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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

  • SEMAA

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 and Lung Cancer. Among its related pathways are Axon guidance and Neuroscience. GO annotations related to this gene include receptor activity. 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

Regulatory Elements for SEMA3B Gene

Enhancers for SEMA3B 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
GH03H050234 2 FANTOM5 Ensembl ENCODE dbSUPER 13.3 -22.3 -22303 21 HDGF FOXA2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 HYAL3 GNAI2 HYAL1 CYB561D2 SEMA3B SEMA3B-AS1 LSMEM2 NAT6 IFRD2 SEMA3F-AS1
GH03H050227 1.9 FANTOM5 Ensembl ENCODE dbSUPER 12.4 -38.4 -38436 4 HDGF ARID4B SIN3A DMAP1 YY1 ZNF207 ZNF143 SP3 SP5 ZHX2 HYAL3 RBM6 SEMA3F-AS1 RBM5 SEMA3B SEMA3B-AS1 LSMEM2 TMEM115 IFRD2 RASSF1
GH03H050201 1.8 FANTOM5 Ensembl ENCODE dbSUPER 12.1 -63.5 -63468 4 HDGF FOXA2 ARID4B DMAP1 YY1 ATF7 SP5 MXD4 NFYC REST RBM6 GNAI2 SEMA3B SEMA3B-AS1 LSMEM2 CYB561D2 HYAL3 SEMA3F SEMA3F-AS1 RBM5
GH03H050192 1.3 Ensembl ENCODE 12.1 -73.1 -73137 4 PKNOX1 FOXA2 ARID4B DMAP1 ZNF2 YY1 SLC30A9 ZNF143 FOS SP5 HYAL3 RBM6 GNAI2 SEMA3F SEMA3F-AS1 SEMA3B SEMA3B-AS1 LSMEM2 HYAL1 IFRD2
GH03H050188 1.1 Ensembl ENCODE 11.7 -78.1 -78106 1 RB1 ARID4B RAD21 RFX5 EGR1 ZNF143 RCOR1 CREM MIXL1 DEK GNAI2 SEMA3F SEMA3F-AS1 SEMA3B SEMA3B-AS1 LSMEM2 IFRD2 HYAL3 MON1A RBM6
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEMA3B on UCSC Golden Path with GeneCards custom track

Genomic Location for SEMA3B Gene

Chromosome:
3
Start:
50,267,558 bp from pter
End:
50,277,546 bp from pter
Size:
9,989 bases
Orientation:
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:
    Q13214-SEM3B_HUMAN
    Recommended name:
    Semaphorin-3B
    Protein Accession:
    Q13214
    Secondary Accessions:
    • Q6GU46
    • Q8TB71
    • Q8TDV7
    • Q93018
    • Q96GX0

    Protein attributes for SEMA3B Gene

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

    Alternative splice isoforms for SEMA3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA3B Gene

Post-translational modifications for SEMA3B Gene

  • Glycosylation at isoforms=282, Asn124, Asn427, and isoforms=2611
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for SEMA3B (Semaphorin 3B)
  • Cell Signaling Technology (CST) Antibodies for SEMA3B (SEMA3B)

No data available for DME Specific Peptides for SEMA3B Gene

Domains & Families for SEMA3B Gene

Gene Families for SEMA3B Gene

HGNC:
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

Q13214

UniProtKB/Swiss-Prot:

SEM3B_HUMAN :
  • Belongs to the semaphorin family.
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

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

Gene Ontology (GO) - Molecular Function for SEMA3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0038191 neuropilin binding IBA --
genes like me logo Genes that share ontologies with SEMA3B: view

Phenotypes for SEMA3B Gene

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

CRISPR Products

miRNA for SEMA3B Gene

miRTarBase miRNAs that target SEMA3B

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SEMA3B
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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:0005615 extracellular space IBA --
GO:0005783 endoplasmic reticulum TAS,IEA --
GO:0070062 extracellular exosome IDA 23376485
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 Cell Signaling Technology pathway for SEMA3B Gene
1 KEGG 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:0007267 cell-cell signaling TAS 8633026
GO:0007411 axon guidance TAS 8633026
GO:0050919 negative chemotaxis 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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for SEMA3B
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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: - - - - -
SP10:
SP11: - - - - - -
SP12:
SP13:
SP14: - - - - - -
SP15:
SP16: - - - -
SP17:

ExUns: 13a · 13b ^ 14a · 14b ^ 15 ^ 16a · 16b · 16c · 16d ^ 17 ^ 18 ^ 19a · 19b · 19c · 19d · 19e
SP1: - -
SP2: - -
SP3: - -
SP4: - -
SP5: - -
SP6: - -
SP7: - - - - -
SP8:
SP9:
SP10: -
SP11: - -
SP12: -
SP13:
SP14:
SP15:
SP16:
SP17:

Relevant External Links for SEMA3B Gene

GeneLoc Exon Structure for
SEMA3B
ECgene alternative splicing isoforms for
SEMA3B

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:

SEMA3B

SOURCE GeneReport for Unigene cluster for SEMA3B Gene:

Hs.82222

mRNA Expression by UniProt/SwissProt for SEMA3B Gene:

Q13214-SEM3B_HUMAN
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

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia SEMA3B 33
  • 97.85 (n)
cow
(Bos Taurus)
Mammalia SEMA3B 33
  • 87.3 (n)
dog
(Canis familiaris)
Mammalia SEMA3B 33
  • 87.12 (n)
rat
(Rattus norvegicus)
Mammalia Sema3b 33
  • 83.49 (n)
mouse
(Mus musculus)
Mammalia Sema3b 33 16
  • 83.13 (n)
chicken
(Gallus gallus)
Aves SEMA3B 33
  • 77.22 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3b 33
  • 63.12 (n)
zebrafish
(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

ENSEMBL:
Gene Tree for SEMA3B (if available)
TreeFam:
Gene Tree for SEMA3B (if available)

Paralogs for SEMA3B Gene

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 Sequence Context AA Info Type
rs2071203 A non-small cell lung cancer cell line 50,274,469(-) CCCCA(A/G)TGGGC nc-transcript-variant, reference, missense
VAR_014221 A non-small cell lung cancer cell line
VAR_014222 A non-small cell lung cancer cell line
rs1000216160 -- 50,268,718(+) CCCCT(C/T)CTGTC intron-variant, upstream-variant-2KB
rs1000553484 -- 50,267,125(+) GCCCA(A/C)GTGTT intron-variant, upstream-variant-2KB

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

Relevant External Links for SEMA3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA3B

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

(2) MalaCards diseases for SEMA3B Gene - From: Novoseek and GeneCards

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

Relevant External Links for SEMA3B

Genetic Association Database (GAD)
SEMA3B
Human Genome Epidemiology (HuGE) Navigator
SEMA3B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEMA3B
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 45 60
  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 45 60
  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 60
  4. 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 60
  5. 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 45 60

Products for SEMA3B Gene

Sources for SEMA3B Gene

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