuantiFast Probe-based Assays in human, mouse, rat SEMA4D
    Flow Cytometry
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    eBioscience FlowRNA Probe Sets ( VA1-12606) for SEMA4D 

    Additional mRNA sequence: 

    AB210030.1 AJ420442.1 AK090804.1 AK091601.1 AK128342.1 AK316107.1 BC054500.1 BC137515.1 
    BC137518.1 BX648216.1 U60800.1 

    16 DOTS entries:

    DT.100707088  DT.425505  DT.216746  DT.99939187  DT.40222164  DT.101981557  DT.99933126  DT.100745499 
    DT.91763078  DT.95118872  DT.95275724  DT.95364573  DT.99939987  DT.121145382  DT.95299118  DT.99969380 

    Selected AceView cDNA sequences (see all 229):

    AA776123 AA262446 AA987949 AA987971 BM312188 BG055243 BI761171 BX094225 
    AA983707 AA631749 AW958939 AI310454 AA757508 BU737916 AA736830 BX109801 
    AI796993 AA435602 AA297504 AI055975 AA742319 AI094654 AK090804 T36191 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SEMA4D (see all 8)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22a · 22b ^
    SP1:                          -     -     -     -                 -                                                                                   -         
    SP2:        -     -           -     -     -     -     -     -     -                                                                                   -         
    SP3:                                                              -                                                                                   -         
    SP4:              -           -     -     -     -     -           -                                                                                             
    SP5:                                -     -     -     -           -                                                                                             

    ExUns: 23 ^ 24a · 24b
    SP1:                  
    SP2:                  
    SP3:                  
    SP4:                  
    SP5:                  


    ECgene alternative splicing isoforms for SEMA4D

    (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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    SEMA4D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SEMA4D Expression
    About this image


    SEMA4D expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Umbilical Cord (Extraembryonic Tissues)
             Umbilical Veins
    SEMA4D Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SEMA4D Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.494406

    UniProtKB/Swiss-Prot: SEM4D_HUMAN, Q92854
    Tissue specificity: Strongly expressed in skeletal muscle, peripheral blood lymphocytes, spleen, and thymus and
    also expressed at lower levels in testes, brain, kidney, small intestine, prostate, heart, placenta, lung and
    pancreas, but not in colon and liver

        Pathway & Disease-focused RT2 Profiler PCR Array including SEMA4D: 
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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 SEMA4D gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sema4d1 , 5 sema domain, immunoglobulin domain (Ig), transmembrane more1, 5 82.89(n)1
    85.6(a)1
      13 (26.16 cM)5
    203541  NM_013660.41  NP_038688.21 
     517012465 
    chicken
    (Gallus gallus)
    Aves SEMA4D1 sema domain, immunoglobulin domain (Ig), transmembrane more 68.17(n)
    69.6(a)
      396331  XM_424426.4  XP_424426.4 
    lizard
    (Anolis carolinensis)
    Reptilia SEMA4D6
    sema domain, immunoglobulin domain (Ig), transmemb...
    67(a)
    1 ↔ 1
    2(36783021-36808585)
    African clawed frog
    (Xenopus laevis)
    Amphibia BU916292.12   -- 76.71(n)    BU916292.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sema4d1 sema domain, immunoglobulin domain (Ig), transmembrane more 57.33(n)
    51.6(a)
      100333323  XM_003200811.2  XP_003200859.2 


    ENSEMBL Gene Tree for SEMA4D (if available)
    TreeFam Gene Tree for SEMA4D (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SEMA4D gene
    SEMA3C2  SEMA4F2  SEMA3E2  SEMA4B2  SEMA4C2  SEMA3F2  SEMA4A2  SEMA4G2  
    SEMA3A2  SEMA3G2  SEMA3D2  
    Selected SIMAP similar genes for SEMA4D using alignment to 6 protein entries:     SEM4D_HUMAN (see all proteins) (see all similar genes):
    SEMA4D variant protein    SEMA6D    DKFZp686A04130    SEMA4G    SEMA4C    SEMA4B
    SEMA4F    DKFZp686D04248    SEMA4A    SEMA3A    SEMA6A    SEMA6C
    SEMA3F    SEMA3C    SEMA3B    SEMA3D    SEMA3E    SEMA5B

    Find genes that share paralogs with SEMA4D           About GenesLikeMe



    (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 SEMA4D (see all 2977)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs764148131,2
    F--91853524(+) AGTAAA/GTAGCA 1 -- int12Minor allele frequency- G:0.03CSA WA 120
    rs1430259221,2
    --91853537(+) TTGTGA/GTAAGT 1 -- int10--------
    rs1137471801,2
    F--91853722(+) TCTAGG/TTCTGT 1 -- int11Minor allele frequency- T:0.50CSA 2
    rs1413332261,2
    --91853728(+) TCTGTC/GATATT 1 -- int10--------
    rs1911908351,2
    --91853903(+) GAGGCC/TACTGC 1 -- int10--------
    rs1507793861,2
    --91853975(+) CCAGGA/GGCGCC 1 -- int10--------
    rs1134748061,2
    C--91853990(+) CAGTCATT/-ATTTA 1 -- cds11Minor allele frequency- -:0.50CSA 2
    rs1381334541,2
    C--91854058(+) AAATTC/TATCCT 1 -- ut310--------
    rs1831539741,2
    --91854110(+) CTTCAA/GGTATG 1 -- ut310--------
    rs1112998041,2
    C,F--91854188(+) CAAGAA/GTATAA 1 -- ut312Minor allele frequency- G:0.05CSA WA 120

    HapMap Linkage Disequilibrium report for SEMA4D (91975702 - 92113045 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SEMA4D (see all 20):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2738731CNV Deletion23290073
    esv2668286CNV Deletion23128226
    esv2738734CNV Deletion23290073
    esv2294805CNV Deletion18987734
    esv2738736CNV Deletion23290073
    esv2738728CNV Deletion23290073
    esv3490CNV Deletion18987735
    esv2738730CNV Deletion23290073
    esv2738735CNV Deletion23290073
    esv2738733CNV Deletion23290073

    Human Gene Mutation Database (HGMD): SEMA4D
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SEMA4D
    DNA2.0 Custom Variant and Variant Library Synthesis for SEMA4D

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601866    OMIM disorders: --


    Find genes that share disorders with SEMA4D           About GenesLikeMe

    4 Novoseek inferred disease relationships for SEMA4D gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    demyelination 26.7 1 14707103 (1)
    carcinoma squamous cell 20.2 4 16754882 (1), 19762474 (1), 17204469 (1)
    cancer 13.1 5 18559453 (1), 17204469 (1), 19805522 (1), 16055703 (1) (see all 5)
    tumors 4.95 16 18559453 (4), 19762474 (3), 16754882 (1), 15569615 (1) (see all 5)

    Genetic Association Database (GAD): SEMA4D
    Human Genome Epidemiology (HuGE) Navigator: SEMA4D (3 documents)

    Export disorders for SEMA4D 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)
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    PubMed articles for SEMA4D gene, integrated from 10 sources (see all 82):
    (articles sorted by number of sources associating them with SEMA4D)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human CD100, a novel leukocyte semaphorin that promotes B-cell aggregation and differentiation. (PubMed id 8876214)1, 2, 3, 9 Hall K.T.... Freeman G.J. (Proc. Natl. Acad. Sci. U.S.A. 1996)
    2. Semaphorin 4D/plexin-B1 induces endothelial cell migration through the activation of PYK2, Src, and the phosphatidylinositol 3-kinase-Akt pathway. (PubMed id 16055703)1, 2, 9 Basile J.R.... Gutkind J.S. (Mol. Cell. Biol. 2005)
    3. Plexins are a large family of receptors for transmembrane, secreted and GPI-anchored semaphorins in vertebrates. (PubMed id 10520995)1, 2, 9 Tamagnone L.... Comoglio P.M. (Cell 1999)
    4. Candidate gene analysis of semaphorins in patients with Alzheimer's disease. (PubMed id 19957197)1, 4 Villa C....Galimberti D. (Neurol. Sci. 2010)
    5. Structural basis of semaphorin-plexin signalling. (PubMed id 20877282)1, 2 Janssen B.J.... Jones E.Y. (Nature 2010)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    7. The semaphorin 4D-plexin-B signalling complex regulates dendritic and axonal complexity in developing neurons via diverse pathways. (PubMed id 19788569)1, 2 Vodrazka P.... Kuner R. (Eur. J. Neurosci. 2009)
    8. Elucidation of N-glycosylation sites on human platelet proteins: a glycoproteomic approach. (PubMed id 16263699)1, 2 Lewandrowski U.... Sickmann A. (Mol. Cell. Proteomics 2006)
    9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    10. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 10507 HGNC: 10732 AceView: SEMA4D Ensembl:ENSG00000187764 euGenes: HUgn10507
    ECgene: SEMA4D Kegg: 10507 H-InvDB: SEMA4D

    (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 SEMA4D Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SEMA4D Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SEMA4D gene:
    Search GeneIP for patents involving SEMA4D

    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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