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 secr... See more...

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
  • Semaphorin-5B 3 4
  • SEMAG 3 4
  • KIAA1445 4
  • SemG 3

External Ids for SEMA5B Gene

Previous HGNC Symbols for SEMA5B Gene

  • SEMAG

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. Diseases associated with SEMA5B include Diffuse Glomerulonephritis and Kallmann Syndrome. Among its related pathways are Metabolism of proteins and O-glycosylation of TSR domain-containing proteins. An important paralog of this gene is SEMA5A.

UniProtKB/Swiss-Prot Summary for SEMA5B Gene

Additional gene information for SEMA5B Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEMA5B Gene

Genomics for SEMA5B Gene

GeneHancer (GH) Regulatory Elements for SEMA5B Gene

Promoters and enhancers for SEMA5B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J123026 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +1.1 1093 3.4 HNRNPK CTCF TEAD4 ZNF639 ZIC2 ZBTB10 ZBTB26 TRIM28 SAP30 REST SEMA5B lnc-HSPBAP1-1 CCDC58 lnc-PDIA5-1
GH03J122997 Promoter/Enhancer 0.7 EPDnew Ensembl 511.9 +31.5 31504 2.2 POLR2A ZBTB20 EZH2 SEMA5B CCDC58 lnc-PDIA5-1 lnc-HSPBAP1-1
GH03J123029 Promoter 0.3 Ensembl 500.7 -0.9 -895 0.2 SEMA5B lnc-HSPBAP1-1 piR-46381-054
GH03J122971 Promoter/Enhancer 1.7 VISTA Ensembl ENCODE CraniofacialAtlas dbSUPER 11.5 +54.7 54655 5 ZNF217 USF1 JUND FOS REST TRIM28 CTBP1 MXI1 ZNF341 OSR2 SEMA5B ADCY5 ENSG00000273454 lnc-PDIA5-1 lnc-HSPBAP1-1 piR-61945-360
GH03J122931 Enhancer 0.9 FANTOM5 Ensembl ENCODE 19 +95.5 95543 4.1 FOS ZNF768 HNF4A CEBPG CEBPB ZNF770 STAT3 CEBPA SEMA5B PARP14 HSPBAP1 SLC49A4 piR-61945-360 lnc-PDIA5-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA5B on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEMA5B

Top Transcription factor binding sites by QIAGEN in the SEMA5B gene promoter:
  • Chx10
  • Ik-1
  • NRSF form 1
  • NRSF form 2
  • Pax-2
  • Pax-2a
  • POU2F1
  • POU2F1a

Genomic Locations for SEMA5B Gene

Genomic Locations for SEMA5B Gene
chr3:122,909,082-123,028,605
(GRCh38/hg38)
Size:
119,524 bases
Orientation:
Minus strand
chr3:122,628,041-122,747,452
(GRCh37/hg19)
Size:
119,412 bases
Orientation:
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:
    Q9P283-SEM5B_HUMAN
    Recommended name:
    Semaphorin-5B
    Protein Accession:
    Q9P283
    Secondary Accessions:
    • A8K5U2
    • B7Z393
    • F8W9U8
    • Q6DD89
    • Q6UY12
    • Q9NW17

    Protein attributes for SEMA5B Gene

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

    Alternative splice isoforms for SEMA5B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA5B Gene

Post-translational modifications for SEMA5B Gene

  • Glycosylation at Asn153, Asn236, Asn345, Asn436, and Thr788
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEMA5B Gene

Domains & Families for SEMA5B Gene

Gene Families for SEMA5B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SEMA5B Gene

Suggested Antigen Peptide Sequences for SEMA5B Gene

GenScript: Design optimal peptide antigens:
  • Semaphorin-5B (SEM5B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9P283

UniProtKB/Swiss-Prot:

SEM5B_HUMAN :
  • Belongs to the semaphorin family.
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.

Phenotypes From GWAS Catalog for SEMA5B Gene

Gene Ontology (GO) - Molecular Function for SEMA5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030215 semaphorin receptor binding IEA --
genes like me logo Genes that share ontologies with SEMA5B: view
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

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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

COMPARTMENTS
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 4
extracellular 3
cytoskeleton 2
nucleus 2
cytosol 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

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,IBA 21873635
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:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0030154 cell differentiation IEA --
GO:0048675 axon extension IBA 21873635
GO:0050908 detection of light stimulus involved in visual perception 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

mRNA/cDNA for SEMA5B Gene

5 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone 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: - -
SP6:
SP7: - - - -
SP8:
SP9:

ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25a · 25b ^ 26a · 26b · 26c ^ 27a · 27b
SP1: -
SP2: - -
SP3: - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for SEMA5B Gene

GeneLoc Exon Structure for
SEMA5B

Expression for SEMA5B Gene

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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEMA5B

SOURCE GeneReport for Unigene cluster for SEMA5B Gene:

Hs.210870

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

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
chimpanzee
(Pan troglodytes)
Mammalia SEMA5B 31 30
  • 98.62 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA5B 31 30
  • 90.88 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Sema5b 17 31 30
  • 89.08 (n)
rat
(Rattus norvegicus)
Mammalia Sema5b 30
  • 88.92 (n)
dog
(Canis familiaris)
Mammalia SEMA5B 31 30
  • 88.57 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SEMA5B 31
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 15 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SEMA5B 31 30
  • 71.99 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA5B 31
  • 78 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia MGC68835 30
zebrafish
(Danio rerio)
Actinopterygii sema5ba 31 30
  • 67.4 (n)
OneToMany
sema5bb 31
  • 63 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Sema-5c 31 32 30
  • 51.04 (n)
OneToMany
Sema-1a 32
  • 40 (a)
CG4383 32
  • 36 (a)
Sema-2a 32
  • 35 (a)
Sema-1b 32
  • 34 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002424 30
  • 50.3 (n)
worm
(Caenorhabditis elegans)
Secernentea C36B7.5b 32
  • 31 (a)
C36B7.5a 32
  • 31 (a)
mab-20 32
  • 27 (a)
smp-2 32
  • 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

ENSEMBL:
Gene Tree for SEMA5B (if available)
TreeFam:
Gene Tree for SEMA5B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEMA5B: view image

Paralogs for SEMA5B Gene

(11) SIMAP similar genes for SEMA5B Gene using alignment to 7 proteins:

  • SEM5B_HUMAN
  • B5ME80_HUMAN
  • C9JKR3_HUMAN
  • C9JTV9_HUMAN
  • C9JTX2_HUMAN
  • F8WAT5_HUMAN
  • H0Y5U2_HUMAN
genes like me logo Genes that share paralogs with SEMA5B: view

Variants for SEMA5B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEMA5B Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs148102705 A breast cancer sample p.Gly42Ser
VAR_037198 A breast cancer sample p.Ile223Met
rs2276774 - p.Ile220Thr
rs2276781 - p.Met742Thr
rs2276782 - p.Val840Asp

Additional dbSNP identifiers (rs#s) for SEMA5B Gene

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)

Additional Variant Information for SEMA5B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA5B

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

Disorders for SEMA5B Gene

MalaCards: The human disease database

(2) MalaCards diseases for SEMA5B Gene - From: DISEASES

Disorder Aliases PubMed IDs
diffuse glomerulonephritis
  • glomerulonephritis diffuse
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA5B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SEMA5B: view

No data available for 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 (Nature genetics 2011) 3 41 54
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  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 SD … DREAM investigators (Diabetes care 2010) 3 41 54
  4. Semaphorin 5B mediates synapse elimination in hippocampal neurons. (PMID: 19463192) O'Connor TP … Bamji SX (Neural development 2009) 3 23 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54

Products for SEMA5B Gene

Sources for SEMA5B Gene