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Aliases for SEMA4D Gene

Aliases for SEMA4D Gene

  • Sema Domain, Immunoglobulin Domain (Ig), Transmembrane Domain (TM) And Short Cytoplasmic Domain, (Semaphorin) 4D 2 3
  • C9orf164 3 4
  • SEMAJ 3 4
  • CD100 3 4
  • BB18 3 4
  • GR3 3 4
  • A8 3 4
  • Sema Domain, Immunoglobulin Domain (Ig), Transmembrane Domain (TM) And Short Cytoplasmic Domain, 4D 3
  • Chromosome 9 Open Reading Frame 164 2
  • CD100 Antigen 4
  • M-Sema G 2
  • M-Sema-G 3
  • Coll-4 3

External Ids for SEMA4D Gene

Previous HGNC Symbols for SEMA4D Gene

  • SEMAJ
  • C9orf164

Previous GeneCards Identifiers for SEMA4D Gene

  • GC09U990094
  • GC09M083868
  • GC09M085576
  • GC09M9O0142
  • GC09M089221
  • GC09M091181
  • GC09M091975
  • GC09M061809

Summaries for SEMA4D Gene

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. Diseases associated with SEMA4D include hemorrhagic fever with renal syndrome. Among its related pathways are Developmental Biology and Guidance Cues and Growth Cone Motility. GO annotations related to this gene include receptor binding and transmembrane signaling receptor activity. An important paralog of this gene is SEMA4G.

UniProtKB/Swiss-Prot for SEMA4D Gene

  • 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

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA4D Gene

Genomics for SEMA4D Gene

Regulatory Elements for SEMA4D Gene

Genomic Location for SEMA4D Gene

Chromosome:
9
Start:
89,360,787 bp from pter
End:
89,498,130 bp from pter
Size:
137,344 bases
Orientation:
Minus strand

Genomic View for SEMA4D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SEMA4D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA4D Gene

Proteins for SEMA4D Gene

  • Protein details for SEMA4D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92854-SEM4D_HUMAN
    Recommended name:
    Semaphorin-4D
    Protein Accession:
    Q92854
    Secondary Accessions:
    • B2RPM6
    • Q7Z5S4
    • Q8N8B0

    Protein attributes for SEMA4D Gene

    Size:
    862 amino acids
    Molecular mass:
    96150 Da
    Quaternary structure:
    • Homodimer. Interacts with PLXNB2 (By similarity). Binds PLXNB1.
    SequenceCaution:
    • Sequence=AAI37516.1; Type=Miscellaneous discrepancy; Note=Cloning artifact.; Evidence={ECO:0000305}; Sequence=AAI37519.1; Type=Miscellaneous discrepancy; Note=Cloning artifact.; Evidence={ECO:0000305}; Sequence=BAC04938.1; Type=Miscellaneous discrepancy; Note=Cloning artifact.; Evidence={ECO:0000305}; Sequence=CAI95794.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SEMA4D Gene

    Alternative splice isoforms for SEMA4D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA4D Gene

Proteomics data for SEMA4D Gene at MOPED

Post-translational modifications for SEMA4D Gene

  • Glycosylation at Asn 49, Asn 74, Asn 77, Asn 139, Asn 191, Asn 329, Asn 379, Asn 419, Asn 613, Asn 632, Thr 657, Thr 663, and Ser 722
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for SEMA4D (Semaphorin 4D/CD100)

No data available for DME Specific Peptides for SEMA4D Gene

Domains & Families for SEMA4D Gene

Suggested Antigen Peptide Sequences for SEMA4D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q92854

UniProtKB/Swiss-Prot:

SEM4D_HUMAN :
  • Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
  • Belongs to the semaphorin family.
Domain:
  • Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
  • Contains 1 PSI domain.
  • Contains 1 Sema domain.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA4D: view

Function for SEMA4D Gene

Molecular function for SEMA4D Gene

GENATLAS Biochemistry:
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)
UniProtKB/Swiss-Prot 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 Ontology (GO) - Molecular Function for SEMA4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity IDA 15613544
GO:0004888 transmembrane signaling receptor activity IMP 20877282
GO:0005102 receptor binding IDA 11254688
GO:0005515 protein binding IPI 20877282
GO:0030215 semaphorin receptor binding ISS --
genes like me logo Genes that share ontologies with SEMA4D: view
genes like me logo Genes that share phenotypes with SEMA4D: view

Animal Models for SEMA4D Gene

MGI Knock Outs for SEMA4D:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SEMA4D

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SEMA4D Gene

Localization for SEMA4D Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA4D Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SEMA4D Gene COMPARTMENTS Subcellular localization image for SEMA4D gene
Compartment Confidence
plasma membrane 5
extracellular 3
endoplasmic reticulum 2

Gene Ontology (GO) - Cellular Components for SEMA4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space ISS --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IDA 8876214
GO:0016020 membrane --
genes like me logo Genes that share ontologies with SEMA4D: view

Pathways & Interactions for SEMA4D Gene

genes like me logo Genes that share pathways with SEMA4D: view

Pathways by source for SEMA4D Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

SIGNOR curated interactions for SEMA4D Gene

Activates:

Gene Ontology (GO) - Biological Process for SEMA4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IMP 22019888
GO:0001755 neural crest cell migration IBA --
GO:0001934 positive regulation of protein phosphorylation IDA 16055703
GO:0006955 immune response TAS 8876214
GO:0007155 cell adhesion TAS 8876214
genes like me logo Genes that share ontologies with SEMA4D: view

Drugs & Compounds for SEMA4D Gene

(3) Drugs for SEMA4D Gene - From: DGIdb and NovoSeek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
VX15/2503 VACCINE Pharma 0
serine Nutra 420
tyrosine Nutra 547

(1) Additional Compounds for SEMA4D Gene - From: NovoSeek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Phosphatidylinositol
genes like me logo Genes that share compounds with SEMA4D: view

Transcripts for SEMA4D Gene

Unigene Clusters for SEMA4D Gene

Sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SEMA4D

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA4D Gene

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: - - - - -
SP6:
SP7:
SP8:

ExUns: 23 ^ 24a · 24b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for SEMA4D Gene

GeneLoc Exon Structure for
SEMA4D
ECgene alternative splicing isoforms for
SEMA4D

Expression for SEMA4D Gene

mRNA expression in normal human tissues for SEMA4D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA4D Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x8.0) and Whole Blood (x6.1).

Protein differential expression in normal tissues from HIPED for SEMA4D Gene

This gene is overexpressed in Lymph node (22.1), CD8 Tcells (11.8), Frontal cortex (10.2), and Peripheral blood mononuclear cells (9.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SEMA4D Gene



SOURCE GeneReport for Unigene cluster for SEMA4D Gene Hs.494406

mRNA Expression by UniProt/SwissProt for SEMA4D Gene

Q92854-SEM4D_HUMAN
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.
genes like me logo Genes that share expression patterns with SEMA4D: view

Protein tissue co-expression partners for SEMA4D Gene

Primer Products

In Situ Assay Products

Orthologs for SEMA4D Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA4D Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia SEMA4D 35
  • 82.05 (n)
  • 79.86 (a)
SEMA4D 36
  • 70 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema4d 35
  • 82.89 (n)
  • 85.6 (a)
Sema4d 16
Sema4d 36
  • 86 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SEMA4D 35
  • 99.65 (n)
  • 99.54 (a)
SEMA4D 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema4d 35
  • 82.21 (n)
  • 84.92 (a)
cow
(Bos Taurus)
Mammalia SEMA4D 36
  • 71 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SEMA4D 36
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA4D 36
  • 36 (a)
OneToOne
chicken
(Gallus gallus)
Aves SEMA4D 35
  • 68.17 (n)
  • 69.6 (a)
SEMA4D 36
  • 61 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA4D 36
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.20164 35
zebrafish
(Danio rerio)
Actinopterygii sema4d 35
  • 57.33 (n)
  • 51.6 (a)
SEMA4D 36
  • 48 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG4383 37
  • 29 (a)
Sema-2a 37
  • 29 (a)
Species with no ortholog for SEMA4D:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SEMA4D Gene

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

Paralogs for SEMA4D Gene

genes like me logo Genes that share paralogs with SEMA4D: view

Variants for SEMA4D Gene

Sequence variations from dbSNP and Humsavar for SEMA4D Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type MAF
rs4304417 -- 89,488,201(+) tggta(C/T)caaca intron-variant
rs4317671 -- 89,443,227(+) TGGAC(A/G)GAGGC intron-variant
rs4320636 -- 89,480,903(+) ATGCC(C/G)CCAAA upstream-variant-2KB, intron-variant
rs4330779 -- 89,434,559(+) CCAGC(A/G)TAGCA intron-variant
rs4360376 -- 89,459,514(+) GTGAG(A/C)AACAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SEMA4D Gene

Variant ID Type Subtype PubMed ID
esv29434 CNV Gain+Loss 19812545
esv7634 CNV Gain 19470904
esv2738727 CNV Deletion 23290073
esv2668286 CNV Deletion 23128226
esv2738728 CNV Deletion 23290073
esv2738730 CNV Deletion 23290073
esv2294805 CNV Deletion 18987734
esv2738731 CNV Deletion 23290073
esv2738732 CNV Deletion 23290073
nsv517495 CNV Loss 19592680
nsv510200 CNV Loss 20534489
esv2738733 CNV Deletion 23290073
esv2738734 CNV Deletion 23290073
nsv893558 CNV Gain 21882294
esv2629900 CNV Insertion 19546169
esv2738735 CNV Deletion 23290073
esv3490 CNV Deletion 18987735
esv2662702 CNV Deletion 23128226
esv2738736 CNV Deletion 23290073
nsv415790 CNV Loss 16902084

Variation tolerance for SEMA4D Gene

Residual Variation Intolerance Score: 28.79% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.89; 91.85% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SEMA4D Gene

HapMap Linkage Disequilibrium report
SEMA4D
Human Gene Mutation Database (HGMD)
SEMA4D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA4D Gene

Disorders for SEMA4D Gene

MalaCards: The human disease database

(1) MalaCards diseases for SEMA4D Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hemorrhagic fever with renal syndrome
  • hfrs
- elite association

Relevant External Links for SEMA4D

Genetic Association Database (GAD)
SEMA4D
Human Genome Epidemiology (HuGE) Navigator
SEMA4D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEMA4D
genes like me logo Genes that share disorders with SEMA4D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA4D Gene

Publications for SEMA4D Gene

  1. Human CD100, a novel leukocyte semaphorin that promotes B-cell aggregation and differentiation. (PMID: 8876214) Hall K.T. … Freeman G.J. (Proc. Natl. Acad. Sci. U.S.A. 1996) 2 23 67
  2. Protein tyrosine phosphatase SHP2 is involved in Semaphorin 4D-induced axon repulsion. (PMID: 19433062) Fuchikawa T. … Goshima Y. (Biochem. Biophys. Res. Commun. 2009) 23 67
  3. Plexin-B1 is a GTPase activating protein for M-Ras, remodelling dendrite morphology. (PMID: 19444311) Saito Y. … Negishi M. (EMBO Rep. 2009) 23 67
  4. Semaphorin 4D signaling requires the recruitment of phospholipase C gamma into the plexin-B1 receptor complex. (PMID: 19805522) Swiercz J.M. … Offermanns S. (Mol. Cell. Biol. 2009) 23 67
  5. Hypoxia-inducible factor-1-mediated regulation of semaphorin 4D affects tumor growth and vascularity. (PMID: 19762474) Sun Q. … Basile J.R. (J. Biol. Chem. 2009) 23 67

Products for SEMA4D Gene

Sources for SEMA4D Gene

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