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SEMA6A semaphorin 6A [ Homo sapiens (human) ]

Gene ID: 57556, updated on 5-Jan-2025

Summary

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, Jan 2025]
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

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

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

Interactions

General gene information

Clone Names

  • KIAA1368

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chemorepellent activity  
enables protein binding PubMed 
enables semaphorin receptor binding  
Process Evidence Code Pubs
involved_in animal organ morphogenesis PubMed 
involved_in apoptotic process PubMed 
involved_in axon guidance  
involved_in axon guidance PubMed 
involved_in cell surface receptor signaling pathway PubMed 
involved_in cellular response to vascular endothelial growth factor stimulus PubMed 
involved_in cytoskeleton organization PubMed 
involved_in negative regulation of ERK1 and ERK2 cascade PubMed 
involved_in negative regulation of angiogenesis PubMed 
involved_in negative regulation of cell adhesion involved in sprouting angiogenesis PubMed 
involved_in negative regulation of sprouting angiogenesis PubMed 
involved_in negative regulation of vascular endothelial growth factor signaling pathway PubMed 
involved_in nervous system development PubMed 
involved_in neural crest cell migration  
involved_in positive regulation of neuron migration  
involved_in semaphorin-plexin signaling pathway  
Component Evidence Code Pubs
located_in axon PubMed 
located_in membrane PubMed 
is_active_in plasma membrane  

General protein information

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_001300780.2NP_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:48513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514544
    PSI; Plexin repeat
  2. NM_020796.5NP_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:48513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514544
    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_005272042.5XP_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:48513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514544
    PSI; Plexin repeat
  2. XM_006714663.3XP_006714726.1  semaphorin-6A isoform X1

    UniProtKB/TrEMBL
    B2RCJ4
    Conserved Domains (2) summary
    cd11266
    Location:48513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514544
    PSI; Plexin repeat
  3. XM_047417451.1XP_047273407.1  semaphorin-6A isoform X2

    UniProtKB/Swiss-Prot
    Q9H2E6, Q9P2H9
    UniProtKB/TrEMBL
    B2RCJ4
    Related
    ENSP00000424388.1, ENST00000510263.5
  4. XM_024446138.2XP_024301906.1  semaphorin-6A isoform X1

    UniProtKB/TrEMBL
    B2RCJ4
    Conserved Domains (2) summary
    cd11266
    Location:48513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514544
    PSI; Plexin repeat
  5. XM_017009675.2XP_016865164.1  semaphorin-6A isoform X1

    UniProtKB/TrEMBL
    B2RCJ4
    Conserved Domains (2) summary
    cd11266
    Location:48513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514544
    PSI; Plexin repeat
  6. XM_047417452.1XP_047273408.1  semaphorin-6A isoform X4

    UniProtKB/TrEMBL
    B2RCJ4

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_054353014.1XP_054208989.1  semaphorin-6A isoform X3

    UniProtKB/TrEMBL
    B2RCJ4
  2. XM_054353010.1XP_054208985.1  semaphorin-6A isoform X1

    UniProtKB/TrEMBL
    B2RCJ4
  3. XM_054353012.1XP_054208987.1  semaphorin-6A isoform X1

    UniProtKB/TrEMBL
    B2RCJ4
  4. XM_054353013.1XP_054208988.1  semaphorin-6A isoform X2

    UniProtKB/Swiss-Prot
    Q9H2E6, Q9P2H9
    UniProtKB/TrEMBL
    B2RCJ4
  5. XM_054353011.1XP_054208986.1  semaphorin-6A isoform X1

    UniProtKB/TrEMBL
    B2RCJ4
  6. XM_054353015.1XP_054208990.1  semaphorin-6A isoform X4

    UniProtKB/TrEMBL
    B2RCJ4

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