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SEMA5A semaphorin 5A [ Homo sapiens (human) ]

Gene ID: 9037, updated on 3-May-2020

Summary

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Official Symbol
SEMA5Aprovided by HGNC
Official Full Name
semaphorin 5Aprovided by HGNC
Primary source
HGNC:HGNC:10736
See related
Ensembl:ENSG00000112902 MIM:609297
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
semF; SEMAF
Summary
This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene.[provided by RefSeq, Jan 2010]
Expression
Broad expression in lung (RPKM 6.9), kidney (RPKM 6.5) and 24 other tissues See more
Orthologs
mouse all

Genomic context

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See SEMA5A in Genome Data Viewer
Location:
5p15.31
Exon count:
28
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (9035030..9546121, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (9035138..9546233, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene MT-CYB pseudogene 37 Neighboring gene uncharacterized LOC101929307 Neighboring gene long intergenic non-protein coding RNA 2199 Neighboring gene microRNA 4636 Neighboring gene SEMA5A antisense RNA 1 Neighboring gene uncharacterized LOC101929359 Neighboring gene small nucleolar RNA, C/D box 123 Neighboring gene small nucleolar RNA host gene 18

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Assessment of the Usefulness of the SEMA5A Concentration Profile Changes as a Molecular Marker in Endometrial Cancer. Dziobek K, et al. Curr Pharm Biotechnol, 2020. PMID 31544715
  2. Semaphorin-5A maintains epithelial phenotype of malignant pancreatic cancer cells. Saxena S, et al. BMC Cancer, 2018 Dec 22. PMID 30577767, Free PMC Article
  3. A de novo microdeletion of SEMA5A in a boy with autism spectrum disorder and intellectual disability. Mosca-Boidron AL, et al. Eur J Hum Genet, 2016 Jun. PMID 26395558, Free PMC Article
  4. Meta analysis of the association of rs7702187 SNP in SEMA5A gene with risk of Parkinson's disease. Yu X, et al. Eur Rev Med Pharmacol Sci, 2014. PMID 24706317
  5. The SEMA5A gene is associated with hippocampal volume, and their interaction is associated with performance on Raven's Progressive Matrices. Zhu B, et al. Neuroimage, 2014 Mar. PMID 24291503

See all (45) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. In our study of SEMA5A expression in endometrial cancer, we observed an increased level of this protein compared to the control. The homogeneity of expression changes at the transcriptome and proteome levels suggests that SEMA5A could be a new potential supplementary molecular marker in endometrial cancer.
    Title: Assessment of the Usefulness of the SEMA5A Concentration Profile Changes as a Molecular Marker in Endometrial Cancer.
  2. Study provide the first evidence that SEMA3C, SEMA5A and SEMA6D can be considered as markers of liver injury in chronic hepatitis C. While serum concentrations of SEMA3C and SEMA6D significantly increased with fibrosis stage in both HCV-g1 and HCV-g3 infections, the concentration of SEMA5A inversely correlated with fibrosis stage in both HCV genotypes.
    Title: The association of semaphorins 3C, 5A and 6D with liver fibrosis stage in chronic hepatitis C.
  3. Collectively, our data suggest that SEMA5A expression maintains epithelial phenotype in the metastatic microenvironment
    Title: Semaphorin-5A maintains epithelial phenotype of malignant pancreatic cancer cells.
  4. Data provide evidences supporting the role of Sema5A in melanoma progression and the involvement of Bcl-2, miR-204 and c-Myb in regulating its expression.
    Title: Semaphorin 5A drives melanoma progression: role of Bcl-2, miR-204 and c-Myb.
  5. SEMA5A gene is associated with hippocampal volume, and their interaction is associated with reasoning ability.
    Title: The SEMA5A gene is associated with hippocampal volume, and their interaction is associated with performance on Raven's Progressive Matrices.
  6. De novo translocation t(5;22)(p15.3;q11.21) associated with a partial deletion of SEMA5A identified in a patient with ASD.
    Title: A de novo microdeletion of SEMA5A in a boy with autism spectrum disorder and intellectual disability.
  7. Our data demonstrated that elevated serum Semaphorin5A (Sema5A) in SLE patients correlated with disease activity and are involved in kidney and blood system damage; ADAM17 might be involved in the release of secreted Sema5A.
    Title: Elevated semaphorin5A in systemic lupus erythematosus is in association with disease activity and lupus nephritis.
  8. data demonstrated that elevated serum Semaphorin5A in systemic lupus erythematosus patients correlated with disease activity and are involved in kidney and blood system damage; ADAM17 might be involved in the release of secreted Sema5A
    Title: Elevated semaphorin5A in systemic lupus erythematosus is in association with disease activity and lupus nephritis.
  9. Multigenerational autosomal dominant inheritance of 5p chromosomal deletions resulting in Cri-du-Chat Syndrome with SEMA5A, CTNND2, and ICE1 deficiencies has been described.
    Title: Multigenerational autosomal dominant inheritance of 5p chromosomal deletions.
  10. The Single-Nucleotide Polymorphism (SNP) of rs7702187 within the SEMA5A gene would be a high-penetrant risk factor for PD development.
    Title: Meta analysis of the association of rs7702187 SNP in SEMA5A gene with risk of Parkinson's disease.
Submit: New GeneRIF Correction See all GeneRIFs (29)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

NHGRI GWAS Catalog

Description
A genome-wide linkage and association scan reveals novel loci for autism.
NHGRI GWA Catalog
Genome-wide association of serum uric acid concentration: replication of sequence variants in an island population of the Adriatic coast of Croatia.
NHGRI GWA Catalog
High-resolution whole-genome association study of Parkinson disease.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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General gene information

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Markers

Homology

Clone Names

  • FLJ12815

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chondroitin sulfate proteoglycan binding ISS
Inferred from Sequence or Structural Similarity
more info
  
heparan sulfate proteoglycan binding ISS
Inferred from Sequence or Structural Similarity
more info
  
semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
semaphorin receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
  
syndecan binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
axon extension IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
axonal fasciculation ISS
Inferred from Sequence or Structural Similarity
more info
  
blood vessel endothelial cell proliferation involved in sprouting angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
cell adhesion TAS
Traceable Author Statement
more info
 PubMed 
cell chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
  
cell-cell signaling TAS
Traceable Author Statement
more info
 PubMed 
diencephalon development ISS
Inferred from Sequence or Structural Similarity
more info
  
negative regulation of axon extension involved in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
negative regulation of cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
  
negative regulation of endothelial cell apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
  
nervous system development TAS
Traceable Author Statement
more info
 PubMed 
positive chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
  
positive regulation of actin filament depolymerization ISS
Inferred from Sequence or Structural Similarity
more info
  
positive regulation of angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
positive regulation of axon extension involved in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
positive regulation of canonical Wnt signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
positive regulation of endothelial cell chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
  
positive regulation of endothelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
  
positive regulation of protein kinase B signaling ISS
Inferred from Sequence or Structural Similarity
more info
  
semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
signal clustering ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
integral component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
semaphorin-5A
Names
sema F
sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A
semaphorin F

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016410.1 RefSeqGene

    Range
    5001..516096
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_003966.3 → NP_003957.2  semaphorin-5A precursor

    See identical proteins and their annotated locations for NP_003957.2

    Status: REVIEWED

    Source sequence(s)
    AC021088, AC022446, AC027335, AC027336, AC034214, AC091906
    Consensus CDS
    CCDS3875.1
    UniProtKB/Swiss-Prot
    Q13591
    UniProtKB/TrEMBL
    X5DR95
    Related
    ENSP00000371936.5, ENST00000382496.10
    Conserved Domains (3) summary
    cd11263
    Location:50 → 485
    Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)
    smart00209
    Location:844 → 896
    TSP1; Thrombospondin type 1 repeats
    pfam01437
    Location:486 → 533
    PSI; Plexin repeat

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    9035030..9546121 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010016.2 → XP_016865505.1  semaphorin-5A isoform X3

  2. XM_011514157.2 → XP_011512459.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_011512459.1

    UniProtKB/Swiss-Prot
    Q13591
    UniProtKB/TrEMBL
    X5DR95
    Conserved Domains (3) summary
    cd11263
    Location:50 → 485
    Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)
    smart00209
    Location:844 → 896
    TSP1; Thrombospondin type 1 repeats
    pfam01437
    Location:486 → 533
    PSI; Plexin repeat

  3. XM_006714506.3 → XP_006714569.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_006714569.1

    UniProtKB/Swiss-Prot
    Q13591
    UniProtKB/TrEMBL
    X5DR95
    Conserved Domains (3) summary
    cd11263
    Location:50 → 485
    Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)
    smart00209
    Location:844 → 896
    TSP1; Thrombospondin type 1 repeats
    pfam01437
    Location:486 → 533
    PSI; Plexin repeat

  4. XM_011514156.2 → XP_011512458.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_011512458.1

    UniProtKB/Swiss-Prot
    Q13591
    UniProtKB/TrEMBL
    X5DR95
    Related
    ENSP00000499013.1, ENST00000652226.1
    Conserved Domains (3) summary
    cd11263
    Location:50 → 485
    Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)
    smart00209
    Location:844 → 896
    TSP1; Thrombospondin type 1 repeats
    pfam01437
    Location:486 → 533
    PSI; Plexin repeat

  5. XM_011514158.2 → XP_011512460.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_011512460.1

    UniProtKB/Swiss-Prot
    Q13591
    UniProtKB/TrEMBL
    X5DR95
    Conserved Domains (3) summary
    cd11263
    Location:50 → 485
    Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)
    smart00209
    Location:844 → 896
    TSP1; Thrombospondin type 1 repeats
    pfam01437
    Location:486 → 533
    PSI; Plexin repeat

  6. XM_011514155.2 → XP_011512457.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_011512457.1

    UniProtKB/Swiss-Prot
    Q13591
    UniProtKB/TrEMBL
    X5DR95
    Conserved Domains (3) summary
    cd11263
    Location:50 → 485
    Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)
    smart00209
    Location:844 → 896
    TSP1; Thrombospondin type 1 repeats
    pfam01437
    Location:486 → 533
    PSI; Plexin repeat

  7. XM_006714507.3 → XP_006714570.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_006714570.1

    UniProtKB/Swiss-Prot
    Q13591
    UniProtKB/TrEMBL
    X5DR95
    Conserved Domains (3) summary
    cd11263
    Location:50 → 485
    Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)
    smart00209
    Location:844 → 896
    TSP1; Thrombospondin type 1 repeats
    pfam01437
    Location:486 → 533
    PSI; Plexin repeat

  8. XM_011514159.2 → XP_011512461.1  semaphorin-5A isoform X2

    Conserved Domains (3) summary
    smart00209
    Location:797 → 849
    TSP1; Thrombospondin type 1 repeats
    pfam01437
    Location:439 → 486
    PSI; Plexin repeat
    cl15693
    Location:34 → 438
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13591.3 GenPept UniProtKB/Swiss-Prot:Q13591

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