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Aliases for SEMA4D Gene

Aliases for SEMA4D Gene

  • Semaphorin 4D 2 3 5
  • 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
  • Semaphorin-4D 3
  • 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 (Semaphorin 4D) is a Protein Coding gene. Diseases associated with SEMA4D include Hemorrhagic Fever With Renal Syndrome and Osteonecrosis Of The Jaw. Among its related pathways are Semaphorin interactions and Development Slit-Robo signaling. GO annotations related to this gene include receptor binding and transmembrane signaling receptor activity. An important paralog of this gene is SEMA4B.

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

Additional gene information for SEMA4D Gene

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

Genomics for SEMA4D Gene

Regulatory Elements for SEMA4D Gene

Enhancers for SEMA4D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09H089417 1.8 FANTOM5 Ensembl ENCODE dbSUPER 24 +74.2 74181 12 HDGF PKNOX1 TBL1XR1 KLF17 BMI1 BATF RAD21 ETS1 HSF1 ZNF143 SEMA4D CKS2 SECISBP2 S1PR3 C9orf47 PA2G4P6 PIR43063
GH09H089439 1.6 FANTOM5 Ensembl ENCODE dbSUPER 21.7 +55.1 55103 6 MXI1 KLF1 MAX EBF1 ZIC2 ZFHX2 POLR2A EED FOS ETV6 SEMA4D PA2G4P6 PIR43063
GH09H089518 1.8 FANTOM5 Ensembl ENCODE dbSUPER 18.4 -24.9 -24943 9 HDGF PKNOX1 TBL1XR1 RB1 SIN3A BATF BRCA1 RFX5 SMARCC2 RCOR1 SECISBP2 SEMA4D SHC3 LOC105376137
GH09H089405 1.3 Ensembl ENCODE dbSUPER 22.3 +89.6 89617 6 SIN3A BATF RAD21 ZNF143 ZNF207 ATF7 ETV6 RUNX3 CREM IKZF2 SEMA4D SECISBP2 PA2G4P6 PIR43063
GH09H089433 1.3 Ensembl ENCODE dbSUPER 21.1 +62.1 62084 4 KLF1 SIN3A MAX CEBPG E2F1 ZFHX2 CTBP1 GATA3 POLR2A FOS SEMA4D SECISBP2 PA2G4P6 PIR43063
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEMA4D on UCSC Golden Path with GeneCards custom track

Promoters for SEMA4D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000237531 430 1401 HDGF SIN3A YBX1 GLI4 GLIS2 ZNF366 SCRT2 ATF7 ZNF391 RUNX3

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

Genes around SEMA4D on UCSC Golden Path with GeneCards custom track

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

Post-translational modifications for SEMA4D Gene

  • Glycosylation at Asn49, Asn74, isoforms=277, isoforms=2139, isoforms=2191, Asn329, Asn379, Asn419, isoforms=613, Asn632, isoforms=657, Thr663, and isoforms=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

Gene Families for SEMA4D Gene

HGNC:
Human Protein Atlas (HPA):
  • CD markers
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

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 :
  • Belongs to the semaphorin family.
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.

Phenotypes From GWAS Catalog for SEMA4D Gene

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

  • Taconic Biosciences Mouse Models for SEMA4D

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SEMA4D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
  • R&D Systems cDNA Clones for SEMA4D (Semaphorin 4D/CD100)

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SEMA4D gene
Compartment Confidence
plasma membrane 5
extracellular 4
endoplasmic reticulum 3
cytoskeleton 1
mitochondrion 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SEMA4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA,ISS --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IDA 8876214
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
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

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:0001934 positive regulation of protein phosphorylation IDA 16055703
GO:0006955 immune response TAS 8876214
GO:0007155 cell adhesion TAS 8876214
GO:0007162 negative regulation of cell adhesion IDA 15218527
genes like me logo Genes that share ontologies with SEMA4D: view

Drugs & Compounds for SEMA4D Gene

(6) Drugs for SEMA4D Gene - From: ClinicalTrials, DGIdb, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Antibodies Pharma 6725
Antibodies, Monoclonal Pharma 4265
Immunoglobulins Pharma 6713
VX15/2503 VACCINE Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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

Clone Products

  • Applied Biological Materials Clones for SEMA4D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
  • R&D Systems cDNA Clones for SEMA4D (Semaphorin 4D/CD100)

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for SEMA4D Gene



Protein tissue co-expression partners for SEMA4D Gene

NURSA nuclear receptor signaling pathways regulating expression of SEMA4D Gene:

SEMA4D

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.

Evidence on tissue expression from TISSUES for SEMA4D Gene

  • Nervous system(4.9)
  • Blood(4.6)
  • Intestine(4.3)
  • Eye(4.1)
  • Lymph node(2.5)
  • Spleen(2.2)
genes like me logo Genes that share expression patterns with SEMA4D: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA4D Gene

Orthologs for SEMA4D Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA4D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA4D 33 34
  • 99.65 (n)
mouse
(Mus musculus)
Mammalia Sema4d 33 16 34
  • 82.89 (n)
rat
(Rattus norvegicus)
Mammalia Sema4d 33
  • 82.21 (n)
dog
(Canis familiaris)
Mammalia SEMA4D 33 34
  • 82.05 (n)
oppossum
(Monodelphis domestica)
Mammalia SEMA4D 34
  • 75 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA4D 34
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA4D 34
  • 36 (a)
OneToOne
chicken
(Gallus gallus)
Aves SEMA4D 33 34
  • 68.17 (n)
lizard
(Anolis carolinensis)
Reptilia SEMA4D 34
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.20164 33
zebrafish
(Danio rerio)
Actinopterygii sema4d 33
  • 57.33 (n)
SEMA4D 34
  • 48 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG4383 35
  • 29 (a)
Sema-2a 35
  • 29 (a)
Species where no ortholog for SEMA4D was found in the sources mined by GeneCards:
  • 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

Variants for SEMA4D Gene

Sequence variations from dbSNP and Humsavar for SEMA4D Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000007036 -- 89,494,634(+) AGGGA(G/T)GAATT intron-variant
rs1000008314 -- 89,432,352(+) AGGAC(C/T)CTGGG intron-variant
rs1000009548 -- 89,474,878(+) AATAG(C/G)GGTCC intron-variant
rs1000009939 -- 89,477,981(+) AAGCA(A/G)AGAGT intron-variant, upstream-variant-2KB
rs1000031902 -- 89,396,118(+) CAGAG(A/G)CCGGA intron-variant

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

Variant ID Type Subtype PubMed ID
esv2294805 CNV deletion 18987734
esv2629900 CNV insertion 19546169
esv2662702 CNV deletion 23128226
esv2668286 CNV deletion 23128226
esv2738727 CNV deletion 23290073
esv2738728 CNV deletion 23290073
esv2738730 CNV deletion 23290073
esv2738731 CNV deletion 23290073
esv2738732 CNV deletion 23290073
esv2738733 CNV deletion 23290073
esv2738734 CNV deletion 23290073
esv2738735 CNV deletion 23290073
esv2738736 CNV deletion 23290073
esv29434 CNV gain+loss 19812545
esv3395094 CNV duplication 20981092
esv3490 CNV loss 18987735
esv3621014 CNV gain 21293372
esv3621027 CNV loss 21293372
esv7634 CNV gain 19470904
nsv1041327 CNV gain 25217958
nsv1142706 CNV deletion 24896259
nsv1147032 CNV deletion 26484159
nsv1154135 CNV duplication 26484159
nsv415790 CNV deletion 16902084
nsv510200 OTHER sequence alteration 20534489
nsv517495 CNV loss 19592680
nsv968724 CNV duplication 23825009

Variation tolerance for SEMA4D Gene

Residual Variation Intolerance Score: 28.8% 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

Human Gene Mutation Database (HGMD)
SEMA4D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA4D

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

Disorders for SEMA4D Gene

MalaCards: The human disease database

(2) MalaCards diseases for SEMA4D Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hemorrhagic fever with renal syndrome
  • hemorrhagic fever, russian
osteonecrosis of the jaw
- elite association - COSMIC cancer census association via MalaCards

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 KT … Freeman GJ (Proceedings of the National Academy of Sciences of the United States of America 1996) 2 3 4 22 60
  2. Semaphorin 4D/plexin-B1 induces endothelial cell migration through the activation of PYK2, Src, and the phosphatidylinositol 3-kinase-Akt pathway. (PMID: 16055703) Basile JR … Gutkind JS (Molecular and cellular biology 2005) 3 4 22 60
  3. Plexins are a large family of receptors for transmembrane, secreted, and GPI-anchored semaphorins in vertebrates. (PMID: 10520995) Tamagnone L … Comoglio PM (Cell 1999) 3 4 22 60
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  5. Structural basis of semaphorin-plexin signalling. (PMID: 20877282) Janssen BJ … Jones EY (Nature 2010) 3 4 60

Products for SEMA4D Gene

Sources for SEMA4D Gene

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