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economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas).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 jlhuret@AtlasGeneticsOncology.org
Donations are also welcome
If each casual visitor gives 3 Euros or Dollars, the Atlas is saved in a week !
If each professional gives 100 Euros or Dollars once a year (now), the Atlas is saved in 2 weeks !
Don't let the Atlas imminent demise
Note: we send fiscal receipts for donations equal or above 50 Euros or Dollars

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SMARCA2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2)

Identity

Other namesBAF190
BRM
NCBRS
SNF2
SNF2L2
SNF2LA
SWI2
Sth1p
hBRM
hSNF2a
HGNC (Hugo) SMARCA2
LocusID (NCBI) 6595
Location 9p24.3
Location_base_pair Starts at 2021945 and ends at 2193623 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)SMARCA2   11098
Cards
Entrez_Gene (NCBI)SMARCA2  6595  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
GeneCards (Weizmann)SMARCA2
Ensembl hg19 (Hinxton)ENSG00000080503 [Gene_View]  chr9:2021945-2193623 [Contig_View]  SMARCA2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000080503 [Gene_View]  chr9:2021945-2193623 [Contig_View]  SMARCA2 [Vega]
ICGC DataPortalENSG00000080503
cBioPortalSMARCA2
AceView (NCBI)SMARCA2
Genatlas (Paris)SMARCA2
WikiGenes6595
SOURCE (Princeton)SMARCA2
Genomic and cartography
GoldenPath hg19 (UCSC)SMARCA2  -     chr9:2021945-2193623 +  9p24.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SMARCA2  -     9p24.3   [Description]    (hg38-Dec_2013)
EnsemblSMARCA2 - 9p24.3 [CytoView hg19]  SMARCA2 - 9p24.3 [CytoView hg38]
Mapping of homologs : NCBISMARCA2 [Mapview hg19]  SMARCA2 [Mapview hg38]
OMIM600014   601358   
Gene and transcription
Genbank (Entrez)AK094076 AK296373 AK298045 AK299683 AK300093
RefSeq transcript (Entrez)NM_001289396 NM_001289397 NM_001289398 NM_001289399 NM_001289400 NM_003070 NM_139045
RefSeq genomic (Entrez)NC_000009 NC_018920 NG_032162 NT_008413 NW_004929342
Consensus coding sequences : CCDS (NCBI)SMARCA2
Cluster EST : UnigeneHs.644901 [ NCBI ]
CGAP (NCI)Hs.644901
Alternative Splicing : Fast-db (Paris)GSHG0029984
Alternative Splicing GalleryENSG00000080503
Gene ExpressionSMARCA2 [ NCBI-GEO ]     SMARCA2 [ SEEK ]   SMARCA2 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP51531 (Uniprot)
NextProtP51531  [Medical]
With graphics : InterProP51531
Splice isoforms : SwissVarP51531 (Swissvar)
Catalytic activity : Enzyme3.6.4.- [ Enzyme-Expasy ]   3.6.4.-3.6.4.- [ IntEnz-EBI ]   3.6.4.- [ BRENDA ]   3.6.4.- [ KEGG ]   
Domaine pattern : Prosite (Expaxy)BROMODOMAIN_1 (PS00633)    BROMODOMAIN_2 (PS50014)    HELICASE_ATP_BIND_1 (PS51192)    HELICASE_CTER (PS51194)    HSA (PS51204)    QLQ (PS51666)   
Domains : Interpro (EBI)BRK_domain    Bromodomain    Bromodomain_CS    Gln-Leu-Gln_QLQ    HAS_subgr    Helicase/SANT-assoc_DNA-bd    Helicase_ATP-bd    Helicase_C    P-loop_NTPase    SMARCA2    SnAC    SNF2_N   
Related proteins : CluSTrP51531
Domain families : Pfam (Sanger)BRK (PF07533)    Bromodomain (PF00439)    Helicase_C (PF00271)    HSA (PF07529)    QLQ (PF08880)    SnAC (PF14619)    SNF2_N (PF00176)   
Domain families : Pfam (NCBI)pfam07533    pfam00439    pfam00271    pfam07529    pfam08880    pfam14619    pfam00176   
Domain families : Smart (EMBL)BRK (SM00592)  BROMO (SM00297)  DEXDc (SM00487)  HELICc (SM00490)  HSA (SM00573)  QLQ (SM00951)  
DMDM Disease mutations6595
Blocks (Seattle)P51531
PDB (SRS)2DAT   
PDB (PDBSum)2DAT   
PDB (IMB)2DAT   
PDB (RSDB)2DAT   
Human Protein AtlasENSG00000080503
Peptide AtlasP51531
HPRD02483
IPIIPI00514648   IPI00386718   IPI00647560   IPI00647028   IPI00641350   IPI00641050   IPI00640353   IPI00642503   IPI00103451   IPI00643691   IPI00640994   IPI00644329   IPI00645885   
Protein Interaction databases
DIP (DOE-UCLA)P51531
IntAct (EBI)P51531
FunCoupENSG00000080503
BioGRIDSMARCA2
IntegromeDBSMARCA2
STRING (EMBL)SMARCA2
Ontologies - Pathways
QuickGOP51531
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  RNA polymerase II transcription coactivator activity  transcription coactivator activity  helicase activity  protein binding  ATP binding  nucleus  nucleoplasm  nucleoplasm  chromatin organization  chromatin remodeling  transcription, DNA-templated  regulation of transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  nervous system development  DNA-dependent ATPase activity  negative regulation of cell proliferation  SWI/SNF complex  negative regulation of cell growth  aortic smooth muscle cell differentiation  histone binding  intracellular membrane-bounded organelle  transcription regulatory region DNA binding  intermediate filament cytoskeleton  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  npBAF complex  nBAF complex  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  RNA polymerase II transcription coactivator activity  transcription coactivator activity  helicase activity  protein binding  ATP binding  nucleus  nucleoplasm  nucleoplasm  chromatin organization  chromatin remodeling  transcription, DNA-templated  regulation of transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  nervous system development  DNA-dependent ATPase activity  negative regulation of cell proliferation  SWI/SNF complex  negative regulation of cell growth  aortic smooth muscle cell differentiation  histone binding  intracellular membrane-bounded organelle  transcription regulatory region DNA binding  intermediate filament cytoskeleton  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  npBAF complex  nBAF complex  
Protein Interaction DatabaseSMARCA2
DoCM (Curated mutations)SMARCA2
Wikipedia pathwaysSMARCA2
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSMARCA2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMARCA2
dbVarSMARCA2
ClinVarSMARCA2
1000_GenomesSMARCA2 
Exome Variant ServerSMARCA2
SNP (GeneSNP Utah)SMARCA2
SNP : HGBaseSMARCA2
Genetic variants : HAPMAPSMARCA2
Genomic Variants (DGV)SMARCA2 [DGVbeta]
Mutations
ICGC Data PortalENSG00000080503 
Somatic Mutations in Cancer : COSMICSMARCA2 
CONAN: Copy Number AnalysisSMARCA2 
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
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)9:2021945-2193623
Mutations and Diseases : HGMDSMARCA2
OMIM600014    601358   
MedgenSMARCA2
NextProtP51531 [Medical]
GENETestsSMARCA2
Disease Genetic AssociationSMARCA2
Huge Navigator SMARCA2 [HugePedia]  SMARCA2 [HugeCancerGEM]
snp3D : Map Gene to Disease6595
DGIdb (Drug Gene Interaction db)SMARCA2
General knowledge
Homologs : HomoloGeneSMARCA2
Homology/Alignments : Family Browser (UCSC)SMARCA2
Phylogenetic Trees/Animal Genes : TreeFamSMARCA2
Chemical/Protein Interactions : CTD6595
Chemical/Pharm GKB GenePA35948
Clinical trialSMARCA2
Cancer Resource (Charite)ENSG00000080503
Other databases
Probes
Litterature
PubMed153 Pubmed reference(s) in Entrez
CoreMineSMARCA2
GoPubMedSMARCA2
iHOPSMARCA2
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
Updated02-2015Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Mar 28 17:22:39 CET 2015

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.