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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. 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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for SEMA4A Gene

Promoters and enhancers for SEMA4A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J156145 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 650.7 +2.0 1994 7.7 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 SEMA4A LMNA CCT3 LOC246784 GON4L SLC25A44 KHDC4 ENSG00000252236 ENSG00000271267 MEX3A
GH01J156153 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 650.4 +7.6 7622 3.5 CTCF PKNOX1 SMAD1 EBF1 ZBTB40 RELA GATA3 POLR2A EED BCLAF1 SEMA4A ENSG00000252236 SLC25A44 LMNA MEX3A BGLAP PAQR6 TSACC CCT3 GC01P156159
GH01J156138 Promoter/Enhancer 0.8 EPDnew dbSUPER 650.4 -8.8 -8763 0.1 ZBTB33 SEMA4A GC01M156123 LMNA
GH01J156137 Promoter/Enhancer 0.8 EPDnew dbSUPER 650.4 -10.2 -10244 0.1 CTCF SEMA4A LMNA MEX3A PAQR6 BGLAP GC01M156123
GH01J156180 Enhancer 1.1 Ensembl ENCODE 50.3 +36.2 36232 7 ATF1 FOXA2 MLX ARID4B DMAP1 TCF12 ZNF121 ATF7 CAVIN1 SP5 SEMA4A BGLAP PAQR6 SLC25A44 GC01M156192 GC01P156159 GC01P156160
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA4A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SEMA4A gene promoter:
  • C/EBPalpha
  • Lmo2
  • HEN1
  • c-Myc
  • Max1
  • Pax-5
  • AP-1
  • c-Fos
  • c-Jun
  • Arnt

Genomic Locations for SEMA4A Gene

Genomic Locations for SEMA4A Gene
chr1:156,147,359-156,177,752
(GRCh38/hg38)
Size:
30,394 bases
Orientation:
Plus strand
chr1:156,117,157-156,147,543
(GRCh37/hg19)
Size:
30,387 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

  • Glycosylation at isoforms=2607, isoforms=2496, posLast=135135, and isoforms=120
  • Ubiquitination at isoforms=2535 and posLast=219219
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for SEMA4A (Semaphorin 4A)
  • Abcam antibodies for SEMA4A
  • Boster Bio Antibodies for SEMA4A

No data available for DME Specific Peptides for SEMA4A Gene

Domains & Families for SEMA4A Gene

Gene Families for SEMA4A Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

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).

Phenotypes From GWAS Catalog for SEMA4A Gene

Gene Ontology (GO) - Molecular Function for SEMA4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI,IEA 17318185
GO:0030215 semaphorin receptor binding IBA --
GO:0038191 NOT neuropilin binding IBA --
GO:0045499 chemorepellent activity IBA --
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

miRNA for SEMA4A Gene

miRTarBase miRNAs that target SEMA4A

Clone 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 4
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SEMA4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA --
GO:0005634 nucleus IDA --
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA,IBA --
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:0001755 neural crest cell migration IBA --
GO:0002250 adaptive immune response IEA --
GO:0002292 T cell differentiation involved in immune response IEA --
GO:0002376 immune system process 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:

Clone 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, 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(2.2)
  • Heart(2.1)
  • Lymph node(2.1)
  • Spleen(2)

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
Regions:
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

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 33
  • 99.49 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA4A 34 33
  • 86.07 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA4A 34 33
  • 85.97 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema4a 33
  • 83.82 (n)
mouse
(Mus musculus)
Mammalia Sema4a 16 34 33
  • 83.46 (n)
oppossum
(Monodelphis domestica)
Mammalia SEMA4A 34
  • 67 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA4A 34
  • 46 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema4a 33
  • 57.5 (n)
Str.10445 33
zebrafish
(Danio rerio)
Actinopterygii sema4ab 34
  • 31 (a)
OneToMany
sema4aa 34
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SEMA4A: view image

Paralogs for SEMA4A Gene

(19) SIMAP similar genes for SEMA4A Gene using alignment to 5 proteins:

  • SEM4A_HUMAN
  • Q5TCI4_HUMAN
  • Q5TCI6_HUMAN
  • Q5TCJ5_HUMAN
  • Q5TCJ7_HUMAN
genes like me logo Genes that share paralogs with SEMA4A: view

Variants for SEMA4A Gene

Sequence variations from dbSNP and Humsavar for SEMA4A Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs113436119 uncertain-significance, Cone-Rod Dystrophy, Recessive, Retinitis Pigmentosa, Recessive 156,153,629(+) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs117762142 uncertain-significance, Retinitis Pigmentosa, Recessive, Cone-Rod Dystrophy, Recessive 156,177,185(+) G/T 3_prime_UTR_variant
rs12401573 benign, not specified, Retinitis Pigmentosa, Recessive, Cone-Rod Dystrophy, Recessive 156,176,427(+) C/T coding_sequence_variant, synonymous_variant
rs144540956 uncertain-significance, Retinitis Pigmentosa, Recessive, Cone-Rod Dystrophy, Recessive 156,176,392(+) C/A/G intron_variant
rs145993678 uncertain-significance, Cone-Rod Dystrophy, Recessive, Retinitis Pigmentosa, Recessive 156,163,046(+) A/C coding_sequence_variant, synonymous_variant

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)

Additional Variant Information 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

(5) MalaCards diseases for SEMA4A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SEM4A_HUMAN
  • 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, ECO:0000269 PubMed:22956603}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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.

Additional Disease Information for SEMA4A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (Journal of medical genetics 2006) 3 4 22 58
  2. On variants and disease-causing mutations: Case studies of a SEMA4A variant identified in inherited blindness. (PMID: 28805479) Bryant L … Bennett J (Ophthalmic genetics 2018) 3 4 58
  3. SEMA4A mutations lead to susceptibility to light irradiation, oxidative stress, and ER stress in retinal pigment epithelial cells. (PMID: 22956603) Tsuruma K … Hara H (Investigative ophthalmology & visual science 2012) 3 4 58
  4. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij JC … Florijn RJ (Ophthalmology 2011) 3 44 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for SEMA4A Gene

Sources for SEMA4A Gene

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