U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    SEMA5A semaphorin 5A [ Homo sapiens (human) ]

    Gene ID: 9037, updated on 10-Dec-2024

    Summary

    Go to the top of the page Help
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

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

    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

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

    Go to the top of the page

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous