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] See more...

Aliases for SEMA6A Gene

Aliases for SEMA6A Gene

  • Semaphorin 6A 2 3 5
  • Sema Domain, Transmembrane Domain (TM), And Cytoplasmic Domain, (Semaphorin) 6A 2 3
  • Semaphorin VIA 3 4
  • Semaphorin-6A 3 4
  • Sema VIa 2 3
  • SEMA6A-1 3 4
  • SEMAQ 3 4
  • Semaphorin 6A-1 3
  • Semaphorin-6A-1 4
  • KIAA1368 4
  • Sema VIA 4
  • SEMA6A1 3
  • HT018 3
  • SEMA 3
  • VIA 3

External Ids for SEMA6A Gene

Previous HGNC Symbols for SEMA6A Gene

  • SEMAQ

Previous GeneCards Identifiers for SEMA6A Gene

  • GC05M115548
  • GC05M116186
  • GC05M115810
  • GC05M115855
  • GC05M115858
  • GC05M115807
  • GC05M110960

Summaries for SEMA6A Gene

Entrez Gene Summary for SEMA6A Gene

  • 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]

GeneCards Summary for SEMA6A Gene

SEMA6A (Semaphorin 6A) is a Protein Coding gene. Diseases associated with SEMA6A include Deafness, Autosomal Recessive 97 and Exfoliation Syndrome. Among its related pathways are Spinal Cord Injury and Developmental Biology. Gene Ontology (GO) annotations related to this gene include semaphorin receptor binding. An important paralog of this gene is SEMA6D.

UniProtKB/Swiss-Prot Summary for SEMA6A Gene

  • Cell surface receptor for PLXNA2 that plays an important role in cell-cell signaling. Required for normal granule cell migration in the developing cerebellum. Promotes reorganization of the actin cytoskeleton and plays an important role in axon guidance in the developing central nervous system. Can act as repulsive axon guidance cue. Has repulsive action towards migrating granular neurons. May play a role in channeling sympathetic axons into the sympathetic chains and controlling the temporal sequence of sympathetic target innervation (By similarity).

Gene Wiki entry for SEMA6A Gene

Additional gene information for SEMA6A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEMA6A Gene

Genomics for SEMA6A Gene

GeneHancer (GH) Regulatory Elements for SEMA6A Gene

Promoters and enhancers for SEMA6A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J116572 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 509.9 +0.5 494 6.9 ZNF217 EP300 CTCF ZSCAN5C SIN3A NRF1 TCF12 MYC POLR2G USF1 SEMA6A SEMA6A-AS2 lnc-ATG12-9 ATG12
GH05J116523 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 513.9 +38.5 38467 25 EP300 ZSCAN5C NCOR1 RBAK ZNF639 ZNF10 KDM6A TCF7 ZNF623 FOXA1 SEMA6A SEMA6A-AS2 SEMA6A-AS1 RNU6-644P lnc-ATG12-8 lnc-ATG12-9 lnc-ATG12-7
GH05J116558 Promoter/Enhancer 1.2 EPDnew ENCODE dbSUPER 500.4 +15.1 15057 2.1 TEAD4 ZIC2 ATF2 POLR2A ZNF585B ZBTB17 ZNF184 YY1 TCF12 ETS1 piR-39493-002 SEMA6A RPS14P8 lnc-ATG12-9
GH05J116453 Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 21.6 +120.9 120933 4.8 ZSCAN5C ZIC2 REST RELA KLF7 ATF2 MXI1 OSR2 BCL11A TCF12 SEMA6A SEMA6A-AS2 COMMD10 SEMA6A-AS1 piR-41239 HQ292167
GH05J116438 Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas dbSUPER 12.5 +133.5 133526 7.2 USF1 JUND TEAD4 ATF2 POLR2A HDAC2 ZNF263 MXI1 RAD21 FEZF1 piR-46105 SEMA6A COMMD10 lnc-ATG12-6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA6A on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEMA6A

Top Transcription factor binding sites by QIAGEN in the SEMA6A gene promoter:
  • FOXO4
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1b
  • Pax-4a
  • POU2F1
  • POU2F1a
  • Sox5
  • Zic1

Genomic Locations for SEMA6A Gene

Genomic Locations for SEMA6A Gene
chr5:116,443,555-116,574,934
(GRCh38/hg38)
Size:
131,380 bases
Orientation:
Minus strand
chr5:115,779,251-115,910,630
(GRCh37/hg19)
Size:
131,380 bases
Orientation:
Minus strand

Genomic View for SEMA6A Gene

Genes around SEMA6A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA6A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA6A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA6A Gene

Proteins for SEMA6A Gene

  • Protein details for SEMA6A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H2E6-SEM6A_HUMAN
    Recommended name:
    Semaphorin-6A
    Protein Accession:
    Q9H2E6
    Secondary Accessions:
    • Q9P2H9

    Protein attributes for SEMA6A Gene

    Size:
    1030 amino acids
    Molecular mass:
    114395 Da
    Quaternary structure:
    • Active as a homodimer or oligomer. The SEMA6A homodimer interacts with a PLXNA2 homodimer, giving rise to a heterotetramer (By similarity). Interacts with EVL.
    SequenceCaution:
    • Sequence=BAA92606.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SEMA6A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA6A Gene

Post-translational modifications for SEMA6A Gene

  • Glycosylation at Asn33, Asn49, Asn65, Asn282, Asn434, Asn461, and Asn937
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • SEM6A_HUMAN (1976)

No data available for DME Specific Peptides for SEMA6A Gene

Domains & Families for SEMA6A Gene

Gene Families for SEMA6A Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SEMA6A Gene

Blocks:
  • Semaphorin/CD100 antigen
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SEMA6A Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ39018 fis, clone NT2RP7002594, highly similar to Semaphorin-6A (B3KU01_HUMAN)
  • Semaphorin-6A-1 (SEM6A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H2E6

UniProtKB/Swiss-Prot:

SEM6A_HUMAN :
  • Belongs to the semaphorin family.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA6A: view

Function for SEMA6A Gene

Molecular function for SEMA6A Gene

UniProtKB/Swiss-Prot Function:
Cell surface receptor for PLXNA2 that plays an important role in cell-cell signaling. Required for normal granule cell migration in the developing cerebellum. Promotes reorganization of the actin cytoskeleton and plays an important role in axon guidance in the developing central nervous system. Can act as repulsive axon guidance cue. Has repulsive action towards migrating granular neurons. May play a role in channeling sympathetic axons into the sympathetic chains and controlling the temporal sequence of sympathetic target innervation (By similarity).

Phenotypes From GWAS Catalog for SEMA6A Gene

Gene Ontology (GO) - Molecular Function for SEMA6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004888 transmembrane signaling receptor activity IEA --
GO:0005515 protein binding IPI,IEA 10993894
GO:0030215 semaphorin receptor binding IBA,IEA 21873635
GO:0045499 chemorepellent activity IBA 21873635
genes like me logo Genes that share ontologies with SEMA6A: view
genes like me logo Genes that share phenotypes with SEMA6A: view

Animal Models for SEMA6A Gene

MGI Knock Outs for SEMA6A:
  • Sema6a Sema6a<tm2e.1(EUCOMM)Hmgu>

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SEMA6A Gene

Localization for SEMA6A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA6A Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SEMA6A gene
Compartment Confidence
plasma membrane 5
extracellular 4
cytoskeleton 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Intermediate filaments (2)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SEMA6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 10993894
genes like me logo Genes that share ontologies with SEMA6A: view

Pathways & Interactions for SEMA6A Gene

genes like me logo Genes that share pathways with SEMA6A: view

Pathways by source for SEMA6A Gene

1 BioSystems pathway for SEMA6A Gene
1 KEGG pathway for SEMA6A Gene

Gene Ontology (GO) - Biological Process for SEMA6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001755 neural crest cell migration IBA 21873635
GO:0001764 neuron migration IEA --
GO:0006915 apoptotic process NAS 10993894
GO:0007010 cytoskeleton organization NAS 10993894
GO:0007166 cell surface receptor signaling pathway NAS 10993894
genes like me logo Genes that share ontologies with SEMA6A: view

No data available for SIGNOR curated interactions for SEMA6A Gene

Drugs & Compounds for SEMA6A Gene

No Compound Related Data Available

Transcripts for SEMA6A Gene

mRNA/cDNA for SEMA6A Gene

3 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA6A Gene

No ASD Table

Relevant External Links for SEMA6A Gene

GeneLoc Exon Structure for
SEMA6A

Expression for SEMA6A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SEMA6A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA6A Gene

This gene is overexpressed in Adrenal Gland (x5.0).

Protein differential expression in normal tissues from HIPED for SEMA6A Gene

This gene is overexpressed in Vitreous humor (57.6) and Peripheral blood mononuclear cells (11.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SEMA6A Gene



Protein tissue co-expression partners for SEMA6A Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEMA6A

SOURCE GeneReport for Unigene cluster for SEMA6A Gene:

Hs.156967

Evidence on tissue expression from TISSUES for SEMA6A Gene

  • Nervous system(4.9)
  • Skin(3.1)
  • Heart(2)
genes like me logo Genes that share expression patterns with SEMA6A: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA6A Gene

Orthologs for SEMA6A Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA6A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA6A 31 30
  • 99.61 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SEMA6A 31
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA6A 31 30
  • 92.3 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA6A 31 30
  • 91.04 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema6a 30
  • 90.06 (n)
mouse
(Mus musculus)
Mammalia Sema6a 17 31 30
  • 89.97 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA6A 31
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves SEMA6A 31 30
  • 82.99 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA6A 31
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema6a 30
  • 74.86 (n)
Str.2597 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.16239 30
zebrafish
(Danio rerio)
Actinopterygii sema6a 31 30
  • 69.5 (n)
OneToOne
wufj46c12 30
fruit fly
(Drosophila melanogaster)
Insecta Sema-1b 32
  • 41 (a)
Sema-1a 32
  • 35 (a)
CG4383 32
  • 35 (a)
Sema-2a 31 32
  • 29 (a)
ManyToMany
Sema-2b 31
  • 26 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea mab-20 32
  • 27 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 29 (a)
OneToMany
Species where no ortholog for SEMA6A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SEMA6A Gene

ENSEMBL:
Gene Tree for SEMA6A (if available)
TreeFam:
Gene Tree for SEMA6A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEMA6A: view image

Paralogs for SEMA6A Gene

(9) SIMAP similar genes for SEMA6A Gene using alignment to 7 proteins:

  • SEM6A_HUMAN
  • B3KU01_HUMAN
  • D6RAG9_HUMAN
  • D6RCR0_HUMAN
  • E7ERF3_HUMAN
  • E9PDV9_HUMAN
  • H0Y8V9_HUMAN
genes like me logo Genes that share paralogs with SEMA6A: view

Variants for SEMA6A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEMA6A Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
709225 Benign: not provided 116,502,230(-) T/C SYNONYMOUS_VARIANT
712532 Likely Benign: not provided 116,446,915(-) C/G MISSENSE_VARIANT
713698 Likely Benign: not provided 116,447,034(-) G/A MISSENSE_VARIANT
718147 Benign: not provided 116,446,797(-) T/G MISSENSE_VARIANT
722892 Likely Benign: not provided 116,477,882(-) T/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SEMA6A Gene

Structural Variations from Database of Genomic Variants (DGV) for SEMA6A Gene

Variant ID Type Subtype PubMed ID
dgv210n6 CNV deletion 16902084
dgv3157n106 CNV deletion 24896259
esv2061795 CNV deletion 18987734
esv2549113 CNV deletion 19546169
esv2730635 CNV deletion 23290073
esv3227 CNV loss 18987735
esv3566513 CNV deletion 23714750
esv5985 CNV loss 19470904
nsv1074326 CNV deletion 25765185
nsv518494 CNV loss 19592680
nsv956446 CNV deletion 24416366
nsv964926 CNV duplication 23825009

Variation tolerance for SEMA6A Gene

Residual Variation Intolerance Score: 9.96% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.46; 64.21% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEMA6A Gene

Human Gene Mutation Database (HGMD)
SEMA6A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA6A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA6A Gene

Disorders for SEMA6A Gene

MalaCards: The human disease database

(5) MalaCards diseases for SEMA6A Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal recessive 97
  • dfnb97
exfoliation syndrome
  • xfs
granulomatosis with polyangiitis
  • gpa
renal cell carcinoma, papillary, 1
  • rccp1
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA6A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SEMA6A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA6A Gene

Publications for SEMA6A Gene

  1. The orthologous human and murine semaphorin 6A-1 proteins (SEMA6A-1/Sema6A-1) bind to the enabled/vasodilator-stimulated phosphoprotein-like protein (EVL) via a novel carboxyl-terminal zyxin-like domain. (PMID: 10993894) Klostermann A … Behl C (The Journal of biological chemistry 2000) 2 3 4 54
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  3. Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis. (PMID: 19451621) Landers JE … Brown RH (Proceedings of the National Academy of Sciences of the United States of America 2009) 3 41 54
  4. The ERAP2 gene is associated with preeclampsia in Australian and Norwegian populations. (PMID: 19578876) Johnson MP … Moses EK (Human genetics 2009) 3 41 54
  5. From plasma membrane to cytoskeleton: a novel function for semaphorin 6A. (PMID: 18187809) Prislei S … Ferlini C (Molecular cancer therapeutics 2008) 3 23 54

Products for SEMA6A Gene

Sources for SEMA6A Gene