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    SEMA6A semaphorin 6A [ Homo sapiens (human) ]

    Gene ID: 57556, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SEMA6Aprovided by HGNC
    Official Full Name
    semaphorin 6Aprovided by HGNC
    Primary source
    HGNC:HGNC:10738
    See related
    Ensembl:ENSG00000092421 MIM:605885; AllianceGenome:HGNC:10738
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    VIA; SEMA; HT018; SEMAQ; SEMA6A1
    Summary
    Predicted to enable identical protein binding activity; signaling receptor binding activity; and transmembrane signaling receptor activity. Involved in cellular response to vascular endothelial growth factor stimulus; negative regulation of cell adhesion involved in sprouting angiogenesis; and negative regulation of signal transduction. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in adrenal (RPKM 13.5), placenta (RPKM 11.0) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SEMA6A in Genome Data Viewer
    Location:
    5q23.1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (116443555..116574823, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (116956014..117086961, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (115779251..115910519, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene COMM domain containing 10 Neighboring gene microRNA 12130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:115696405-115697201 Neighboring gene uncharacterized LOC101927190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16258 Neighboring gene SEMA6A antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:115823690-115824889 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:115853599-115854798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:115858520-115859094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:115859095-115859667 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:115894513-115895385 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:115895386-115896257 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:115907796-115908577 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16259 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:115913215-115913850 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:115913851-115914484 Neighboring gene SEMA6A antisense RNA 2 Neighboring gene ribosomal protein S14 pseudogene 8 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:115964490-115965301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22946 Neighboring gene NANOG hESC enhancer GRCh37_chr5:115975944-115976532 Neighboring gene Sharpr-MPRA regulatory region 8609 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:115996497-115996997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22948 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:116040271-116040997 Neighboring gene ribosomal protein S17 pseudogene 2 Neighboring gene long intergenic non-protein coding RNA 2214

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genome-Wide CRISPR Screen Identifies Semaphorin 6A and 6B as Receptors for Paeniclostridium sordellii Toxin TcsL.
      Title: Genome-Wide CRISPR Screen Identifies Semaphorin 6A and 6B as Receptors for Paeniclostridium sordellii Toxin TcsL.
    2. Semaphorin 6A Attenuates the Migration Capability of Lung Cancer Cells via the NRF2/HMOX1 Axis.
      Title: Semaphorin 6A Attenuates the Migration Capability of Lung Cancer Cells via the NRF2/HMOX1 Axis.
    3. RNA-guided epigenetic editing of Sema6a gene promoters via a dCas9-SunTag system with C11orf46 binding normalized SEMA6A expression and rescued transcallosal dysconnectivity via repressive chromatin remodeling by the SETDB1 repressor complex.
      Title: In vivo epigenetic editing of Sema6a promoter reverses transcallosal dysconnectivity caused by C11orf46/Arl14ep risk gene.
    4. The A alleles of SEMA6A and POMP genes are likely the risk factors of disease development in Georgians
      Title: NEW GENETIC MARKERS ASSOCIATED WITH SUSCEPTIBILITY TO EXFOLIATION SYNDROME AMONG GEORGIAN POPULATION.
    5. describes the experiments and methods enabling the characterization of Semaphorin 6A as a critical regulator of endothelial cell survival and vessel function
      Title: Characterization of Semaphorin 6A-Mediated Effects on Angiogenesis Through Regulation of VEGF Signaling.
    6. miR-203 induces the apoptosis of YD-38 human oral cancer cells by directly targeting SEMA6A.
      Title: Suppression of Oral Carcinoma Oncogenic Activity by microRNA-203 via Down-regulation of SEMA6A.
    7. our findings indicated that SEMA6A may be a potential prognostic biomarker in the treatment of Glioblastoma multiforme
      Title: SEMA6A is a prognostic biomarker in glioblastoma.
    8. Data suggest that Sema6A and Mical1 may represent new potential therapeutic targets in BRAFV600E melanoma.
      Title: Sema6A and Mical1 control cell growth and survival of BRAFV600E human melanoma cells.
    9. We identified the SEMA6A and HLA-DP loci as significant contributors to risk for granulomatosis with polyangiitis.
      Title: Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis.
    10. Data show that miR-27a/b regulated the expression of the angiogenesis inhibitor semaphorin 6A (SEMA6A) in vitro and in vivo and targeted the 3'-untranslated region of SEMA6A.
      Title: MicroRNA-27a/b controls endothelial cell repulsion and angiogenesis by targeting semaphorin 6A.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization and their interaction with birth order.
    EBI GWAS Catalog
    Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis.
    EBI GWAS Catalog
    Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease.
    EBI GWAS Catalog
    Genome-wide association study of chronic periodontitis in a general German population.
    EBI GWAS Catalog
    Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis.
    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1368

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in animal organ morphogenesis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in apoptotic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in axon guidance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cell surface receptor signaling pathway NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cellular response to vascular endothelial growth factor stimulus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cytoskeleton organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of ERK1 and ERK2 cascade IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of angiogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in negative regulation of cell adhesion involved in sprouting angiogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in negative regulation of sprouting angiogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of vascular endothelial growth factor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nervous system development NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of neuron migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in axon NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    semaphorin-6A
    Names
    SEMA6A-1
    sema VIa
    sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A
    semaphorin 6A-1
    semaphorin VIA

    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.

    mRNA and Protein(s)

    1. NM_001300780.2 → NP_001287709.1  semaphorin-6A isoform 1 precursor

      See identical proteins and their annotated locations for NP_001287709.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB037789, AF279656, AI110626, AL544905, BC032619
      Consensus CDS
      CCDS75288.1
      UniProtKB/TrEMBL
      A0A0A0MQU6, B2RCJ4
      Related
      ENSP00000257414.8, ENST00000257414.12
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 544
      PSI; Plexin repeat

    2. NM_020796.5 → NP_065847.1  semaphorin-6A isoform 2 precursor

      See identical proteins and their annotated locations for NP_065847.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AB037789, AF279656, AI110626, AL544905, BC032619
      Consensus CDS
      CCDS47256.1
      UniProtKB/Swiss-Prot
      Q9H2E6, Q9P2H9
      UniProtKB/TrEMBL
      B2RCJ4
      Related
      ENSP00000345512.6, ENST00000343348.11
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 544
      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
      116443555..116574823 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005272042.5 → XP_005272099.2  semaphorin-6A isoform X3

      See identical proteins and their annotated locations for XP_005272099.2

      UniProtKB/TrEMBL
      B2RCJ4
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 544
      PSI; Plexin repeat

    2. XM_006714663.3 → XP_006714726.1  semaphorin-6A isoform X1

      UniProtKB/TrEMBL
      B2RCJ4
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 544
      PSI; Plexin repeat

    3. XM_047417451.1 → XP_047273407.1  semaphorin-6A isoform X2

      UniProtKB/Swiss-Prot
      Q9H2E6, Q9P2H9
      Related
      ENSP00000424388.1, ENST00000510263.5

    4. XM_024446138.2 → XP_024301906.1  semaphorin-6A isoform X1

      UniProtKB/TrEMBL
      B2RCJ4
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 544
      PSI; Plexin repeat

    5. XM_017009675.2 → XP_016865164.1  semaphorin-6A isoform X1

      UniProtKB/TrEMBL
      B2RCJ4
      Conserved Domains (2) summary
      cd11266
      Location:48 → 513
      Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
      pfam01437
      Location:514 → 544
      PSI; Plexin repeat

    6. XM_047417452.1 → XP_047273408.1  semaphorin-6A isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      116956014..117086961 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353014.1 → XP_054208989.1  semaphorin-6A isoform X3

    2. XM_054353010.1 → XP_054208985.1  semaphorin-6A isoform X1

    3. XM_054353012.1 → XP_054208987.1  semaphorin-6A isoform X1

    4. XM_054353013.1 → XP_054208988.1  semaphorin-6A isoform X2

      UniProtKB/Swiss-Prot
      Q9H2E6, Q9P2H9

    5. XM_054353011.1 → XP_054208986.1  semaphorin-6A isoform X1

    6. XM_054353015.1 → XP_054208990.1  semaphorin-6A isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_020681.1: Suppressed sequence

      Description
      NM_020681.1: This RefSeq was permanently suppressed because it is primarily UTR sequence.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H2E6.3 GenPept UniProtKB/Swiss-Prot:Q9H2E6

    Gene LinkOut

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

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