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Aliases for SEMA5B Gene

Aliases for SEMA5B Gene

  • Semaphorin 5B 2 3
  • Sema Domain, Seven Thrombospondin Repeats (Type 1 And Type 1-Like), Transmembrane Domain (TM) And Short Cytoplasmic Domain, (Semaphorin) 5B 2 3 5
  • 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. Among its related pathways are Axon guidance and O-glycosylation of TSR domain-containing proteins. GO annotations related to this gene include receptor activity. An important paralog of this gene is SEMA6C.

UniProtKB/Swiss-Prot for SEMA5B Gene

  • May act as positive axonal guidance cues.

No data available for 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

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

ENSRs around SEMA5B on UCSC Golden Path with GeneCards custom track

Genomic Location for SEMA5B Gene

Chromosome:
3
Start:
122,909,193 bp from pter
End:
123,028,605 bp from pter
Size:
119,413 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

Proteomics data for SEMA5B Gene at MOPED

Post-translational modifications for SEMA5B Gene

  • Glycosylation at Asn 153, Asn 236, Asn 345, Asn 436, and Thr 788
  • Modification sites at PhosphoSitePlus

Antibody Products

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

Q9P283

UniProtKB/Swiss-Prot:

SEM5B_HUMAN :
  • Contains 1 PSI domain.
  • Belongs to the semaphorin family.
Domain:
  • Contains 1 PSI domain.
  • Contains 1 Sema domain.
  • Contains 5 TSP type-1 domains.
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

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

COMPARTMENTS
Jensen Localization Image for SEMA5B Gene COMPARTMENTS Subcellular localization image for SEMA5B gene
Compartment Confidence
plasma membrane 3
cytosol 2
extracellular 1
nucleus 1
peroxisome 1

No data available for Gene Ontology (GO) - Cellular Components for SEMA5B Gene

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:0001755 neural crest cell migration IBA --
GO:0030335 positive regulation of cell migration IBA --
GO:0048843 negative regulation of axon extension involved in axon guidance IBA --
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

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:

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
ECgene alternative splicing isoforms for
SEMA5B

Expression for SEMA5B Gene

mRNA expression in normal human tissues 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



SOURCE GeneReport for Unigene cluster for SEMA5B Gene Hs.210870

genes like me logo Genes that share expression patterns with SEMA5B: view

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners 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
cow
(Bos Taurus)
Mammalia SEMA5B 35
  • 90.88 (n)
  • 94.57 (a)
SEMA5B 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA5B 35
  • 88.57 (n)
  • 90.88 (a)
SEMA5B 36
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema5b 35
  • 89.08 (n)
  • 93.6 (a)
Sema5b 16
Sema5b 36
  • 94 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SEMA5B 35
  • 98.62 (n)
  • 98.37 (a)
SEMA5B 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema5b 35
  • 88.92 (n)
  • 93.37 (a)
oppossum
(Monodelphis domestica)
Mammalia SEMA5B 36
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 15 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SEMA5B 35
  • 71.99 (n)
  • 78.52 (a)
SEMA5B 36
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA5B 36
  • 78 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia MGC68835 35
zebrafish
(Danio rerio)
Actinopterygii sema5ba 35
  • 67.4 (n)
  • 69.18 (a)
sema5ba 36
  • 66 (a)
OneToMany
sema5bb 36
  • 63 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG4383 37
  • 36 (a)
Sema-1a 37
  • 40 (a)
Sema-1b 37
  • 34 (a)
Sema-2a 37
  • 35 (a)
Sema-5c 37
  • 37 (a)
Sema-5c 35
  • 51.04 (n)
  • 42.73 (a)
Sema-5c 36
  • 37 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002424 35
  • 50.3 (n)
  • 41.01 (a)
worm
(Caenorhabditis elegans)
Secernentea C36B7.5a 37
  • 31 (a)
C36B7.5b 37
  • 31 (a)
mab-20 37
  • 27 (a)
smp-2 37
  • 25 (a)
Species with no ortholog for SEMA5B:
  • 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)

Paralogs for SEMA5B Gene

Paralogs for SEMA5B Gene

Pseudogenes.org Pseudogenes 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
VAR_037196 A breast cancer sample
rs2276774 - 122,927,981(-) GACTA(C/T)TGAGA nc-transcript-variant, reference, missense
VAR_037198 A breast cancer sample
rs2276781 - 122,913,589(-) GGGCA(C/T)GCAGT nc-transcript-variant, reference, missense
rs2276782 - 122,913,049(-) GGAGG(A/C/T)CCTCC nc-transcript-variant, reference, missense

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

Variant ID Type Subtype PubMed ID
nsv829706 CNV Gain 17160897
nsv877393 CNV Gain 21882294
esv998863 CNV Insertion 20482838
nsv517695 CNV Loss 19592680
nsv460835 CNV Gain 19166990
nsv460836 CNV Loss 19166990
esv2678374 CNV Deletion 23128226

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

HapMap Linkage Disequilibrium report
SEMA5B

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)
SEMA5B
Human Genome Epidemiology (HuGE) Navigator
SEMA5B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEMA5B

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 48 67
  2. Semaphorin 5B mediates synapse elimination in hippocampal neurons. (PMID: 19463192) O'Connor T.P. … Bamji S.X. (Neural Dev 2009) 3 23
  3. A novel class of murine semaphorins with homology to thrombospondin is differentially expressed during early embryogenesis. (PMID: 8817451) Adams R.H. … PA1schel A.W. (Mech. Dev. 1996) 2 3
  4. Kelch Domain of Gigaxonin Interacts with Intermediate Filament Proteins Affected in Giant Axonal Neuropathy. (PMID: 26460568) Johnson-Kerner B.L. … Wichterle H. (PLoS ONE 2015) 3
  5. A directed protein interaction network for investigating intracellular signal transduction. (PMID: 21900206) Vinayagam A. … Wanker E.E. (Sci Signal 2011) 3

Products for SEMA5B Gene

Sources for SEMA5B Gene

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