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 port... See more...

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 4
  • KIAA1479 2 4
  • FLJ11598 2
  • SEMA6D 5

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. Diseases associated with SEMA6D include Kallmann Syndrome. Among its related pathways are Axon guidance and Developmental Biology. Gene Ontology (GO) annotations related to this gene include semaphorin receptor binding. An important paralog of this gene is SEMA6A.

UniProtKB/Swiss-Prot Summary 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.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEMA6D Gene

Genomics for SEMA6D Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SEMA6D 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
GH15J047715 Promoter/Enhancer 2.5 VISTA EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600 +537.8 537847 12.9 PRDM10 ZNF629 ZNF692 FOXA1 PRDM1 ZIC2 ZSCAN4 POLR2A PATZ1 CTCF SEMA6D piR-39972-011 L13714-145 SLC24A5
GH15J047183 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +0.6 612 2.2 PRDM10 ZNF692 ZIC2 POLR2A PATZ1 ZNF501 EZH2 KLF9 ZBTB20 SP2 SEMA6D RF00100-045 RN7SKP139 lnc-SLC24A5-9 SLC24A5
GH15J047312 Promoter 0.3 EPDnew 600.1 +128.1 128136 0.1 SEMA6D lnc-MYEF2-5 ENSG00000259221 SLC24A5
GH15J047184 Enhancer 0.2 Ensembl 600.7 -0.8 -788 0.2 SEMA6D LOC107984733
GH15J047383 Enhancer 0.8 Ensembl ENCODE 20 +200.1 200112 2.4 ZIC2 POLR2A CEBPA SCRT2 ZBTB44 CEBPB FOS MAX ZFHX2 BHLHE40 SEMA6D ENSG00000259221 lnc-MYEF2-5 SLC24A5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA6D on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEMA6D

Top Transcription factor binding sites by QIAGEN in the SEMA6D gene promoter:
  • AML1a
  • C/EBPalpha
  • Cdc5
  • CUTL1
  • Evi-1
  • FOXL1
  • IRF-7A
  • Nkx2-5
  • S8

Genomic Locations for SEMA6D Gene

Genomic Locations for SEMA6D Gene
chr15:47,184,089-47,774,228
(GRCh38/hg38)
Size:
590,140 bases
Orientation:
Plus strand
chr15:47,476,298-48,066,420
(GRCh37/hg19)
Size:
590,123 bases
Orientation:
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:
    Q8NFY4-SEM6D_HUMAN
    Recommended name:
    Semaphorin-6D
    Protein Accession:
    Q8NFY4
    Secondary Accessions:
    • A6NF10
    • A6NM95
    • A6NNK1
    • A7E2A0
    • Q8NFY3
    • Q8NFY5
    • Q8NFY6
    • Q8NFY7
    • Q9P249

    Protein attributes for SEMA6D Gene

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

    Alternative splice isoforms for SEMA6D Gene

neXtProt entry for SEMA6D Gene

Post-translational modifications for SEMA6D Gene

  • Glycosylation at Asn51, Asn283, Asn435, Asn461, Thr613, and Asn631
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEMA6D Gene

Domains & Families for SEMA6D Gene

Gene Families for SEMA6D Gene

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

Protein Domains for SEMA6D Gene

InterPro:
Blocks:
  • Semaphorin/CD100 antigen
ProtoNet:

Suggested Antigen Peptide Sequences for SEMA6D Gene

GenScript: Design optimal peptide antigens:
  • Semaphorin-6D (SEM6D_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NFY4

UniProtKB/Swiss-Prot:

SEM6D_HUMAN :
  • Belongs to the semaphorin family.
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:0005515 protein binding IEA --
GO:0030215 semaphorin receptor binding IBA 21873635
GO:0045499 chemorepellent activity IBA 21873635
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

CRISPR Products

miRNA for SEMA6D Gene

miRTarBase miRNAs that target SEMA6D

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products 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

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 SEMA6D gene
Compartment Confidence
plasma membrane 5
extracellular 4
golgi apparatus 4
cytoskeleton 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
peroxisome 1
endosome 1
lysosome 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:0005615 extracellular space IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005794 Golgi apparatus IDA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA 21873635
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:0001755 neural crest cell migration IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0007411 axon guidance IBA 21873635
GO:0014911 positive regulation of smooth muscle cell migration 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

mRNA/cDNA for SEMA6D Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SEMA6D

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
SEMA6D

Expression for SEMA6D Gene

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



Protein tissue co-expression partners for SEMA6D Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEMA6D

SOURCE GeneReport for Unigene cluster for SEMA6D Gene:

Hs.511265

Evidence on tissue expression from TISSUES for SEMA6D Gene

  • Nervous system(4.9)
  • Heart(2.7)
  • Kidney(2.7)
  • Eye(2.6)
  • Muscle(2.4)
  • Lung(2.2)
  • Blood(2.1)
  • Skin(2.1)
  • Intestine(2)
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
Chimpanzee
(Pan troglodytes)
Mammalia SEMA6D 30 31
  • 99.63 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SEMA6D 31
  • 95 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SEMA6D 30 31
  • 93.45 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SEMA6D 30 31
  • 93.23 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sema6d 30 17 31
  • 88.75 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sema6d 30
  • 88.39 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SEMA6D 31
  • 79 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SEMA6D 30 31
  • 81.52 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SEMA6D 31
  • 92 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sema6d 30
  • 76.06 (n)
Str.10846 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.22993 30
Zebrafish
(Danio rerio)
Actinopterygii sema6dl 30 31
  • 68.5 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Sema-2a 31
  • 28 (a)
ManyToMany
Sema-2b 31
  • 26 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 29 (a)
OneToMany
Species where no ortholog for SEMA6D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for SEMA6D (if available)
TreeFam:
Gene Tree for SEMA6D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEMA6D: view image

Paralogs for SEMA6D Gene

(18) SIMAP similar genes for SEMA6D Gene using alignment to 7 proteins:

  • SEM6D_HUMAN
  • A6NM95_HUMAN
  • H0YL82_HUMAN
  • H0YM97_HUMAN
  • H0YMA6_HUMAN
  • H0YMP7_HUMAN
  • H0YMV0_HUMAN
genes like me logo Genes that share paralogs with SEMA6D: view

Variants for SEMA6D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEMA6D Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
rs1555428181 Uncertain Significance: not provided 47,764,915(+) C/T MISSENSE_VARIANT
rs16960074 - p.Ser969Thr
rs3743279 - p.Asn307Ser
rs532598 - p.Ser478Asn

Additional dbSNP identifiers (rs#s) for SEMA6D Gene

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)
SEMA6D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA6D

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

Disorders for SEMA6D Gene

MalaCards: The human disease database

(1) MalaCards diseases for SEMA6D Gene - From: DISEASES

Disorder Aliases PubMed IDs
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA6D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SEMA6D: view

No data available for 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
  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 41
  3. Expression of semaphorin 6D in gastric carcinoma and its significance. (PMID: 17143962) Zhao XY … Li YH (World journal of gastroenterology 2006) 3 23
  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
  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

Products for SEMA6D Gene

  • Boster Bio Antibodies for SEMA6D
  • Boster Bio ELISA Kits for SEMA6D

Sources for SEMA6D Gene