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Aliases for SEMA6D Gene

Aliases for SEMA6D Gene

  • Semaphorin 6D 2 3 5
  • Sema Domain, Transmembrane Domain (TM), And Cytoplasmic Domain, (Semaphorin) 6D 2 3
  • Semaphorin-6D 3
  • KIAA1479 4

External Ids for SEMA6D Gene

Previous GeneCards Identifiers for SEMA6D Gene

  • GC15P043610
  • GC15P041056
  • GC15P045589
  • GC15P045726
  • GC15P045797
  • GC15P048010
  • GC15P024843
  • GC15P047704
  • GC15P047476

Summaries for SEMA6D Gene

Entrez Gene Summary for SEMA6D Gene

  • Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]

GeneCards Summary for SEMA6D Gene

SEMA6D (Semaphorin 6D) is a Protein Coding gene. Among its related pathways are Semaphorin interactions and Developmental Biology. Gene Ontology (GO) annotations related to this gene include receptor activity and semaphorin receptor binding. An important paralog of this gene is SEMA6A.

UniProtKB/Swiss-Prot for SEMA6D Gene

  • Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections.

Additional gene information for SEMA6D Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA6D Gene

Genomics for SEMA6D Gene

GeneHancer (GH) Regulatory Elements for SEMA6D Gene

Promoters and enhancers for SEMA6D Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15I047715 Promoter/Enhancer 2.5 VISTA EPDnew Ensembl ENCODE dbSUPER 550 +535.7 535663 8.6 PKNOX1 SIN3A FEZF1 GLI4 ZNF2 GLIS2 SP3 ZNF488 MAFF GLIS1 SEMA6D RPL7AP62 LOC105370804
GH15I047183 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 550.8 +0.7 666 1.7 SIN3A ZNF2 ZNF335 ZNF121 GLIS2 ZNF366 EGR2 SP3 YY2 ZBTB11 SEMA6D GC15M047252
GH15I047312 Promoter 0.5 EPDnew 550.1 +128.1 128124 0.1 SEMA6D GC15M047291 GC15M047333
GH15I047465 Enhancer 0.7 Ensembl ENCODE 25.6 +282.4 282385 2 GATA3 JUND JUN FOS FOXA1 SEMA6D GC15P047454 PIR62302
GH15I047383 Enhancer 0.8 Ensembl ENCODE 20 +200.0 200016 1.9 ZNF362 JUN MAX CEBPB CEBPG FEZF1 ZIC2 ZKSCAN1 ZFP69B ZFHX2 GC15M047386 GC15M047387 GC15M047388 GC15M047389 PIR54210 SEMA6D ENSG00000259221 GC15M047332
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SEMA6D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SEMA6D gene promoter:

Genomic Locations for SEMA6D Gene

Genomic Locations for SEMA6D Gene
590,123 bases
Plus strand

Genomic View for SEMA6D Gene

Genes around SEMA6D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA6D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA6D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA6D Gene

Proteins for SEMA6D Gene

  • Protein details for SEMA6D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A6NF10
    • A6NM95
    • A6NNK1
    • A7E2A0
    • Q8NFY3
    • Q8NFY5
    • Q8NFY6
    • Q8NFY7
    • Q9P249

    Protein attributes for SEMA6D Gene

    1073 amino acids
    Molecular mass:
    119872 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA96003.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for SEMA6D Gene

neXtProt entry for SEMA6D Gene

Post-translational modifications for SEMA6D Gene

  • Glycosylation at isoforms=2, 3, 4, 5, 6, 7, 851, posLast=283283, isoforms=2, 3, 4, 5, 6, 7, 8435, isoforms=2, 3, 4, 5, 6, 7, 8461, posLast=613613, and isoforms=6631
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEMA6D Gene

Domains & Families for SEMA6D Gene

Gene Families for SEMA6D Gene

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

Suggested Antigen Peptide Sequences for SEMA6D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the semaphorin family.
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA6D: view

Function for SEMA6D Gene

Molecular function for SEMA6D Gene

UniProtKB/Swiss-Prot Function:
Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections.

Phenotypes From GWAS Catalog for SEMA6D Gene

Gene Ontology (GO) - Molecular Function for SEMA6D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030215 semaphorin receptor binding IEA --
genes like me logo Genes that share ontologies with SEMA6D: view
genes like me logo Genes that share phenotypes with SEMA6D: view

Animal Models for SEMA6D Gene

MGI Knock Outs for SEMA6D:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA6D

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SEMA6D Gene

Localization for SEMA6D Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA6D Gene

Isoform 1: Cell membrane; Single-pass type I membrane protein.
Isoform 2: Cell membrane; Single-pass type I membrane protein.
Isoform 3: Cell membrane; Single-pass type I membrane protein.
Isoform 4: Cell membrane; Single-pass type I membrane protein.
Isoform 5: Cell membrane; Single-pass type I membrane protein.
Isoform 7: Cytoplasm.

Subcellular locations from

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 SEMA6D gene
Compartment Confidence
plasma membrane 5
golgi apparatus 4
extracellular 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
  • Golgi apparatus (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SEMA6D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 Golgi apparatus IDA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SEMA6D: view

Pathways & Interactions for SEMA6D Gene

genes like me logo Genes that share pathways with SEMA6D: view

Pathways by source for SEMA6D Gene

1 KEGG pathway for SEMA6D Gene

Gene Ontology (GO) - Biological Process for SEMA6D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0014911 positive regulation of smooth muscle cell migration IEA --
GO:0014912 negative regulation of smooth muscle cell migration IEA --
GO:0021591 ventricular system development IEA --
genes like me logo Genes that share ontologies with SEMA6D: view

No data available for SIGNOR curated interactions for SEMA6D Gene

Drugs & Compounds for SEMA6D Gene

No Compound Related Data Available

Transcripts for SEMA6D Gene

Unigene Clusters for SEMA6D Gene

Sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA6D Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19
SP1: -
SP2: - -
SP3: - -
SP4: - - -

Relevant External Links for SEMA6D Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SEMA6D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SEMA6D Gene

Protein differential expression in normal tissues from HIPED for SEMA6D Gene

This gene is overexpressed in Esophagus (45.3), Vitreous humor (12.7), and Fetal Brain (11.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SEMA6D Gene

Protein tissue co-expression partners for SEMA6D Gene

NURSA nuclear receptor signaling pathways regulating expression of SEMA6D Gene:


SOURCE GeneReport for Unigene cluster for SEMA6D Gene:


Evidence on tissue expression from TISSUES for SEMA6D Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with SEMA6D: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA6D Gene

Orthologs for SEMA6D Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA6D Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SEMA6D 33 34
  • 99.63 (n)
(Monodelphis domestica)
Mammalia SEMA6D 34
  • 95 (a)
(Bos Taurus)
Mammalia SEMA6D 33 34
  • 93.45 (n)
(Canis familiaris)
Mammalia SEMA6D 33 34
  • 93.23 (n)
(Mus musculus)
Mammalia Sema6d 33 16 34
  • 88.75 (n)
(Rattus norvegicus)
Mammalia Sema6d 33
  • 88.39 (n)
(Ornithorhynchus anatinus)
Mammalia SEMA6D 34
  • 79 (a)
(Gallus gallus)
Aves SEMA6D 33 34
  • 81.52 (n)
(Anolis carolinensis)
Reptilia SEMA6D 34
  • 92 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sema6d 33
  • 76.06 (n)
Str.10846 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.22993 33
(Danio rerio)
Actinopterygii sema6dl 33 34
  • 68.5 (n)
fruit fly
(Drosophila melanogaster)
Insecta Sema-2a 34
  • 28 (a)
Sema-2b 34
  • 26 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 29 (a)
Species where no ortholog for SEMA6D 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)
  • worm (Caenorhabditis elegans)

Evolution for SEMA6D Gene

Gene Tree for SEMA6D (if available)
Gene Tree for SEMA6D (if available)

Paralogs for SEMA6D Gene

Paralogs for SEMA6D Gene

genes like me logo Genes that share paralogs with SEMA6D: view

Variants for SEMA6D Gene

Sequence variations from dbSNP and Humsavar for SEMA6D Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1000001005 -- 47,457,919(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000010256 -- 47,645,744(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000011264 -- 47,375,316(+) C/G genic_upstream_transcript_variant, intron_variant
rs1000014806 -- 47,473,569(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000015120 -- 47,183,305(+) A/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SEMA6D Gene

Variant ID Type Subtype PubMed ID
dgv1207n106 CNV deletion 24896259
dgv4513n54 CNV loss 21841781
dgv4514n54 CNV loss 21841781
dgv739e212 CNV loss 25503493
esv1010172 CNV deletion 20482838
esv1571390 CNV insertion 17803354
esv2032789 CNV deletion 18987734
esv2660412 CNV deletion 23128226
esv2660518 CNV deletion 23128226
esv2665614 CNV deletion 23128226
esv2665943 CNV deletion 23128226
esv2670559 CNV deletion 23128226
esv2670993 CNV deletion 23128226
esv2749653 CNV deletion 23290073
esv2749654 CNV deletion 23290073
esv2749655 CNV deletion 23290073
esv2749656 CNV deletion 23290073
esv2761943 CNV loss 21179565
esv2763098 CNV loss 21179565
esv2893 CNV loss 18987735
esv29723 CNV loss 19812545
esv3303262 CNV mobile element insertion 20981092
esv33210 CNV gain 17666407
esv3326619 CNV insertion 20981092
esv3389217 CNV insertion 20981092
esv3435123 CNV insertion 20981092
esv3552407 CNV deletion 23714750
esv3552408 CNV deletion 23714750
esv3552409 CNV deletion 23714750
esv3552413 CNV deletion 23714750
esv3636383 CNV loss 21293372
esv3636385 CNV loss 21293372
esv3636389 CNV loss 21293372
esv3636391 CNV loss 21293372
esv3636395 CNV loss 21293372
esv3636396 CNV loss 21293372
esv3636398 CNV loss 21293372
esv993814 CNV insertion 20482838
nsv1042048 CNV loss 25217958
nsv1046813 CNV loss 25217958
nsv1070696 CNV deletion 25765185
nsv1133051 OTHER inversion 24896259
nsv1134444 CNV deletion 24896259
nsv1525 CNV insertion 18451855
nsv1526 CNV insertion 18451855
nsv457129 CNV loss 19166990
nsv510875 OTHER complex 20534489
nsv569329 CNV loss 21841781
nsv569330 CNV loss 21841781
nsv569331 CNV loss 21841781
nsv569332 CNV loss 21841781
nsv569333 CNV loss 21841781
nsv832996 CNV loss 17160897
nsv984067 CNV duplication 23825009

Variation tolerance for SEMA6D Gene

Residual Variation Intolerance Score: 2.99% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.22; 76.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEMA6D Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA6D Gene

Disorders for SEMA6D Gene

Additional Disease Information for SEMA6D

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SEMA6D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SEMA6D Gene

Publications for SEMA6D Gene

  1. Identification, characterization, and functional study of the two novel human members of the semaphorin gene family. (PMID: 12110693) Qu X … He F (The Journal of biological chemistry 2002) 2 3 4 58
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  3. Expression of semaphorin 6D in gastric carcinoma and its significance. (PMID: 17143962) Zhao XY … Li YH (World journal of gastroenterology 2006) 3 22 58
  4. Dual roles of Sema6D in cardiac morphogenesis through region-specific association of its receptor, Plexin-A1, with off-track and vascular endothelial growth factor receptor type 2. (PMID: 14977921) Toyofuku T … Kikutani H (Genes & development 2004) 2 3 58
  5. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4 58

Products for SEMA6D Gene

Sources for SEMA6D Gene

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