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SEMA3D (semaphorin 3D)

Identity

Alias_namessema domain
Alias_symbol (synonym)coll-2
Sema-Z2
Other alias
HGNC (Hugo) SEMA3D
LocusID (NCBI) 223117
Atlas_Id 50589
Location 7q21.11  [Link to chromosome band 7q21]
Location_base_pair Starts at 84995556 and ends at 85121931 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
DMTF1 (7q21.12) / SEMA3D (7q21.11)NUCKS1 (1q32.1) / SEMA3D (7q21.11)DMTF1 7q21.12 / SEMA3D 7q21.11

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  DMTF1/SEMA3D (7q21)


External links

Nomenclature
HGNC (Hugo)SEMA3D   10726
Cards
Entrez_Gene (NCBI)SEMA3D  223117  semaphorin 3D
AliasesSema-Z2; coll-2
GeneCards (Weizmann)SEMA3D
Ensembl hg19 (Hinxton)ENSG00000153993 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000153993 [Gene_View]  ENSG00000153993 [Sequence]  chr7:84995556-85121931 [Contig_View]  SEMA3D [Vega]
ICGC DataPortalENSG00000153993
TCGA cBioPortalSEMA3D
AceView (NCBI)SEMA3D
Genatlas (Paris)SEMA3D
WikiGenes223117
SOURCE (Princeton)SEMA3D
Genetics Home Reference (NIH)SEMA3D
Genomic and cartography
GoldenPath hg38 (UCSC)SEMA3D  -     chr7:84995556-85121931 -  7q21.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SEMA3D  -     7q21.11   [Description]    (hg19-Feb_2009)
EnsemblSEMA3D - 7q21.11 [CytoView hg19]  SEMA3D - 7q21.11 [CytoView hg38]
Mapping of homologs : NCBISEMA3D [Mapview hg19]  SEMA3D [Mapview hg38]
OMIM609907   
Gene and transcription
Genbank (Entrez)AK021802 AK309116 AY358937 BC029590 BX648652
RefSeq transcript (Entrez)NM_152754
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SEMA3D
Cluster EST : UnigeneHs.664064 [ NCBI ]
CGAP (NCI)Hs.664064
Alternative Splicing GalleryENSG00000153993
Gene ExpressionSEMA3D [ NCBI-GEO ]   SEMA3D [ EBI - ARRAY_EXPRESS ]   SEMA3D [ SEEK ]   SEMA3D [ MEM ]
Gene Expression Viewer (FireBrowse)SEMA3D [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)223117
GTEX Portal (Tissue expression)SEMA3D
Human Protein AtlasENSG00000153993-SEMA3D [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO95025   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO95025  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO95025
Splice isoforms : SwissVarO95025
PhosPhoSitePlusO95025
Domaine pattern : Prosite (Expaxy)IG_LIKE (PS50835)    SEMA (PS51004)   
Domains : Interpro (EBI)Ig-like_dom    Ig-like_dom_sf    Ig-like_fold    Ig_sub    PSI    Semap_dom    Semap_dom_sf    Semaphorin    WD40/YVTN_repeat-like_dom_sf   
Domain families : Pfam (Sanger)Sema (PF01403)   
Domain families : Pfam (NCBI)pfam01403   
Domain families : Smart (EMBL)IG (SM00409)  PSI (SM00423)  Sema (SM00630)  
Conserved Domain (NCBI)SEMA3D
DMDM Disease mutations223117
Blocks (Seattle)SEMA3D
SuperfamilyO95025
Human Protein Atlas [tissue]ENSG00000153993-SEMA3D [tissue]
Peptide AtlasO95025
HPRD15321
IPIIPI00028213   IPI00925624   
Protein Interaction databases
DIP (DOE-UCLA)O95025
IntAct (EBI)O95025
FunCoupENSG00000153993
BioGRIDSEMA3D
STRING (EMBL)SEMA3D
ZODIACSEMA3D
Ontologies - Pathways
QuickGOO95025
Ontology : AmiGOneural crest cell migration  extracellular space  integral component of plasma membrane  semaphorin receptor binding  positive regulation of cell migration  neuropilin binding  chemorepellent activity  negative regulation of axon extension involved in axon guidance  negative chemotaxis  semaphorin-plexin signaling pathway  
Ontology : EGO-EBIneural crest cell migration  extracellular space  integral component of plasma membrane  semaphorin receptor binding  positive regulation of cell migration  neuropilin binding  chemorepellent activity  negative regulation of axon extension involved in axon guidance  negative chemotaxis  semaphorin-plexin signaling pathway  
Pathways : KEGGAxon guidance   
NDEx NetworkSEMA3D
Atlas of Cancer Signalling NetworkSEMA3D
Wikipedia pathwaysSEMA3D
Orthology - Evolution
OrthoDB223117
GeneTree (enSembl)ENSG00000153993
Phylogenetic Trees/Animal Genes : TreeFamSEMA3D
HOVERGENO95025
HOGENOMO95025
Homologs : HomoloGeneSEMA3D
Homology/Alignments : Family Browser (UCSC)SEMA3D
Gene fusions - Rearrangements
Fusion : MitelmanDMTF1/SEMA3D [7q21.12/7q21.11]  [t(7;7)(q21;q21)]  
Fusion PortalDMTF1 7q21.12 SEMA3D 7q21.11 LGG
Fusion : QuiverSEMA3D
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSEMA3D [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SEMA3D
dbVarSEMA3D
ClinVarSEMA3D
1000_GenomesSEMA3D 
Exome Variant ServerSEMA3D
ExAC (Exome Aggregation Consortium)ENSG00000153993
GNOMAD BrowserENSG00000153993
Varsome BrowserSEMA3D
Genetic variants : HAPMAP223117
Genomic Variants (DGV)SEMA3D [DGVbeta]
DECIPHERSEMA3D [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSEMA3D 
Mutations
ICGC Data PortalSEMA3D 
TCGA Data PortalSEMA3D 
Broad Tumor PortalSEMA3D
OASIS PortalSEMA3D [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSEMA3D  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSEMA3D
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SEMA3D
DgiDB (Drug Gene Interaction Database)SEMA3D
DoCM (Curated mutations)SEMA3D (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SEMA3D (select a term)
intoGenSEMA3D
Cancer3DSEMA3D(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609907   
Orphanet647   
DisGeNETSEMA3D
MedgenSEMA3D
Genetic Testing Registry SEMA3D
NextProtO95025 [Medical]
TSGene223117
GENETestsSEMA3D
Target ValidationSEMA3D
Huge Navigator SEMA3D [HugePedia]
snp3D : Map Gene to Disease223117
BioCentury BCIQSEMA3D
ClinGenSEMA3D
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD223117
Chemical/Pharm GKB GenePA35648
Clinical trialSEMA3D
Miscellaneous
canSAR (ICR)SEMA3D (select the gene name)
Probes
Litterature
PubMed19 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSEMA3D
EVEXSEMA3D
GoPubMedSEMA3D
iHOPSEMA3D
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 6 11:38:06 CET 2018

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