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Aliases for SEMA3A Gene

Aliases for SEMA3A Gene

  • Semaphorin 3A 2 3 5
  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3A 2 3
  • Semaphorin III 3 4
  • Sema III 2 4
  • SEMAD 3 4
  • Semaphorin-3A 3
  • Semaphorin D 3
  • Semaphorin L 3
  • Collapsin 1 3
  • Hsema-III 3
  • Hsema-I 3
  • Coll-1 3
  • COLL1 3
  • SEMA1 3
  • SEMAL 3
  • HH16 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 (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 Apoptotic Pathways in Synovial Fibroblasts and Development Slit-Robo signaling. Gene Ontology (GO) annotations related to this gene include receptor activity and chemorepellent activity. An important paralog of this gene is SEMA3D.

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

Additional gene information for SEMA3A Gene

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

Genomics for SEMA3A Gene

GeneHancer (GH) Regulatory Elements for SEMA3A Gene

Promoters and enhancers for SEMA3A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07I084189 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.1 +299.3 299333 6.8 PKNOX1 ZSCAN4 MZF1 SIN3A FEZF1 ZNF2 ZNF335 ZNF302 ZNF366 SCRT2 SEMA3A GC07P084322 GC07P083837
GH07I084492 Enhancer 0.5 ENCODE 550.8 -0.1 -116 0.2 POLR2A FOXP2 PRDM10 RCOR1 PRDM4 CHD2 ZBTB17 SEMA3A RPL7P30
GH07I084491 Enhancer 0.3 ENCODE 550.8 +1.8 1824 0.2 CTCF SEMA3A GC07M084394
GH07I084524 Enhancer 0.8 Ensembl ENCODE 11.6 -32.5 -32468 1.4 SIX5 CEBPB REST EP300 SP1 JUND MAFF FOSL2 NFE2 NFE2L2 SEMA3A RPL7P30
GH07I084057 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 4.2 +433.0 432953 3.8 FOXA2 ZFP64 ATF7 ZNF680 SP3 ZBTB11 CEBPB ZC3H11A REST ELF1 ENSG00000232019 SEMA3A GC07P083837 GC07P084322
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SEMA3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SEMA3A gene promoter:

Genomic Locations for SEMA3A Gene

Genomic Locations for SEMA3A Gene
536,948 bases
Minus strand

Genomic View for SEMA3A Gene

Genes around SEMA3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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:

    Protein attributes for SEMA3A Gene

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

neXtProt entry for SEMA3A Gene

Post-translational modifications for SEMA3A Gene

  • Glycosylation at posLast=5353, isoforms=125, and isoforms=590
  • Modification sites at PhosphoSitePlus

Protein Products

No data available for DME Specific Peptides for SEMA3A Gene

Domains & Families for SEMA3A Gene

Gene Families for SEMA3A Gene

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

Suggested Antigen Peptide Sequences for SEMA3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Strong binding to neuropilin is mediated by the carboxy third of the protein.
  • Belongs to the semaphorin family.
  • Strong binding to neuropilin is mediated by the carboxy third of the protein.
  • 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

Phenotypes From GWAS Catalog for SEMA3A Gene

Gene Ontology (GO) - Molecular Function for SEMA3A Gene

GO ID Qualified GO term Evidence PubMed IDs
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

Human Phenotype Ontology for SEMA3A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SEMA3A Gene

MGI Knock Outs for SEMA3A:

Animal Model Products

CRISPR Products

miRNA for SEMA3A Gene

miRTarBase miRNAs that target SEMA3A

Inhibitory RNA Products

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

Localization for SEMA3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA3A Gene


Subcellular locations from

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 SEMA3A gene
Compartment Confidence
extracellular 5
nucleus 3
plasma membrane 2
cytoskeleton 2
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SEMA3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IBA --
GO:0030424 axon IBA --
GO:0030425 dendrite IEA --
genes like me logo Genes that share ontologies with SEMA3A: view

Pathways & Interactions for SEMA3A Gene

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

SIGNOR curated interactions for SEMA3A Gene


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 organism development IEA --
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with SEMA3A: view

Drugs & Compounds for SEMA3A Gene

(3) Drugs for SEMA3A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for SEMA3A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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:

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x5.4), Esophagus - Gastroesophageal Junction (x5.4), and Esophagus - Muscularis (x5.4).

Protein differential expression in normal tissues from HIPED for SEMA3A Gene

This gene is overexpressed in Lung (28.3), Amniocyte (20.5), and Vitreous humor (20.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SEMA3A Gene

Protein tissue co-expression partners for SEMA3A Gene

NURSA nuclear receptor signaling pathways regulating expression of SEMA3A Gene:


SOURCE GeneReport for Unigene cluster for SEMA3A Gene:


Evidence on tissue expression from TISSUES for SEMA3A Gene

  • Nervous system(4.8)
  • Heart(2.4)
  • Muscle(2.2)
  • Eye(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA3A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • face
  • head
  • hypothalamus
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • olfactory bulb
  • pharynx
  • pituitary gland
  • skull
  • vocal cord
  • breast
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
  • kidney
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vas deferens
  • vulva
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns 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 33 34
  • 99.74 (n)
(Bos Taurus)
Mammalia SEMA3A 33 34
  • 93.3 (n)
(Monodelphis domestica)
Mammalia SEMA3A 34
  • 93 (a)
(Ornithorhynchus anatinus)
Mammalia SEMA3A 34
  • 92 (a)
(Canis familiaris)
Mammalia SEMA3A 33 34
  • 91.96 (n)
(Rattus norvegicus)
Mammalia Sema3a 33
  • 89.41 (n)
(Mus musculus)
Mammalia Sema3a 33 16 34
  • 88.63 (n)
(Gallus gallus)
Aves SEMA3A 33 34
  • 81.88 (n)
(Anolis carolinensis)
Reptilia SEMA3A 34
  • 88 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3a 33
  • 79.16 (n)
African clawed frog
(Xenopus laevis)
Amphibia sema3a-A 33
(Danio rerio)
Actinopterygii sema3ab 33 34
  • 70.52 (n)
sema3aa 34
  • 65 (a)
fruit fly
(Drosophila melanogaster)
Insecta Sema-2a 35 33
  • 46.57 (n)
Sema-1a 35
  • 34 (a)
CG4383 35
  • 33 (a)
Sema-1b 35
  • 32 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006634 33
  • 45.9 (n)
Species where no ortholog for SEMA3A was found in the sources mined by GeneCards:
  • 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

Variants for SEMA3A Gene

Sequence variations from dbSNP and Humsavar for SEMA3A Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs137871935 Hypogonadotropic hypogonadism 16 with or without anosmia (HH16) [MIM:614897] 84,001,957(-) G/A coding_sequence_variant, missense_variant
rs138952094 likely-pathogenic, Delayed puberty 83,961,537(-) G/A coding_sequence_variant, missense_variant
rs139295139 not-provided, not provided, Hypogonadotropic hypogonadism 16 with or without anosmia (HH16) [MIM:614897] 84,060,554(-) T/C coding_sequence_variant, missense_variant
rs143007146 A breast cancer sample 84,110,532(-) C/T coding_sequence_variant, missense_variant
rs147436181 risk-factor, not-provided, benign, Hypogonadotropic hypogonadism 16 with or without anosmia, not provided, not specified, Hypogonadotropic hypogonadism 16 with or without anosmia (HH16) [MIM:614897] 84,005,396(-) C/T coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
dgv3606n106 CNV deletion 24896259
esv1251085 CNV deletion 17803354
esv1617967 CNV deletion 17803354
esv1729347 CNV insertion 17803354
esv2086328 CNV deletion 18987734
esv2359570 CNV deletion 18987734
esv2584536 CNV deletion 19546169
esv2657057 CNV deletion 23128226
esv2734760 CNV deletion 23290073
esv2734762 CNV deletion 23290073
esv2734763 CNV deletion 23290073
esv275427 CNV gain+loss 21479260
esv3024 CNV loss 18987735
esv3362773 CNV insertion 20981092
esv3542016 CNV deletion 23714750
esv3542018 CNV deletion 23714750
esv3571947 CNV loss 25503493
esv3613949 CNV loss 21293372
esv3613952 CNV loss 21293372
esv3613954 CNV loss 21293372
esv3613956 CNV loss 21293372
esv3613958 CNV loss 21293372
esv8729 CNV loss 19470904
esv989952 CNV insertion 20482838
esv993949 CNV deletion 20482838
esv994067 CNV deletion 20482838
nsv1020784 CNV loss 25217958
nsv1075041 CNV deletion 25765185
nsv1075977 CNV deletion 25765185
nsv1114981 CNV deletion 24896259
nsv1161576 CNV deletion 26073780
nsv442055 CNV loss 18776908
nsv508464 CNV deletion 20534489
nsv514429 CNV loss 21397061
nsv517852 CNV loss 19592680
nsv519788 CNV loss 19592680
nsv523680 CNV gain 19592680
nsv527413 CNV loss 19592680
nsv607707 CNV gain 21841781
nsv824196 CNV loss 20364138
nsv957055 CNV deletion 24416366
nsv957578 CNV deletion 24416366

Variation tolerance for SEMA3A Gene

Residual Variation Intolerance Score: 75.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.27; 52.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEMA3A Gene

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

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

Disorders for SEMA3A Gene

MalaCards: The human disease database

(19) MalaCards diseases for SEMA3A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hypogonadotropic hypogonadism 16 with or without anosmia
  • hh16
kallmann syndrome
  • familial hypogonadism with anosmia
spondyloepimetaphyseal dysplasia, sponastrime type
  • spondylar and nasal alterations with striated metaphyses
angiomatous meningioma
spondyloepimetaphyseal dysplasia, missouri type
  • semd, missouri type
- elite association - COSMIC cancer census association via MalaCards


  • 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.

Additional Disease Information for SEMA3A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SEMA3A: view

No data available for Genatlas for SEMA3A Gene

Publications for SEMA3A Gene

  1. The semaphorin genes encode a family of transmembrane and secreted growth cone guidance molecules. (PMID: 8269517) Kolodkin AL … Goodman CS (Cell 1993) 2 3 4 58
  2. SEMA3A deletion in a family with Kallmann syndrome validates the role of semaphorin 3A in human puberty and olfactory system development. (PMID: 22416012) Young J … Guiochon-Mantel A (Human reproduction (Oxford, England) 2012) 3 4 58
  3. SEMA3A, a gene involved in axonal pathfinding, is mutated in patients with Kallmann syndrome. (PMID: 22927827) Hanchate NK … Dodé C (PLoS genetics 2012) 3 4 58
  4. Genome-wide association study in multiple human prion diseases suggests genetic risk factors additional to PRNP. (PMID: 22210626) Mead S … Collinge J (Human molecular genetics 2012) 3 44 58
  5. Genome-wide association study of the child behavior checklist dysregulation profile. (PMID: 21784300) Mick E … Faraone SV (Journal of the American Academy of Child and Adolescent Psychiatry 2011) 3 44 58

Products for SEMA3A Gene

Sources for SEMA3A Gene

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