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Aliases for SEMA5B Gene

Aliases for SEMA5B Gene

  • Semaphorin 5B 2 3 5
  • Sema Domain, Seven Thrombospondin Repeats (Type 1 And Type 1-Like), Transmembrane Domain (TM) And Short Cytoplasmic Domain, (Semaphorin) 5B 2 3
  • SEMAG 3 4
  • Semaphorin-5B 3
  • KIAA1445 4
  • SemG 3

External Ids for SEMA5B Gene

Previous HGNC Symbols for SEMA5B Gene


Previous GeneCards Identifiers for SEMA5B Gene

  • GC03M119346
  • GC03M122576
  • GC03M123909
  • GC03M123948
  • GC03M124110
  • GC03M122628
  • GC03M120001

Summaries for SEMA5B Gene

Entrez Gene Summary for SEMA5B Gene

  • This gene encodes a member of the semaphorin protein family which regulates axon growth during development of the nervous system. The encoded protein has a characteristic Sema domain near the N-terminus, through which semaphorins bind to plexin, and five thrombospondin type 1 repeats in the C-terminal region of the protein. The protein product may be cleaved and exist as a secreted molecule (PMID: 19463192). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

GeneCards Summary for SEMA5B Gene

SEMA5B (Semaphorin 5B) is a Protein Coding gene. Among its related pathways are O-glycosylation of TSR domain-containing proteins and Diseases of glycosylation. GO annotations related to this gene include receptor activity. An important paralog of this gene is SEMA5A.

UniProtKB/Swiss-Prot for SEMA5B Gene

  • May act as positive axonal guidance cues.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA5B Gene

Genomics for SEMA5B Gene

Regulatory Elements for SEMA5B Gene

Enhancers for SEMA5B 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
GH03G122971 1.7 VISTA Ensembl ENCODE dbSUPER 11.5 +54.7 54656 5.0 HDGF PKNOX1 FOXA2 MLX ZFP64 SIN3A FEZF1 GATA2 FOS ZNF263 SEMA5B ADCY5 ENSG00000273454 GC03P122991 LINC02035
GH03G123079 1.5 Ensembl ENCODE dbSUPER 11.2 -52.5 -52482 4.8 FOXA2 ATF1 PKNOX1 CREB3L1 FEZF1 TCF12 ZNF766 GATA2 FOS ZNF263 SEMA5B PDIA5 GC03P123071 MIR7110
GH03G123076 1.5 Ensembl ENCODE dbSUPER 11.1 -48.2 -48213 1.9 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 FEZF1 KLF13 SP3 SP5 REST SEMA5B PDIA5 GC03P123071 MIR7110
GH03G122977 1.4 Ensembl ENCODE dbSUPER 11.4 +50.1 50102 1.4 ELF3 HDGF NFIB ARID4B GLI4 GLIS2 EGR2 SP5 MXD4 ZEB2 SEMA5B SEC22A GC03P122991 LINC02035
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEMA5B on UCSC Golden Path with GeneCards custom track

Promoters for SEMA5B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000157390 905 601 CTCF RB1 SUZ12 TEAD4 RBBP5 RAD21 ZFHX2 GLIS2 POLR2A PRDM10

Genomic Location for SEMA5B Gene

122,909,193 bp from pter
123,028,605 bp from pter
119,413 bases
Minus strand

Genomic View for SEMA5B Gene

Genes around SEMA5B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA5B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA5B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA5B Gene

Proteins for SEMA5B Gene

  • Protein details for SEMA5B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A8K5U2
    • B7Z393
    • F8W9U8
    • Q6DD89
    • Q6UY12
    • Q9NW17

    Protein attributes for SEMA5B Gene

    1151 amino acids
    Molecular mass:
    125913 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA91570.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA95969.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SEMA5B Gene


neXtProt entry for SEMA5B Gene

Post-translational modifications for SEMA5B Gene

  • Glycosylation at Asn153, Asn236, Asn345, isoforms=2, 3, 4436, and isoforms=2, 3, 4788
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEMA5B Gene

Domains & Families for SEMA5B Gene

Gene Families for SEMA5B Gene

Suggested Antigen Peptide Sequences for SEMA5B 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 SEMA5B: view

Function for SEMA5B Gene

Molecular function for SEMA5B Gene

UniProtKB/Swiss-Prot Function:
May act as positive axonal guidance cues.
genes like me logo Genes that share phenotypes with SEMA5B: view

Animal Models for SEMA5B Gene

MGI Knock Outs for SEMA5B:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA5B

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SEMA5B Gene

Localization for SEMA5B Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA5B Gene

Membrane; Single-pass type III membrane protein.

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 SEMA5B gene
Compartment Confidence
plasma membrane 3
cytosol 2
extracellular 1
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SEMA5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SEMA5B: view

Pathways & Interactions for SEMA5B Gene

genes like me logo Genes that share pathways with SEMA5B: view

Interacting Proteins for SEMA5B Gene

Gene Ontology (GO) - Biological Process for SEMA5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007399 nervous system development IEA --
GO:0030154 cell differentiation IEA --
GO:0048675 axon extension IEA --
GO:0050908 detection of light stimulus involved in visual perception IEA --
GO:0097485 neuron projection guidance IEA --
genes like me logo Genes that share ontologies with SEMA5B: view

No data available for SIGNOR curated interactions for SEMA5B Gene

Drugs & Compounds for SEMA5B Gene

No Compound Related Data Available

Transcripts for SEMA5B Gene

Unigene Clusters for SEMA5B Gene

Sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA5B Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^
SP1: - - - - - - -
SP2: - - - -
SP3: - -
SP4: - - - - - -
SP5: - -
SP7: - - - -

ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25a · 25b ^ 26a · 26b · 26c ^ 27a · 27b
SP1: -
SP2: - -
SP3: - -

Relevant External Links for SEMA5B Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SEMA5B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SEMA5B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA5B Gene

This gene is overexpressed in Brain - Cortex (x5.5) and Brain - Hippocampus (x4.2).

Protein differential expression in normal tissues from HIPED for SEMA5B Gene

This gene is overexpressed in Adipocyte (24.2), Esophagus (17.9), and CD4 Tcells (16.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SEMA5B Gene

NURSA nuclear receptor signaling pathways regulating expression of SEMA5B Gene:


SOURCE GeneReport for Unigene cluster for SEMA5B Gene:


Evidence on tissue expression from TISSUES for SEMA5B Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with SEMA5B: view

Primer Products

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA5B Gene

Orthologs for SEMA5B Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA5B Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SEMA5B 34 35
  • 98.62 (n)
(Bos Taurus)
Mammalia SEMA5B 34 35
  • 90.88 (n)
(Mus musculus)
Mammalia Sema5b 34 16 35
  • 89.08 (n)
(Rattus norvegicus)
Mammalia Sema5b 34
  • 88.92 (n)
(Canis familiaris)
Mammalia SEMA5B 34 35
  • 88.57 (n)
(Monodelphis domestica)
Mammalia SEMA5B 35
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 15 (a)
(Gallus gallus)
Aves SEMA5B 34 35
  • 71.99 (n)
(Anolis carolinensis)
Reptilia SEMA5B 35
  • 78 (a)
African clawed frog
(Xenopus laevis)
Amphibia MGC68835 34
(Danio rerio)
Actinopterygii sema5ba 34 35
  • 67.4 (n)
sema5bb 35
  • 63 (a)
fruit fly
(Drosophila melanogaster)
Insecta Sema-5c 36 34 35
  • 51.04 (n)
Sema-1a 36
  • 40 (a)
CG4383 36
  • 36 (a)
Sema-2a 36
  • 35 (a)
Sema-1b 36
  • 34 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002424 34
  • 50.3 (n)
(Caenorhabditis elegans)
Secernentea C36B7.5a 36
  • 31 (a)
C36B7.5b 36
  • 31 (a)
mab-20 36
  • 27 (a)
smp-2 36
  • 25 (a)
Species where no ortholog for SEMA5B 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for SEMA5B Gene

Gene Tree for SEMA5B (if available)
Gene Tree for SEMA5B (if available)

Paralogs for SEMA5B Gene

Paralogs for SEMA5B Gene

genes like me logo Genes that share paralogs with SEMA5B: view

Variants for SEMA5B Gene

Sequence variations from dbSNP and Humsavar for SEMA5B Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs148102705 A breast cancer sample 122,961,140(+) CTTAC(A/C/T)CCTGA intron-variant, nc-transcript-variant, reference, missense
VAR_037198 A breast cancer sample
rs1000027337 -- 123,026,299(+) TGCTG(A/C)TCTCA intron-variant
rs1000035081 -- 122,966,533(+) TAAGA(A/T)TGTTT intron-variant
rs1000057489 -- 123,027,670(+) GATGC(A/G)CTGCC intron-variant, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for SEMA5B Gene

Variant ID Type Subtype PubMed ID
esv2678374 CNV deletion 23128226
esv3597618 CNV gain 21293372
esv998863 CNV insertion 20482838
nsv1127989 CNV deletion 24896259
nsv460835 CNV gain 19166990
nsv460836 CNV loss 19166990
nsv517695 CNV loss 19592680
nsv591409 CNV gain 21841781
nsv591410 CNV loss 21841781
nsv829706 CNV gain 17160897

Variation tolerance for SEMA5B Gene

Residual Variation Intolerance Score: 71.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.22; 90.50% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SEMA5B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA5B Gene

Disorders for SEMA5B Gene

Relevant External Links for SEMA5B

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SEMA5B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SEMA5B Gene

Publications for SEMA5B Gene

  1. Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations. (PMID: 21642993) Wu C. … Lin D. (Nat. Genet. 2011) 3 46 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  4. Semaphorin 5B mediates synapse elimination in hippocampal neurons. (PMID: 19463192) O'Connor T.P. … Bamji S.X. (Neural Dev 2009) 3 22 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for SEMA5B Gene

Sources for SEMA5B Gene

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