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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 Developmental Biology and Semaphorin interactions. 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.

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

Regulatory Elements for SEMA6D Gene

Enhancers for SEMA6D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15G047465 0.9 Ensembl ENCODE 25.5 +282.4 282386 2.0 GATA3 JUND SMARCA4 GATA2 NFIB JUN FOS FOXA1 SEMA6D GC15P047454 PIR62302
GH15G047383 1 Ensembl ENCODE 20 +200.0 200016 1.9 JUN MAX FEZF1 CEBPG ZIC2 ZKSCAN1 ZFHX2 POLR2A GATA2 SCRT2 SEMA6D GC15M047389 GC15M047388 GC15M047387 GC15M047386 GC15M047332
GH15G047472 0.7 Ensembl ENCODE 22.9 +289.6 289649 1.7 REST NR2F2 SEMA6D ENSG00000259488 GC15P047454 PIR62302
GH15G047513 1.2 Ensembl ENCODE dbSUPER 12.7 +330.4 330425 1.6 TBP NFYA JUN RFX5 OSR2 JUND MAFF NFYB ZNF629 STAT3 SEMA6D PIR62302 PIR43524
GH15G047443 0.6 ENCODE 21.9 +259.9 259930 1.8 ZNF335 OSR2 ZFHX2 MAFF ZNF585B FOXP2 MAFK WT1 NFE2L2 SEMA6D GC15P047454 ENSG00000259360
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEMA6D on UCSC Golden Path with GeneCards custom track

Genomic Location for SEMA6D Gene

Chromosome:
15
Start:
47,184,101 bp from pter
End:
47,774,223 bp from pter
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=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, Asn283, Asn435, Asn461, isoforms=6613, 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

Suggested Antigen Peptide Sequences for SEMA6D Gene

GenScript: Design optimal peptide antigens:

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.

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

CRISPR 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
golgi apparatus 4
extracellular 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

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: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:

CRISPR 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
ECgene alternative splicing isoforms for
SEMA6D

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:

SEMA6D

SOURCE GeneReport for Unigene cluster for SEMA6D Gene:

Hs.511265

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

Primer Products

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 34 35
  • 99.63 (n)
oppossum
(Monodelphis domestica)
Mammalia SEMA6D 35
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA6D 34 35
  • 93.45 (n)
dog
(Canis familiaris)
Mammalia SEMA6D 34 35
  • 93.23 (n)
mouse
(Mus musculus)
Mammalia Sema6d 34 16 35
  • 88.75 (n)
rat
(Rattus norvegicus)
Mammalia Sema6d 34
  • 88.39 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA6D 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves SEMA6D 34 35
  • 81.52 (n)
lizard
(Anolis carolinensis)
Reptilia SEMA6D 35
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema6d 34
  • 76.06 (n)
Str.10846 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.22993 34
zebrafish
(Danio rerio)
Actinopterygii sema6dl 34 35
  • 68.5 (n)
fruit fly
(Drosophila melanogaster)
Insecta Sema-2a 35
  • 28 (a)
ManyToMany
Sema-2b 35
  • 26 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 29 (a)
OneToMany
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

ENSEMBL:
Gene Tree for SEMA6D (if available)
TreeFam:
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 Sequence Context AA Info Type
rs1000001005 -- 47,457,919(+) TCGCA(A/G)TGAAT intron-variant
rs1000010256 -- 47,645,744(+) GGGTG(A/G)TTGGC intron-variant
rs1000011264 -- 47,375,316(+) GCTGC(C/G)TGTTT intron-variant
rs1000014806 -- 47,473,569(+) TGGTA(C/T)CAGCA intron-variant
rs1000015120 -- 47,183,305(+) CTTTA(A/C)ATACC upstream-variant-2KB

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)

Relevant External Links 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

Relevant External Links for SEMA6D

Genetic Association Database (GAD)
SEMA6D
Human Genome Epidemiology (HuGE) Navigator
SEMA6D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEMA6D

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. (J. Biol. Chem. 2002) 2 3 4 64
  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 S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  3. Expression of semaphorin 6D in gastric carcinoma and its significance. (PMID: 17143962) Zhao X.Y. … Li Y.H. (World J. Gastroenterol. 2006) 3 22 64
  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 Dev. 2004) 2 3 64
  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 Res. 2000) 3 4 64

Products for SEMA6D Gene

Sources for SEMA6D Gene

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