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SEMA6A semaphorin 6A [ Homo sapiens (human) ]

Gene ID: 57556, updated on 4-Jul-2021

Summary

Official Symbol
SEMA6Aprovided by HGNC
Official Full Name
semaphorin 6Aprovided by HGNC
Primary source
HGNC:HGNC:10738
See related
Ensembl:ENSG00000092421 MIM:605885
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
The transmembrane semaphorin SEMA6A is expressed in developing neural tissue and is required for proper development of the thalamocortical projection (Leighton et al., 2001 [PubMed 11242070]).[supplied by OMIM, Feb 2011]
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:
23
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (116443555..116574823, complement)
105.20201022 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 uncharacterized LOC101927190 Neighboring gene SEMA6A antisense RNA 1 Neighboring gene SEMA6A antisense RNA 2 Neighboring gene ribosomal protein S14 pseudogene 8 Neighboring gene Sharpr-MPRA regulatory region 8609 Neighboring gene ribosomal protein S17 pseudogene 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization and their interaction with birth order.
GeneReviews: Not available
Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis.
GeneReviews: Not available
Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease.
GeneReviews: Not available
Genome-wide association study of chronic periodontitis in a general German population.
GeneReviews: Not available
Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
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 axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
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
PubMed 
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of neuron migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in axon NAS
Non-traceable Author Statement
more info
PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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/Swiss-Prot
    Q9H2E6
    UniProtKB/TrEMBL
    A0A0A0MQU6
    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
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    116443555..116574823 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    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_017009675.1XP_016865164.1  semaphorin-6A isoform X1

    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_005272042.4XP_005272099.2  semaphorin-6A isoform X2

    See identical proteins and their annotated locations for XP_005272099.2

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

    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

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.
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