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Aliases for SEMA3B Gene

Aliases for SEMA3B Gene

  • Semaphorin 3B 2 3 5
  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3B 2 3
  • Semaphorin-V 3 4
  • Sema A(V) 3 4
  • SEMAA 3 4
  • SEMA5 3 4
  • Semaphorin-3B 3
  • Semaphorin A 3
  • LUCA-1 3
  • Sema V 4
  • SemaV 3
  • SemA 3

External Ids for SEMA3B Gene

Previous HGNC Symbols for SEMA3B Gene


Previous GeneCards Identifiers for SEMA3B Gene

  • GC03M049672
  • GC03M049841
  • GC03P050159
  • GC03P050265
  • GC03P050281
  • GC03P050304

Summaries for SEMA3B Gene

Entrez Gene Summary for SEMA3B Gene

  • The protein encoded by this gene belongs to the class-3 semaphorin/collapsin family, whose members function in growth cone guidance during neuronal development. This family member inhibits axonal extension and has been shown to act as a tumor suppressor by inducing apoptosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014]

GeneCards Summary for SEMA3B Gene

SEMA3B (Semaphorin 3B) is a Protein Coding gene. Diseases associated with SEMA3B include Phencyclidine Abuse. Among its related pathways are Neuroscience and Axon guidance. An important paralog of this gene is SEMA3A.

UniProtKB/Swiss-Prot for SEMA3B Gene

  • Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons.

Gene Wiki entry for SEMA3B Gene

Additional gene information for SEMA3B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA3B Gene

Genomics for SEMA3B Gene

GeneHancer (GH) Regulatory Elements for SEMA3B Gene

Promoters and enhancers for SEMA3B 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
GH03J050257 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 652.5 -0.1 -57 19.3 CLOCK DMAP1 IRF4 E2F8 ZNF143 SP3 SSRP1 ZNF610 GLIS1 RCOR2 SEMA3B SEMA3B-AS1 HYAL3 CYB561D2 RBM6 RBM5 IFRD2 GNAI2 SEMA3F-AS1 AMT
GH03J050234 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 13.3 -22.3 -22302 21.2 HDGF FOXA2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF213 ZNF207 GNAI2 RBM5 RBM6 SEMA3F-AS1 HYAL3 TMEM115 HYAL1 CYB561D2 RHOA-IT1 AMT
GH03J050227 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 12.4 -38.6 -38558 4.8 HDGF ARID4B SIN3A DMAP1 YY1 E2F8 ZNF207 ZNF143 SP3 SP5 MIR5787 RBM6 RBM5 SEMA3F-AS1 HYAL3 SEMA3B SEMA3B-AS1 LSMEM2 TMEM115 IFRD2
GH03J050201 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.1 -63.5 -63468 4.8 HDGF FOXA2 ARID4B DMAP1 ZNF48 YY1 ATF7 NFKBIZ RXRA SP5 SLC38A3 RBM6 GNAI2 SEMA3B SEMA3B-AS1 LSMEM2 CYB561D2 HYAL3 SEMA3F SEMA3F-AS1
GH03J050192 Enhancer 1.2 Ensembl ENCODE 12.1 -73.1 -73136 4.3 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 FOS HYAL3 RBM6 GNAI2 SEMA3F-AS1 SEMA3F SEMA3B SEMA3B-AS1 LSMEM2 HYAL1 IFRD2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SEMA3B gene promoter:
  • GR
  • CUTL1
  • GATA-1
  • GR-alpha
  • GR-beta
  • Nkx2-5
  • Olf-1
  • Lmo2
  • LCR-F1

Genomic Locations for SEMA3B Gene

Genomic Locations for SEMA3B Gene
9,989 bases
Plus strand
9,988 bases
Plus strand

Genomic View for SEMA3B Gene

Genes around SEMA3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA3B Gene

Proteins for SEMA3B Gene

  • Protein details for SEMA3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q6GU46
    • Q8TB71
    • Q8TDV7
    • Q93018
    • Q96GX0

    Protein attributes for SEMA3B Gene

    749 amino acids
    Molecular mass:
    83122 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAC02731.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for SEMA3B Gene


neXtProt entry for SEMA3B Gene

Post-translational modifications for SEMA3B Gene

  • Glycosylation at posLast=611611, posLast=427427, isoforms=2124, and posLast=8282
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEMA3B Gene

Domains & Families for SEMA3B Gene

Gene Families for SEMA3B Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for SEMA3B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the semaphorin family.
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA3B: view

Function for SEMA3B Gene

Molecular function for SEMA3B Gene

UniProtKB/Swiss-Prot Function:
Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons.
GENATLAS Biochemistry:
semaphorin 3B,secreted,expressed in neuronal and non neuronal tissues,repellent of the nerve growth cone guidance

Phenotypes From GWAS Catalog for SEMA3B Gene

Gene Ontology (GO) - Molecular Function for SEMA3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030215 semaphorin receptor binding IBA --
GO:0038191 neuropilin binding IBA --
GO:0045499 chemorepellent activity IBA --
genes like me logo Genes that share ontologies with SEMA3B: view
genes like me logo Genes that share phenotypes with SEMA3B: view

Animal Models for SEMA3B Gene

MGI Knock Outs for SEMA3B:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA3B

miRNA for SEMA3B Gene

miRTarBase miRNAs that target SEMA3B

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SEMA3B Gene

Localization for SEMA3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA3B Gene

Secreted. Endoplasmic reticulum. Note=Accumulates in the endoplasmic reticulum.

Gene Ontology (GO) - Cellular Components for SEMA3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA --
GO:0005783 endoplasmic reticulum IEA,TAS --
GO:0070062 extracellular exosome HDA --
genes like me logo Genes that share ontologies with SEMA3B: view

No data available for Subcellular locations from COMPARTMENTS and Subcellular locations from the Human Protein Atlas (HPA) for SEMA3B Gene

Pathways & Interactions for SEMA3B Gene

SuperPathways for SEMA3B Gene

SuperPathway Contained pathways
1 Axon guidance
2 Neuroscience
genes like me logo Genes that share pathways with SEMA3B: view

Pathways by source for SEMA3B Gene

1 KEGG pathway for SEMA3B Gene
1 Cell Signaling Technology pathway for SEMA3B Gene

Interacting Proteins for SEMA3B Gene

Gene Ontology (GO) - Biological Process for SEMA3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001755 neural crest cell migration IBA --
GO:0007267 cell-cell signaling TAS 8633026
GO:0007411 axon guidance TAS 8633026
GO:0030335 positive regulation of cell migration IBA --
GO:0048843 negative regulation of axon extension involved in axon guidance IBA --
genes like me logo Genes that share ontologies with SEMA3B: view

No data available for SIGNOR curated interactions for SEMA3B Gene

Drugs & Compounds for SEMA3B Gene

(1) Drugs for SEMA3B Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for SEMA3B Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SEMA3B: view

Transcripts for SEMA3B Gene

Unigene Clusters for SEMA3B Gene

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

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA3B Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c · 8d ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c ^ 12a · 12b · 12c ^
SP1: - - - - - - -
SP2: - - - - - - -
SP3: - - - - - -
SP4: - - - - -
SP5: - - - - -
SP6: - -
SP7: - - - - - - -
SP8: - - - -
SP9: - - - - -
SP11: - - - - - -
SP14: - - - - - -
SP16: - - - -

ExUns: 13a · 13b ^ 14a · 14b ^ 15 ^ 16a · 16b · 16c · 16d ^ 17 ^ 18 ^ 19a · 19b · 19c · 19d · 19e
SP1: - -
SP2: - -
SP3: - -
SP4: - -
SP5: - -
SP6: - -
SP7: - - - - -
SP10: -
SP11: - -
SP12: -

Relevant External Links for SEMA3B Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SEMA3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SEMA3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA3B Gene

This gene is overexpressed in Nerve - Tibial (x6.0) and Adrenal Gland (x4.5).

Protein differential expression in normal tissues from HIPED for SEMA3B Gene

This gene is overexpressed in Testis (68.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SEMA3B Gene

NURSA nuclear receptor signaling pathways regulating expression of SEMA3B Gene:


SOURCE GeneReport for Unigene cluster for SEMA3B Gene:


mRNA Expression by UniProt/SwissProt for SEMA3B Gene:

Tissue specificity: Expressed abundantly but differentially in a variety of neural and nonneural tissues.
genes like me logo Genes that share expression patterns with SEMA3B: view

No data available for Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA3B Gene

Orthologs for SEMA3B Gene

This gene was present in the common ancestor of chordates.

Orthologs for SEMA3B Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SEMA3B 33
  • 97.85 (n)
(Bos Taurus)
Mammalia SEMA3B 33
  • 87.3 (n)
(Canis familiaris)
Mammalia SEMA3B 33
  • 87.12 (n)
(Rattus norvegicus)
Mammalia Sema3b 33
  • 83.49 (n)
(Mus musculus)
Mammalia Sema3b 16 33
  • 83.13 (n)
(Gallus gallus)
Aves SEMA3B 33
  • 77.22 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3b 33
  • 63.12 (n)
(Danio rerio)
Actinopterygii si:ch211-106g4.2 33
  • 63.95 (n)
Species where no ortholog for SEMA3B 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)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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 SEMA3B Gene

Gene Tree for SEMA3B (if available)
Gene Tree for SEMA3B (if available)
Evolutionary constrained regions (ECRs) for SEMA3B: view image

Paralogs for SEMA3B Gene

(16) SIMAP similar genes for SEMA3B Gene using alignment to 2 proteins:

  • Q6PI51_HUMAN
genes like me logo Genes that share paralogs with SEMA3B: view

Variants for SEMA3B Gene

Sequence variations from dbSNP and Humsavar for SEMA3B Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs2071203 A non-small cell lung cancer cell line 50,274,469(+) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
VAR_014221 A non-small cell lung cancer cell line p.Arg348Cys
VAR_014222 A non-small cell lung cancer cell line p.Asp397His
rs1000216160 -- 50,268,718(+) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000553484 -- 50,267,125(+) A/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SEMA3B Gene

Variant ID Type Subtype PubMed ID
dgv602n27 CNV loss 19166990
dgv8316n54 CNV loss 21841781
dgv8317n54 CNV loss 21841781
esv2759148 CNV loss 17122850
nsv460531 CNV loss 19166990
nsv470561 CNV loss 18288195
nsv523560 CNV loss 19592680
nsv523662 CNV loss 19592680
nsv590255 CNV loss 21841781
nsv834692 CNV loss 17160897
nsv834693 CNV loss 17160897
nsv954855 CNV deletion 24416366

Additional Variant Information for SEMA3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SEMA3B Gene

Disorders for SEMA3B Gene

MalaCards: The human disease database

(1) MalaCards diseases for SEMA3B Gene - From: GeneCards

Disorder Aliases PubMed IDs
phencyclidine abuse
  • pcp abuse
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA3B

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 SEMA3B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA3B Gene

Publications for SEMA3B Gene

  1. Semaphorin 3B and 3F single nucleotide polymorphisms are associated with prostate cancer risk and poor prognosis. (PMID: 19683737) Beuten J … Naylor SL (The Journal of urology 2009) 3 22 44 58
  2. The race associated allele of Semaphorin 3B (SEMA3B) T415I and its role in lung cancer in African-Americans and Latino-Americans. (PMID: 15831529) Marsit CJ … Kelsey KT (Carcinogenesis 2005) 3 22 44 58
  3. Human semaphorins A(V) and IV reside in the 3p21.3 small cell lung cancer deletion region and demonstrate distinct expression patterns. (PMID: 8633026) Sekido Y … Minna JD (Proceedings of the National Academy of Sciences of the United States of America 1996) 2 3 4 58
  4. Identification of neuroglycan C and interacting partners as potential susceptibility genes for schizophrenia in a Southern Chinese population. (PMID: 19367581) So HC … Sham PC (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2010) 3 44 58
  5. Hormonal regulation and distinct functions of semaphorin-3B and semaphorin-3F in ovarian cancer. (PMID: 20124444) Joseph D … Syed V (Molecular cancer therapeutics 2010) 3 22 58

Products for SEMA3B Gene

Sources for SEMA3B Gene

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