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GCID:
GC03M122909
GIFtS:
53

SEMA5B Gene(Protein Coding)

Sema Domain, Seven Thrombospondin Repeats (Type 1 And Type 1-Like), Transmembrane Domain (TM) And Short Cytoplasmic Domain, (Semaphorin) 5B

Aliases for SEMA5B Gene

Aliases for SEMA5B Gene

  • 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 Symbols for SEMA5B Gene

  • SEMAG

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 (Sema Domain, Seven Thrombospondin Repeats (Type 1 And Type 1-Like), Transmembrane Domain (TM) And Short Cytoplasmic Domain, (Semaphorin) 5B) is a Protein Coding gene. Among its related pathways are Axon guidance. 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

Genomic Location for SEMA5B Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SEMA5B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA5B Gene

Regulatory Elements 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

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

No data available for DME Specific Peptides for SEMA5B Gene

Domains for SEMA5B Gene

Gene Families for SEMA5B Gene

HGNC:

UniProtKB/Swiss-Prot:

SEM5B_HUMAN
Domain:
  • Contains 1 PSI domain.:
    • Q9P283
  • Contains 1 Sema domain.:
    • Q9P283
  • Contains 5 TSP type-1 domains.:
    • Q9P283
Family:
  • Belongs to the semaphorin family.:
    • Q9P283
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.

Gene Ontology (GO) - Molecular Function for SEMA5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity IEA --
GO:0005515 protein binding --
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:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting 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

Gene Ontology (GO) - Cellular Components for SEMA5B Gene

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

Pathways for SEMA5B Gene

SuperPathways for SEMA5B Gene

Superpath Contained pathways
1 Axon guidance
genes like me logo Genes that share pathways with SEMA5B: view

Pathways by source for SEMA5B Gene

1 KEGG pathway for SEMA5B Gene

Interacting Proteins for SEMA5B Gene

Gene Ontology (GO) - Biological Process for SEMA5B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organismal development --
GO:0007399 nervous system development IEA --
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with SEMA5B: view

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 (5.5) and Brain - Hippocampus (4.2).

Integrated Proteomics: protein expression 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 expressions with SEMA5B: view

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 36
  • 98.62 (n)
  • 98.37 (a)
SEMA5B 37
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA5B 36
  • 90.88 (n)
  • 94.57 (a)
SEMA5B 37
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA5B 36
  • 88.57 (n)
  • 90.88 (a)
SEMA5B 37
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema5b 36
  • 89.08 (n)
  • 93.6 (a)
Sema5b 16
Sema5b 37
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SEMA5B 37
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 15 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Sema5b 36
  • 88.92 (n)
  • 93.37 (a)
chicken
(Gallus gallus)
Aves SEMA5B 36
  • 71.99 (n)
  • 78.52 (a)
SEMA5B 37
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA5B 37
  • 78 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia MGC68835 36
zebrafish
(Danio rerio)
Actinopterygii sema5ba 36
  • 67.4 (n)
  • 69.18 (a)
sema5ba 37
  • 66 (a)
OneToMany
sema5bb 37
  • 63 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002424 36
  • 50.3 (n)
  • 41.01 (a)
fruit fly
(Drosophila melanogaster)
Insecta Sema-5c 36
  • 51.04 (n)
  • 42.73 (a)
Sema-5c 37
  • 37 (a)
OneToMany
Sema-1b 38
  • 34 (a)
Sema-5c 38
  • 37 (a)
Sema-1a 38
  • 40 (a)
Sema-2a 38
  • 35 (a)
CG4383 38
  • 36 (a)
worm
(Caenorhabditis elegans)
Secernentea C36B7.5a 38
  • 31 (a)
mab-20 38
  • 27 (a)
C36B7.5b 38
  • 31 (a)
smp-2 38
  • 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 MAF
rs17171 -- 122,963,083(-) TGAGT(A/G)TGTAG intron-variant
rs745442 -- 122,947,507(+) TCCGC(A/G)TGTCC intron-variant
rs767293 -- 122,931,147(-) TGGGA(A/G)GAGTG intron-variant
rs891672 -- 122,944,380(-) CTTTA(C/G)CCTGG intron-variant
rs895074 -- 122,975,553(+) AAAAC(C/T)ACACA intron-variant

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

Relevant External Links for SEMA5B Gene

HapMap Linkage Disequilibrium report
SEMA5B

Disorders for SEMA5B Gene

Relevant External Links for SEMA5B

Genetic Association Database (GAD)
SEMA5B
Human Genome Epidemiology (HuGE) Navigator
SEMA5B
genes like me logo Genes that share disorders with SEMA5B: view

No data available for UniProtKB/Swiss-Prot for SEMA5B Gene

Publications for SEMA5B Gene

  1. Semaphorin 5B mediates synapse elimination in hippocampal neurons. (PMID: 19463192) O'Connor T.P. … Bamji S.X. (Neural Dev 2009) 3 23
  2. 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
  3. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T. … Ohara O. (DNA Res. 2000) 3 4
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4

Products for SEMA5B Gene

Sources for SEMA5B Gene

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