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SEMA5B Gene(Protein Coding)

Semaphorin 5B

GCID:
GC03M122909
GIFtS:
48
Genes Participants
UDN Logo

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

  • 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 Metabolism of proteins and O-linked glycosylation. Gene Ontology (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.

Additional gene information for SEMA5B Gene

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

Products:

  1. Regulatory Element

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
GH03I123027 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 +0.3 293 1.8 RB1 MZF1 SIN3A ZNF2 RAD21 ZNF335 GLIS2 ZNF366 ZNF143 ZNF391 SEMA5B GC03P122991
GH03I122992 Promoter/Enhancer 0.8 EPDnew ENCODE 562.1 +35.3 35341 0.8 POLR2A SEMA5B GC03P122991
GH03I122989 Promoter 0.5 EPDnew 562.1 +39.4 39350 0.1 SEMA5B GC03P122991 LINC02035
GH03I122971 Enhancer 1.4 VISTA Ensembl ENCODE dbSUPER 11.5 +54.7 54655 5 HDGF PKNOX1 CLOCK ZFP64 FEZF1 ZNF335 ZNF366 SCRT2 RCOR1 FOS SEMA5B ADCY5 ENSG00000273454 GC03P122991 LINC02035
GH03I123079 Enhancer 1.4 Ensembl ENCODE dbSUPER 11.2 -52.5 -52482 4.8 ATF1 FEZF1 NCOA2 TCF12 ZNF766 GATA2 FOS RUNX3 NCOA1 ZNF592 SEMA5B PDIA5 GC03P123071 MIR7110
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SEMA5B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SEMA5B gene promoter:

Genomic Locations for SEMA5B Gene

Genomic Locations for SEMA5B Gene
chr3:122,909,193-123,028,605
(GRCh38/hg38)
Size:
119,413 bases
Orientation:
Minus strand
chr3:122,628,041-122,747,452
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for SEMA5B Gene

Proteins for SEMA5B Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for SEMA5B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SEMA5B Gene

  • Glycosylation at posLast=153153, posLast=236236, isoforms=2, 3, 4345, isoforms=2, 3, 4436, and isoforms=2, 3, 4788

Other Protein References for SEMA5B Gene

ENSEMBL proteins:
REFSEQ proteins:

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

InterPro:
Blocks:
ProtoNet:

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 :
  • 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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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:0038191 neuropilin binding IBA --
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

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
extracellular 4
plasma membrane 3
cytosol 2
peroxisome 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SEMA5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA --
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

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000350215%0d%0a9606.ENSP00000257359%0d%0a9606.ENSP00000251582%0d%0a9606.ENSP00000272643%0d%0a9606.ENSP00000362304%0d%0a9606.ENSP00000422554%0d%0a
Selected Interacting proteins: Q9P283-SEM5B_HUMAN ENSP00000350215 for SEMA5B Gene via MINT STRING IID

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 IEA --
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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SEMA5B Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SEMA5B Gene

(7) REFSEQ mRNAs :
(11) Additional mRNA sequences :
(53) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links where relevant :

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:

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
ECgene alternative splicing isoforms for
SEMA5B

Expression for SEMA5B Gene

Products:

  1. Primer

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

mRNA expression in normal human tissues for SEMA5B Gene
mRNA expression by BioGPS for SEMA5B GenemRNA expression by GTEx 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:

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 33 34
  • 98.62 (n)
cow
(Bos Taurus)
 Mammalia SEMA5B 33 34
  • 90.88 (n)
mouse
(Mus musculus)
 Mammalia Sema5b 33 16 34
  • 89.08 (n)
rat
(Rattus norvegicus)
 Mammalia Sema5b 33
  • 88.92 (n)
dog
(Canis familiaris)
 Mammalia SEMA5B 33 34
  • 88.57 (n)
oppossum
(Monodelphis domestica)
 Mammalia SEMA5B 34
  • 83 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 34
  • 15 (a)
 ManyToMany
chicken
(Gallus gallus)
 Aves SEMA5B 33 34
  • 71.99 (n)
lizard
(Anolis carolinensis)
 Reptilia SEMA5B 34
  • 78 (a)
 OneToOne
African clawed frog
(Xenopus laevis)
 Amphibia MGC68835 33
zebrafish
(Danio rerio)
 Actinopterygii sema5ba 33 34
  • 67.4 (n)
sema5bb 34
  • 63 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta Sema-5c 35 33 34
  • 51.04 (n)
Sema-1a 35
  • 40 (a)
CG4383 35
  • 36 (a)
Sema-2a 35
  • 35 (a)
Sema-1b 35
  • 34 (a)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP002424 33
  • 50.3 (n)
worm
(Caenorhabditis elegans)
 Secernentea C36B7.5a 35
  • 31 (a)
C36B7.5b 35
  • 31 (a)
mab-20 35
  • 27 (a)
smp-2 35
  • 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)

Paralogs for SEMA5B Gene

Paralogs for SEMA5B Gene

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

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 Variation AA Info Type
rs148102705 A breast cancer sample 122,961,140(-) C/A/T coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
VAR_037198 A breast cancer sample p.Ile223Met
rs1000027337 -- 123,026,299(-) C/A genic_upstream_transcript_variant, intron_variant
rs1000035081 -- 122,966,533(-) A/T intron_variant
rs1000057489 -- 123,027,670(-) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant

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

Additional Disease Information for SEMA5B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 (Nature genetics 2011) 3 44 58
  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 44 58
  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 44 58
  4. Semaphorin 5B mediates synapse elimination in hippocampal neurons. (PMID: 19463192) O'Connor TP … Bamji SX (Neural development 2009) 3 22 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for SEMA5B Gene

Sources for SEMA5B Gene

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