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SEMA6A semaphorin 6A [ Homo sapiens (human) ]

Gene ID: 57556, updated on 2-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
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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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Related articles in PubMed

  1. The class 6 semaphorin SEMA6A is induced by interferon-gamma and defines an activation status of langerhans cells observed in pathological situations. Gautier G, et al. Am J Pathol, 2006 Feb. PMID 16436660, Free PMC Article
  2. From plasma membrane to cytoskeleton: a novel function for semaphorin 6A. Prislei S, et al. Mol Cancer Ther, 2008 Jan. PMID 18187809
  3. SEMA6A is a prognostic biomarker in glioblastoma. Zhao J, et al. Tumour Biol, 2015 Nov. PMID 26014517
  4. Characterization of Semaphorin 6A-Mediated Effects on Angiogenesis Through Regulation of VEGF Signaling. Ohnuki H, et al. Methods Mol Biol, 2017. PMID 27787863, Free PMC Article
  5. Semaphorin 6A Attenuates the Migration Capability of Lung Cancer Cells via the NRF2/HMOX1 Axis. Chen LH, et al. Sci Rep, 2019 Sep 16. PMID 31527696, Free PMC Article

See all (49) citations in PubMed

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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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 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)

Genotypes

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 neuropilin binding 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 chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
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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