Atlas of Genetics and Cytogenetics in Oncology and Haematology

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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome

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SMAD9 (SMAD family member 9)

Identity

Other namesMADH6
MADH9
PPH2
SMAD8
SMAD8A
SMAD8B
HGNC (Hugo) SMAD9
LocusID (NCBI) 4093
Location 13q13.3
Location_base_pair Starts at 37418968 and ends at 37494409 bp from pter ( according to hg19-Feb_2009)
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

 

External links

Nomenclature
HGNC (Hugo)SMAD9   6774
Cards
Entrez_Gene (NCBI)SMAD9  4093  SMAD family member 9
GeneCards (Weizmann)SMAD9
Ensembl hg19 (Hinxton)ENSG00000120693 [Gene_View]  chr13:37418968-37494409 [Contig_View]  SMAD9 [Vega]
Ensembl hg38 (Hinxton)ENSG00000120693 [Gene_View]  chr13:37418968-37494409 [Contig_View]  SMAD9 [Vega]
ICGC DataPortalENSG00000120693
cBioPortalSMAD9
AceView (NCBI)SMAD9
Genatlas (Paris)SMAD9
WikiGenes4093
SOURCE (Princeton)SMAD9
Genomic and cartography
GoldenPath hg19 (UCSC)SMAD9  -     chr13:37418968-37494409 -  13q13.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SMAD9  -     13q13.3   [Description]    (hg38-Dec_2013)
EnsemblSMAD9 - 13q13.3 [CytoView hg19]  SMAD9 - 13q13.3 [CytoView hg38]
Mapping of homologs : NCBISMAD9 [Mapview hg19]  SMAD9 [Mapview hg38]
OMIM603295   615342   
Gene and transcription
Genbank (Entrez)AK311686 AK314920 AW191604 BC011559 BC067766
RefSeq transcript (Entrez)NM_001127217 NM_005905
RefSeq genomic (Entrez)AC_000145 NC_000013 NC_018924 NG_016963 NT_024524 NW_001838073 NW_004929388
Consensus coding sequences : CCDS (NCBI)SMAD9
Cluster EST : UnigeneHs.123119 [ NCBI ]
CGAP (NCI)Hs.123119
Alternative Splicing : Fast-db (Paris)GSHG0008423
Alternative Splicing GalleryENSG00000120693
Gene ExpressionSMAD9 [ NCBI-GEO ]     SMAD9 [ SEEK ]   SMAD9 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO15198 (Uniprot)
NextProtO15198  [Medical]
With graphics : InterProO15198
Splice isoforms : SwissVarO15198 (Swissvar)
Domaine pattern : Prosite (Expaxy)MH1 (PS51075)    MH2 (PS51076)   
Domains : Interpro (EBI)Dwarfin    MAD_homology1_Dwarfin-type    MAD_homology_MH1    SMAD_dom-like    SMAD_dom_Dwarfin-type    SMAD_FHA_domain   
Related proteins : CluSTrO15198
Domain families : Pfam (Sanger)MH1 (PF03165)    MH2 (PF03166)   
Domain families : Pfam (NCBI)pfam03165    pfam03166   
Domain families : Smart (EMBL)DWA (SM00523)  DWB (SM00524)  
DMDM Disease mutations4093
Blocks (Seattle)O15198
Human Protein AtlasENSG00000120693
Peptide AtlasO15198
IPIIPI00005223   IPI00216093   
Protein Interaction databases
DIP (DOE-UCLA)O15198
IntAct (EBI)O15198
FunCoupENSG00000120693
BioGRIDSMAD9
IntegromeDBSMAD9
STRING (EMBL)SMAD9
Ontologies - Pathways
QuickGOO15198
Ontology : AmiGOureteric bud development  response to hypoxia  Mullerian duct regression  DNA binding  sequence-specific DNA binding transcription factor activity  protein binding  intracellular  nucleus  nucleoplasm  transcription factor complex  cytosol  transcription, DNA-templated  protein phosphorylation  transforming growth factor beta receptor signaling pathway  BMP signaling pathway  transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity  midbrain development  hindbrain development  intracellular signal transduction  positive regulation of cell differentiation  positive regulation of transcription, DNA-templated  metal ion binding  cartilage development  bone development  cellular response to organic cyclic compound  
Ontology : EGO-EBIureteric bud development  response to hypoxia  Mullerian duct regression  DNA binding  sequence-specific DNA binding transcription factor activity  protein binding  intracellular  nucleus  nucleoplasm  transcription factor complex  cytosol  transcription, DNA-templated  protein phosphorylation  transforming growth factor beta receptor signaling pathway  BMP signaling pathway  transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity  midbrain development  hindbrain development  intracellular signal transduction  positive regulation of cell differentiation  positive regulation of transcription, DNA-templated  metal ion binding  cartilage development  bone development  cellular response to organic cyclic compound  
Pathways : KEGGTGF-beta signaling pathway   
Protein Interaction DatabaseSMAD9
DoCM (Curated mutations)SMAD9
Wikipedia pathwaysSMAD9
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSMAD9 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMAD9
dbVarSMAD9
ClinVarSMAD9
1000_GenomesSMAD9 
Exome Variant ServerSMAD9
SNP (GeneSNP Utah)SMAD9
SNP : HGBaseSMAD9
Genetic variants : HAPMAPSMAD9
Genomic Variants (DGV)SMAD9 [DGVbeta]
Mutations
ICGC Data PortalENSG00000120693 
Somatic Mutations in Cancer : COSMICSMAD9 
CONAN: Copy Number AnalysisSMAD9 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)13:37418968-37494409
Mutations and Diseases : HGMDSMAD9
OMIM603295    615342   
MedgenSMAD9
NextProtO15198 [Medical]
GENETestsSMAD9
Disease Genetic AssociationSMAD9
Huge Navigator SMAD9 [HugePedia]  SMAD9 [HugeCancerGEM]
snp3D : Map Gene to Disease4093
DGIdb (Drug Gene Interaction db)SMAD9
General knowledge
Homologs : HomoloGeneSMAD9
Homology/Alignments : Family Browser (UCSC)SMAD9
Phylogenetic Trees/Animal Genes : TreeFamSMAD9
Chemical/Protein Interactions : CTD4093
Chemical/Pharm GKB GenePA30531
Clinical trialSMAD9
Cancer Resource (Charite)ENSG00000120693
Other databases
Probes
Litterature
PubMed36 Pubmed reference(s) in Entrez
CoreMineSMAD9
GoPubMedSMAD9
iHOPSMAD9
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated12-2014Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Feb 14 18:39:11 CET 2015
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