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SEMA5A semaphorin 5A [ Homo sapiens (human) ]

Gene ID: 9037, updated on 2-Nov-2024

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; AllianceGenome:HGNC:10736
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
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Genomic context

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See SEMA5A in Genome Data Viewer
Location:
5p15.31
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (9035033..9546075, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (8974898..9485916, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (9035145..9546187, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr5:8627353-8627526 Neighboring gene MT-CYB pseudogene 37 Neighboring gene uncharacterized LOC101929307 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:8828894-8830093 Neighboring gene long intergenic non-protein coding RNA 2199 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:9013731-9014930 Neighboring gene microRNA 4636 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9122300-9122841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22348 Neighboring gene uncharacterized LOC124901170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9196848-9197348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9197349-9197849 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:9222365-9222985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22349 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:9456145-9456684 Neighboring gene SEMA5A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15910 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 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. 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
  2. High gene expression of semaphorin 5A in pancreatic cancer is associated with tumor growth, invasion and metastasis. Sadanandam A, et al. Int J Cancer, 2010 Sep 1. PMID 20073063, Free PMC Article
  3. [Correlation study of semaphorin 5a with risk of Parkinson's disease in a Chinese Han population]. Dong HR, et al. Zhonghua Yi Xue Za Zhi, 2009 Jun 16. PMID 19957501
  4. Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women. Lu TP, et al. Cancer Epidemiol Biomarkers Prev, 2010 Oct. PMID 20802022
  5. Association study of semaphorin 5A with risk of Parkinson's disease in a Chinese Han population. Ding H, et al. Brain Res, 2008 Dec 15. PMID 18950607

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circular RNA circSEMA5A facilitates colorectal cancer development by regulating microRNA-195-5p to target CCNE1 axis.
    Title: Circular RNA circSEMA5A facilitates colorectal cancer development by regulating microRNA-195-5p to target CCNE1 axis.
  2. SEMA5A-PLXNB3 Axis Promotes PDAC Liver Metastasis Outgrowth through Enhancing the Warburg Effect.
    Title: SEMA5A-PLXNB3 Axis Promotes PDAC Liver Metastasis Outgrowth through Enhancing the Warburg Effect.
  3. Semaphorin 5A suppresses ferroptosis through activation of PI3K-AKT-mTOR signaling in rheumatoid arthritis.
    Title: Semaphorin 5A suppresses ferroptosis through activation of PI3K-AKT-mTOR signaling in rheumatoid arthritis.
  4. TSP1 is the essential domain of SEMA5A involved in pannus formation in rheumatoid arthritis.
    Title: TSP1 is the essential domain of SEMA5A involved in pannus formation in rheumatoid arthritis.
  5. Relationship between disease and disease severity and semaphorin 5A and hemogram level in obsessive-compulsive disorder.
    Title: Relationship between disease and disease severity and semaphorin 5A and hemogram level in obsessive-compulsive disorder.
  6. The Expression of IL-17, in Chronic Spontaneous Urticaria Is Linked to Semaphorin5A.
    Title: The Expression of IL-17, in Chronic Spontaneous Urticaria Is Linked to Semaphorin5A.
  7. Circular RNA circSEMA5A promotes bladder cancer progression by upregulating ENO1 and SEMA5A expression.
    Title: Circular RNA circSEMA5A promotes bladder cancer progression by upregulating ENO1 and SEMA5A expression.
  8. Semaphorin 5A suppresses the proliferation and migration of lung adenocarcinoma cells.
    Title: Semaphorin 5A suppresses the proliferation and migration of lung adenocarcinoma cells.
  9. High Expression Levels of Long Noncoding RNA Small Nucleolar RNA Host Gene 18 and Semaphorin 5A Indicate Poor Prognosis in Multiple Myeloma.
    Title: High Expression Levels of Long Noncoding RNA Small Nucleolar RNA Host Gene 18 and Semaphorin 5A Indicate Poor Prognosis in Multiple Myeloma.
  10. Semaphorin-5A downregulation is associated with enhanced migration and invasion of BRAF-positive melanoma cells under vemurafenib treatment in melanomas with heterogeneous BRAF status
    Title: Semaphorin-5A downregulation is associated with enhanced migration and invasion of BRAF-positive melanoma cells under vemurafenib treatment in melanomas with heterogeneous BRAF status.
Submit: New GeneRIF Correction See all GeneRIFs (39)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide linkage and association scan reveals novel loci for autism.
EBI GWAS Catalog
Genome-wide association of serum uric acid concentration: replication of sequence variants in an island population of the Adriatic coast of Croatia.
EBI GWAS Catalog
High-resolution whole-genome association study of Parkinson disease.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS 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
enables chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables chondroitin sulfate proteoglycan binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables heparan sulfate proteoglycan binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables semaphorin receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables syndecan binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in axon extension IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in axonal fasciculation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in blood vessel endothelial cell proliferation involved in sprouting angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell adhesion TAS
Traceable Author Statement
more info
 PubMed 
involved_in cell chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell-cell signaling TAS
Traceable Author Statement
more info
 PubMed 
involved_in diencephalon development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative chemotaxis IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of axon extension involved in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of endothelial cell apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in nervous system development TAS
Traceable Author Statement
more info
 PubMed 
involved_in neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of actin filament depolymerization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of axon extension involved in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of canonical Wnt signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of endothelial cell chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of endothelial cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in signal clustering ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in 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_016410.2 RefSeqGene

    Range
    5000..516042
    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
    D3DTC6, O60408, Q13591, Q1RLL9
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    9035033..9546075 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514158.3 → XP_011512460.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_011512460.1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    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

  2. XM_011514157.3 → XP_011512459.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_011512459.1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    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_006714506.4 → XP_006714569.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_006714569.1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    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_011514156.3 → XP_011512458.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_011512458.1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    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_011514155.3 → XP_011512457.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_011512457.1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    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_047417865.1 → XP_047273821.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  7. XM_047417866.1 → XP_047273822.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  8. XM_006714507.4 → XP_006714570.1  semaphorin-5A isoform X1

    See identical proteins and their annotated locations for XP_006714570.1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    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

  9. XM_047417867.1 → XP_047273823.1  semaphorin-5A isoform X3

  10. XM_011514159.3 → 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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    8974898..9485916 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054353761.1 → XP_054209736.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  2. XM_054353762.1 → XP_054209737.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  3. XM_054353758.1 → XP_054209733.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  4. XM_054353759.1 → XP_054209734.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  5. XM_054353757.1 → XP_054209732.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  6. XM_054353755.1 → XP_054209730.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  7. XM_054353756.1 → XP_054209731.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  8. XM_054353760.1 → XP_054209735.1  semaphorin-5A isoform X1

    UniProtKB/Swiss-Prot
    D3DTC6, O60408, Q13591, Q1RLL9
    UniProtKB/TrEMBL
    X5DR95

  9. XM_054353764.1 → XP_054209739.1  semaphorin-5A isoform X3

  10. XM_054353763.1 → XP_054209738.1  semaphorin-5A isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13591.3 GenPept UniProtKB/Swiss-Prot:Q13591

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