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Aliases for SEMA3A Gene

Aliases for SEMA3A Gene

  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3A 2 3
  • SEMAD 3 4 6
  • Semaphorin III 3 4
  • Sema III 2 4
  • COLL1 3 6
  • HH16 3 6
  • Semaphorin-3A 3
  • Semaphorin L 3
  • Semaphorin D 3
  • Collapsin 1 3
  • Hsema-III 3
  • Hsema-I 3
  • Coll-1 3
  • SEMAL 3
  • SEMA1 3
  • SemD 3

External Ids for SEMA3A Gene

Previous HGNC Symbols for SEMA3A Gene


Previous GeneCards Identifiers for SEMA3A Gene

  • GC07M082125
  • GC07M083188
  • GC07M083202
  • GC07M083235
  • GC07M083428
  • GC07M083587
  • GC07M078196

Summaries for SEMA3A Gene

Entrez Gene Summary for SEMA3A Gene

  • This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease. [provided by RefSeq, Jul 2008]

GeneCards Summary for SEMA3A Gene

SEMA3A (Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3A) is a Protein Coding gene. Diseases associated with SEMA3A include hypogonadotropic hypogonadism 16 with or without anosmia and kallmann syndrome. Among its related pathways are L1CAM interactions and NF-KappaB Family Pathway. GO annotations related to this gene include receptor activity and chemorepellent activity. An important paralog of this gene is SEMA4G.

UniProtKB/Swiss-Prot for SEMA3A Gene

  • Involved in the development of the olfactory system and in neuronal control of puberty. Induces the collapse and paralysis of neuronal growth cones. Could serve as a ligand that guides specific growth cones by a motility-inhibiting mechanism. Binds to the complex neuropilin-1/plexin-1.

Gene Wiki entry for SEMA3A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA3A Gene

Genomics for SEMA3A Gene

Regulatory Elements for SEMA3A Gene

Genomic Location for SEMA3A Gene

83,955,777 bp from pter
84,492,768 bp from pter
536,992 bases
Minus strand

Genomic View for SEMA3A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SEMA3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA3A Gene

Proteins for SEMA3A Gene

  • Protein details for SEMA3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:

    Protein attributes for SEMA3A Gene

    771 amino acids
    Molecular mass:
    88889 Da
    Quaternary structure:
    • Interacts with PLXND1.

neXtProt entry for SEMA3A Gene

Proteomics data for SEMA3A Gene at MOPED

Post-translational modifications for SEMA3A Gene

  • Glycosylation at Asn53, Asn125, and Asn590
  • Modification sites at PhosphoSitePlus

Other Protein References for SEMA3A Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for SEMA3A Gene

Domains for SEMA3A Gene

Gene Families for SEMA3A Gene

  • IGD :Immunoglobulin superfamily / Immunoglobulin-like domain containing
  • SEMA :Semaphorins

Suggested Antigen Peptide Sequences for SEMA3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Q14563
  • Strong binding to neuropilin is mediated by the carboxy third of the protein
  • Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
  • Contains 1 PSI domain.
  • Contains 1 Sema domain.
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA3A: view

Function for SEMA3A Gene

Molecular function for SEMA3A Gene

GENATLAS Biochemistry: semaphorin 3A,secreted,repellent of the nerve growth cone guidance
UniProtKB/Swiss-Prot Function: Involved in the development of the olfactory system and in neuronal control of puberty. Induces the collapse and paralysis of neuronal growth cones. Could serve as a ligand that guides specific growth cones by a motility-inhibiting mechanism. Binds to the complex neuropilin-1/plexin-1.

LifeMap Function Summary for SEMA3A Gene

During embryonic development, SEMA3A as signaling molecule is secreted from the following cells

Gene Ontology (GO) - Molecular Function for SEMA3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity IEA --
GO:0005515 protein binding --
GO:0030215 semaphorin receptor binding IEA --
GO:0038191 neuropilin binding ISS --
GO:0045499 chemorepellent activity TAS 19909241
genes like me logo Genes that share ontologies with SEMA3A: view
genes like me logo Genes that share phenotypes with SEMA3A: view

Animal Models for SEMA3A Gene

MGI Knock Outs for SEMA3A:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for SEMA3A Gene

Localization for SEMA3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA3A Gene


Subcellular locations from

Jensen Localization Image for SEMA3A Gene COMPARTMENTS Subcellular localization image for SEMA3A gene
Compartment Confidence
extracellular 4
cytoskeleton 2
cytosol 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SEMA3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0016020 membrane IEA --
GO:0030424 axon IEA --
GO:0030425 dendrite IEA --
genes like me logo Genes that share ontologies with SEMA3A: view

Pathways for SEMA3A Gene

genes like me logo Genes that share pathways with SEMA3A: view

Gene Ontology (GO) - Biological Process for SEMA3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001764 neuron migration ISS --
GO:0002027 regulation of heart rate IEA --
GO:0006915 apoptotic process IEA --
GO:0007275 multicellular organismal development --
GO:0007411 axon guidance TAS 19909241
genes like me logo Genes that share ontologies with SEMA3A: view

Compounds for SEMA3A Gene

(5) Novoseek inferred chemical compound relationships for SEMA3A Gene

Compound -log(P) Hits PubMed IDs
vegf 49.2 23
guanylate 3.34 2
calcium 0 3
tyrosine 0 5
serine 0 1
genes like me logo Genes that share compounds with SEMA3A: view

Transcripts for SEMA3A Gene

Unigene Clusters for SEMA3A Gene

Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA3A Gene

No ASD Table

Relevant External Links for SEMA3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SEMA3A Gene

mRNA expression in normal human tissues for SEMA3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA3A Gene

This gene is overexpressed in Colon - Sigmoid (5.4), Esophagus - Gastroesophageal Junction (5.4), and Esophagus - Muscularis (5.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for SEMA3A Gene

SOURCE GeneReport for Unigene cluster for SEMA3A Gene Hs.252451

genes like me logo Genes that share expressions with SEMA3A: view

No data available for mRNA Expression by UniProt/SwissProt for SEMA3A Gene

Orthologs for SEMA3A Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SEMA3A 35
  • 99.74 (n)
  • 100 (a)
  • 100 (a)
(Bos Taurus)
Mammalia SEMA3A 35
  • 93.3 (n)
  • 96.89 (a)
  • 96 (a)
(Canis familiaris)
Mammalia SEMA3A 35
  • 91.96 (n)
  • 95.72 (a)
  • 96 (a)
(Mus musculus)
Mammalia Sema3a 35
  • 88.63 (n)
  • 95.59 (a)
Sema3a 16
Sema3a 36
  • 95 (a)
(Monodelphis domestica)
Mammalia SEMA3A 36
  • 93 (a)
(Ornithorhynchus anatinus)
Mammalia SEMA3A 36
  • 92 (a)
(Rattus norvegicus)
Mammalia Sema3a 35
  • 89.41 (n)
  • 95.98 (a)
(Gallus gallus)
Aves SEMA3A 35
  • 81.88 (n)
  • 88.59 (a)
  • 85 (a)
(Anolis carolinensis)
Reptilia SEMA3A 36
  • 88 (a)
African clawed frog
(Xenopus laevis)
Amphibia sema3a-A 35
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3a 35
  • 79.16 (n)
  • 85.34 (a)
(Danio rerio)
Actinopterygii sema3aa 36
  • 65 (a)
sema3ab 35
  • 70.52 (n)
  • 77.66 (a)
sema3ab 36
  • 76 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006634 35
  • 45.9 (n)
  • 38.08 (a)
fruit fly
(Drosophila melanogaster)
Insecta Sema-2a 35
  • 46.57 (n)
  • 38.96 (a)
Sema-1b 37
  • 32 (a)
Sema-1a 37
  • 34 (a)
Sema-2a 37
  • 32 (a)
CG4383 37
  • 33 (a)
Species with no ortholog for SEMA3A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 SEMA3A Gene

Gene Tree for SEMA3A (if available)
Gene Tree for SEMA3A (if available)

Paralogs for SEMA3A Gene

genes like me logo Genes that share paralogs with SEMA3A: view

Variants for SEMA3A Gene

Sequence variations from dbSNP and Humsavar for SEMA3A Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type MAF
rs447 -- 84,143,099(-) CCAGG(A/G)AAGAC intron-variant
rs464 -- 84,157,144(-) TTCTT(C/T)TACTG intron-variant
rs3029 -- 84,127,102(+) AGATT(C/G)TCTCC intron-variant
rs16687 -- 84,258,562(+) ACACA(-/CA)TTTTC intron-variant
rs471152 -- 84,262,680(-) GTCAC(C/T)CATAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SEMA3A Gene

Variant ID Type Subtype PubMed ID
nsv888620 CNV Gain 21882294
nsv888622 CNV Gain 21882294
dgv7370n71 CNV Loss 21882294
esv275427 CNV Gain+Loss 21479260
dgv7371n71 CNV Loss 21882294
nsv888628 CNV Loss 21882294
esv268440 CNV Insertion 20981092
nsv523680 CNV Gain 19592680
nsv527413 CNV Loss 19592680
nsv508464 CNV Loss 20534489
nsv824196 CNV Loss 20364138
esv2359570 CNV Deletion 18987734
esv3024 CNV Deletion 18987735
esv2734760 CNV Deletion 23290073
esv993949 CNV Deletion 20482838
esv1617967 CNV Deletion 17803354
esv8729 CNV Loss 19470904
esv2734762 CNV Deletion 23290073
esv1729347 CNV Insertion 17803354
nsv888629 CNV Loss 21882294
esv2734763 CNV Deletion 23290073
esv994067 CNV Deletion 20482838
esv2584536 CNV Deletion 19546169
esv2657057 CNV Deletion 23128226
esv1251085 CNV Deletion 17803354
esv2086328 CNV Deletion 18987734
nsv442055 CNV CNV 18776908
nsv519788 CNV Loss 19592680
nsv517852 CNV Loss 19592680
nsv514429 CNV Loss 21397061
nsv888630 CNV Loss 21882294
esv989952 CNV Insertion 20482838

Relevant External Links for SEMA3A Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA3A Gene

Disorders for SEMA3A Gene

(1) OMIM Diseases for SEMA3A Gene (603961)


  • Hypogonadotropic hypogonadism 16 with or without anosmia (HH16) [MIM:614897]: A disorder characterized by absent or incomplete sexual maturation by the age of 18 years, in conjunction with low levels of circulating gonadotropins and testosterone and no other abnormalities of the hypothalamic-pituitary axis. In some cases, it is associated with non-reproductive phenotypes, such as anosmia, cleft palate, and sensorineural hearing loss. Anosmia or hyposmia is related to the absence or hypoplasia of the olfactory bulbs and tracts. Hypogonadism is due to deficiency in gonadotropin-releasing hormone and probably results from a failure of embryonic migration of gonadotropin-releasing hormone-synthesizing neurons. In the presence of anosmia, idiopathic hypogonadotropic hypogonadism is referred to as Kallmann syndrome, whereas in the presence of a normal sense of smell, it has been termed normosmic idiopathic hypogonadotropic hypogonadism (nIHH). {ECO:0000269 PubMed:22416012, ECO:0000269 PubMed:22927827, ECO:0000269 PubMed:25077900}. Note=The disease may be caused by mutations affecting distinct genetic loci, including the gene represented in this entry.

(5) Novoseek inferred disease relationships for SEMA3A Gene

Disease -log(P) Hits PubMed IDs
scar 6.27 2
neurodegenerative diseases 0 1
metastasis 0 1
tumors 0 9
cancer 0 6

Relevant External Links for SEMA3A

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SEMA3A: view

Publications for SEMA3A Gene

  1. The semaphorin genes encode a family of transmembrane and secreted growth cone guidance molecules. (PMID: 8269517) Kolodkin A.L. … Goodman C.S. (Cell 1993) 2 3 4
  2. Genome-wide association study of the child behavior checklist dysregulation profile. (PMID: 21784300) Mick E. … Faraone S.V. (J Am Acad Child Adolesc Psychiatry 2011) 3 48
  3. GWAS findings for human iris patterns: associations with variants in genes that influence normal neuronal pattern development. (PMID: 21835309) Larsson M. … Medland S.E. (Am. J. Hum. Genet. 2011) 3 48
  4. SEMA3A, a gene involved in axonal pathfinding, is mutated in patients with Kallmann syndrome. (PMID: 22927827) Hanchate N.K. … Dode C. (PLoS Genet. 2012) 3 4
  5. Up-regulation of semaphorin 3A in human corneal fibroblasts by epidermal growth factor released from cocultured human corneal epithelial cells. (PMID: 18831963) Ko J.A. … Nishida T. (Biochem. Biophys. Res. Commun. 2008) 3 23

Products for SEMA3A Gene

Sources for SEMA3A Gene

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