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Aliases for SEMA4A Gene

Aliases for SEMA4A Gene

  • Semaphorin 4A 2 3 5
  • Sema Domain, Immunoglobulin Domain (Ig), Transmembrane Domain (TM) And Short Cytoplasmic Domain, (Semaphorin) 4A 2 3
  • Semaphorin-B 3 4
  • Sema B 3 4
  • SEMAB 3 4
  • SEMB 3 4
  • Semaphorin-4A 3
  • CORD10 3
  • RP35 3

External Ids for SEMA4A Gene

Previous HGNC Symbols for SEMA4A Gene

  • SEMAB

Previous GeneCards Identifiers for SEMA4A Gene

  • GC00U990481
  • GC01P153341
  • GC01P152934
  • GC01P154386
  • GC01P127481

Summaries for SEMA4A Gene

Entrez Gene Summary for SEMA4A Gene

  • This gene encodes a member of the semaphorin family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass type I membrane protein containing an immunoglobulin-like C2-type domain, a PSI domain and a sema domain. It inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. It is an activator of T-cell-mediated immunity and suppresses vascular endothelial growth factor (VEGF)-mediated endothelial cell migration and proliferation in vitro and angiogenesis in vivo. Mutations in this gene are associated with retinal degenerative diseases including retinitis pigmentosa type 35 (RP35) and cone-rod dystrophy type 10 (CORD10). Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]

GeneCards Summary for SEMA4A Gene

SEMA4A (Semaphorin 4A) is a Protein Coding gene. Diseases associated with SEMA4A include Cone-Rod Dystrophy 10 and Retinitis Pigmentosa 35. Among its related pathways are Developmental Biology and Semaphorin interactions. GO annotations related to this gene include receptor activity. An important paralog of this gene is SEMA4B.

UniProtKB/Swiss-Prot for SEMA4A Gene

  • Cell surface receptor for PLXNB1, PLXNB2, PLXNB3 and PLXND1 that plays an important role in cell-cell signaling. Plays a role in priming antigen-specific T-cells, promotes differentiation of Th1 T-helper cells, and thereby contributes to adaptive immunity. Promotes phosphorylation of TIMD2. Inhibits angiogenesis. Promotes axon growth cone collapse. Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons (By similarity).

Gene Wiki entry for SEMA4A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA4A Gene

Genomics for SEMA4A Gene

Regulatory Elements for SEMA4A Gene

Enhancers for SEMA4A 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
GH01G156180 1.3 Ensembl ENCODE 50.3 +36.2 36233 7.0 HDGF PKNOX1 ATF1 FOXA2 MLX ARID4B DMAP1 TCF12 ZNF121 CAVIN1 SEMA4A BGLAP PAQR6 SLC25A44 GC01M156192 GC01P156159 GC01P156160
GH01G156225 1.3 Ensembl ENCODE 20.6 +78.4 78401 0.7 HDGF FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZNF48 YY1 SLC25A44 SEMA4A ENSG00000252236 MEX3A LMNA GLMP UBQLN4 LAMTOR2 PMF1 BGLAP
GH01G156220 1.1 dbSUPER 21.2 +75.3 75293 3.9 HDGF FOXA2 PKNOX1 ARNT CREB3L1 ARID4B SIN3A ZNF2 YY1 ZNF766 SLC25A44 SEMA4A ENSG00000252236 MEX3A LMNA GLMP UBQLN4 LAMTOR2 TSACC CCT3
GH01G156281 1.8 FANTOM5 ENCODE dbSUPER 10.8 +135.9 135899 4.4 MLX CREB3L1 ZFP64 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 GLMP SMG5 SLC25A44 PAQR6 BGLAP ENSG00000252236 SEMA4A TSACC CCT3 KIAA0907
GH01G156212 1.4 ENCODE dbSUPER 9.5 +66.2 66198 2.8 HDGF PKNOX1 FOXA2 CREB3L1 MLX AGO1 SIN3A ARID4B FEZF1 DMAP1 SLC25A44 SEMA4A PAQR6 GBAP1 PMF1 BGLAP
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEMA4A on UCSC Golden Path with GeneCards custom track

Genomic Location for SEMA4A Gene

Chromosome:
1
Start:
156,147,359 bp from pter
End:
156,177,752 bp from pter
Size:
30,394 bases
Orientation:
Plus strand

Genomic View for SEMA4A Gene

Genes around SEMA4A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA4A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA4A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA4A Gene

Proteins for SEMA4A Gene

  • Protein details for SEMA4A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H3S1-SEM4A_HUMAN
    Recommended name:
    Semaphorin-4A
    Protein Accession:
    Q9H3S1
    Secondary Accessions:
    • B2RDH8
    • B3KR76
    • Q5TCI5
    • Q5TCJ6
    • Q8WUA9

    Protein attributes for SEMA4A Gene

    Size:
    761 amino acids
    Molecular mass:
    83574 Da
    Quaternary structure:
    • Interacts with PLXNB1, PLXNB2, PLXNB3 and PLXND1. Probable ligand for TIMD2 (By similarity).

    Alternative splice isoforms for SEMA4A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA4A Gene

Post-translational modifications for SEMA4A Gene

  • Ubiquitination at Lys219 and isoforms=2535
  • Glycosylation at Asn120, Asn135, Asn496, and Asn607
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for SEMA4A (Semaphorin 4A)

No data available for DME Specific Peptides for SEMA4A Gene

Domains & Families for SEMA4A Gene

Gene Families for SEMA4A Gene

Suggested Antigen Peptide Sequences for SEMA4A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H3S1

UniProtKB/Swiss-Prot:

SEM4A_HUMAN :
  • Belongs to the semaphorin family.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA4A: view

Function for SEMA4A Gene

Molecular function for SEMA4A Gene

UniProtKB/Swiss-Prot Function:
Cell surface receptor for PLXNB1, PLXNB2, PLXNB3 and PLXND1 that plays an important role in cell-cell signaling. Plays a role in priming antigen-specific T-cells, promotes differentiation of Th1 T-helper cells, and thereby contributes to adaptive immunity. Promotes phosphorylation of TIMD2. Inhibits angiogenesis. Promotes axon growth cone collapse. Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons (By similarity).

Gene Ontology (GO) - Molecular Function for SEMA4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17318185
genes like me logo Genes that share ontologies with SEMA4A: view
genes like me logo Genes that share phenotypes with SEMA4A: view

Human Phenotype Ontology for SEMA4A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SEMA4A Gene

MGI Knock Outs for SEMA4A:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA4A

CRISPR Products

miRNA for SEMA4A Gene

miRTarBase miRNAs that target SEMA4A

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SEMA4A Gene

Localization for SEMA4A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA4A 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 SEMA4A gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytosol 5
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SEMA4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SEMA4A: view

Pathways & Interactions for SEMA4A Gene

genes like me logo Genes that share pathways with SEMA4A: view

Pathways by source for SEMA4A Gene

1 KEGG pathway for SEMA4A Gene

Gene Ontology (GO) - Biological Process for SEMA4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IEA --
GO:0002250 adaptive immune response IEA --
GO:0002292 T cell differentiation involved in immune response IEA --
GO:0002376 immune system process IEA --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with SEMA4A: view

No data available for SIGNOR curated interactions for SEMA4A Gene

Drugs & Compounds for SEMA4A Gene

No Compound Related Data Available

Transcripts for SEMA4A Gene

Unigene Clusters for SEMA4A Gene

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

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA4A Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e · 6f · 6g · 6h ^ 7a · 7b · 7c ^ 8a · 8b ^ 9a · 9b · 9c · 9d · 9e ^
SP1: - - - - - - - - - - - - -
SP2: - - -
SP3: - -
SP4: - - - - -
SP5: - - - - - - - - - - - - - -
SP6: - - - - - - - - - - - - - - - - - -
SP7: - - - - - - - - - - - - - - - - -
SP8: - - - - -
SP9: - - -
SP10: - - - - -
SP11: - - - - - -
SP12: - - - -
SP13: - - - - -
SP14: - - - - - -
SP15: - - - - - - - - -
SP16: - - - - - - - - - - - - - - - -
SP17: - - - -
SP18: - - - - -
SP19: - -
SP20:
SP21:

ExUns: 10 ^ 11a · 11b ^ 12a · 12b · 12c ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^ 21a · 21b · 21c
SP1: - - -
SP2: - - -
SP3: - - -
SP4: - - - -
SP5: - -
SP6: - -
SP7: -
SP8: -
SP9: - -
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:

Relevant External Links for SEMA4A Gene

GeneLoc Exon Structure for
SEMA4A
ECgene alternative splicing isoforms for
SEMA4A

Expression for SEMA4A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SEMA4A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA4A Gene

This gene is overexpressed in Whole Blood (x16.4).

Protein differential expression in normal tissues from HIPED for SEMA4A Gene

This gene is overexpressed in Heart (37.2), Monocytes (15.7), and Lymph node (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SEMA4A Gene



NURSA nuclear receptor signaling pathways regulating expression of SEMA4A Gene:

SEMA4A

SOURCE GeneReport for Unigene cluster for SEMA4A Gene:

Hs.408846

Evidence on tissue expression from TISSUES for SEMA4A Gene

  • Intestine(4.3)
  • Nervous system(3.6)
  • Blood(2.1)
  • Heart(2.1)
  • Lymph node(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA4A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • lacrimal apparatus
  • middle ear
  • nose
  • outer ear
  • pituitary gland
  • skull
Thorax:
  • breast
Pelvis:
  • ovary
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
General:
  • blood
  • blood vessel
  • hair
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with SEMA4A: view

Primer Products

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SEMA4A Gene

Orthologs for SEMA4A Gene

This gene was present in the common ancestor of chordates.

Orthologs for SEMA4A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA4A 34 35
  • 99.49 (n)
cow
(Bos Taurus)
Mammalia SEMA4A 34 35
  • 86.07 (n)
dog
(Canis familiaris)
Mammalia SEMA4A 34 35
  • 85.97 (n)
rat
(Rattus norvegicus)
Mammalia Sema4a 34
  • 83.82 (n)
mouse
(Mus musculus)
Mammalia Sema4a 34 16 35
  • 83.46 (n)
oppossum
(Monodelphis domestica)
Mammalia SEMA4A 35
  • 67 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA4A 35
  • 46 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema4a 34
  • 57.5 (n)
Str.10445 34
zebrafish
(Danio rerio)
Actinopterygii sema4aa 35
  • 31 (a)
OneToMany
sema4ab 35
  • 31 (a)
OneToMany
Species where no ortholog for SEMA4A 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)
  • chicken (Gallus gallus)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • 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 SEMA4A Gene

ENSEMBL:
Gene Tree for SEMA4A (if available)
TreeFam:
Gene Tree for SEMA4A (if available)

Paralogs for SEMA4A Gene

Variants for SEMA4A Gene

Sequence variations from dbSNP and Humsavar for SEMA4A Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs267607033 Pathogenic, Cone-rod dystrophy 10 (CORD10) [MIM:610283], Retinitis pigmentosa 35 (RP35) [MIM:610282] 156,162,993(+) TCTTG(C/G)ACATT reference, missense
rs267607034 Pathogenic, Cone-rod dystrophy 10 (CORD10) [MIM:610283], Retinitis pigmentosa 35 (RP35) [MIM:610282] 156,163,009(+) TGTCT(G/T)TAAGG reference, missense
rs41265017 Pathogenic, Retinitis pigmentosa 35 (RP35) [MIM:610282] 156,176,849(+) GGCTC(A/G)GGGCA reference, missense
rs2075164 Likely benign 156,175,180(-) GGTCC(C/G/T)GGGCA reference, missense
rs41265023 Likely benign 156,177,034(+) GCACC(C/T)GGCCA utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for SEMA4A Gene

Variant ID Type Subtype PubMed ID
nsv509513 CNV insertion 20534489

Variation tolerance for SEMA4A Gene

Residual Variation Intolerance Score: 43.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.63; 65.55% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SEMA4A Gene

Human Gene Mutation Database (HGMD)
SEMA4A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA4A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA4A Gene

Disorders for SEMA4A Gene

MalaCards: The human disease database

(6) MalaCards diseases for SEMA4A Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cone-rod dystrophy 10
  • cord10
retinitis pigmentosa 35
  • rp35
familial colorectal cancer type x
  • fcctx
sema4a-related retinitis pigmentosa
  • retinitis pigmentosa 35
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SEM4A_HUMAN
  • Cone-rod dystrophy 10 (CORD10) [MIM:610283]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269 PubMed:16199541}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa 35 (RP35) [MIM:610282]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:16199541}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SEMA4A

Genetic Association Database (GAD)
SEMA4A
Human Genome Epidemiology (HuGE) Navigator
SEMA4A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEMA4A
genes like me logo Genes that share disorders with SEMA4A: view

No data available for Genatlas for SEMA4A Gene

Publications for SEMA4A Gene

  1. Identification of novel mutations in the SEMA4A gene associated with retinal degenerative diseases. (PMID: 16199541) Abid A. … Khaliq S. (J. Med. Genet. 2006) 3 4 22 64
  2. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij J.C. … Florijn R.J. (Ophthalmology 2011) 3 46 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 3 4 64

Products for SEMA4A Gene

Sources for SEMA4A Gene

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