Atlas of Genetics and Cytogenetics in Oncology and Haematology


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ATRX (alpha thalassemia/mental retardation syndrome X-linked)

Identity

Other namesATR2
JMS
MRX52
MRXHF1
RAD54
RAD54L
SFM1
SHS
XH2
XNP
ZNF-HX
HGNC (Hugo) ATRX
LocusID (NCBI) 546
Atlas_Id 729
Location Xq21.1
Location_base_pair Starts at 76760356 and ends at 77041755 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2015)
ATRX Xq21.1 / BCL2 18q21.33ATRX Xq21.1 / ZNF304 19q13.43

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)ATRX   886
Cards
Entrez_Gene (NCBI)ATRX  546  alpha thalassemia/mental retardation syndrome X-linked
GeneCards (Weizmann)ATRX
Ensembl hg19 (Hinxton)ENSG00000085224 [Gene_View]  chrX:76760356-77041755 [Contig_View]  ATRX [Vega]
Ensembl hg38 (Hinxton)ENSG00000085224 [Gene_View]  chrX:76760356-77041755 [Contig_View]  ATRX [Vega]
ICGC DataPortalENSG00000085224
TCGA cBioPortalATRX
AceView (NCBI)ATRX
Genatlas (Paris)ATRX
WikiGenes546
SOURCE (Princeton)ATRX
Genomic and cartography
GoldenPath hg19 (UCSC)ATRX  -     chrX:76760356-77041755 -  Xq21.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)ATRX  -     Xq21.1   [Description]    (hg38-Dec_2013)
EnsemblATRX - Xq21.1 [CytoView hg19]  ATRX - Xq21.1 [CytoView hg38]
Mapping of homologs : NCBIATRX [Mapview hg19]  ATRX [Mapview hg38]
OMIM300448   300504   301040   309580   
Gene and transcription
Genbank (Entrez)AA484729 AA732359 AB102641 AB208928 AB209545
RefSeq transcript (Entrez)NM_000489 NM_138270 NM_138271
RefSeq genomic (Entrez)NC_000023 NC_018934 NG_008838 NT_011651 NW_004929444
Consensus coding sequences : CCDS (NCBI)ATRX
Cluster EST : UnigeneHs.653797 [ NCBI ]
CGAP (NCI)Hs.653797
Alternative Splicing : Fast-db (Paris)GSHG0032191
Alternative Splicing GalleryENSG00000085224
Gene ExpressionATRX [ NCBI-GEO ]     ATRX [ SEEK ]   ATRX [ MEM ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)546
Protein : pattern, domain, 3D structure
UniProt/SwissProtP46100 (Uniprot)
NextProtP46100  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP46100
Splice isoforms : SwissVarP46100 (Swissvar)
Catalytic activity : Enzyme3.6.4.12 [ Enzyme-Expasy ]   3.6.4.12 [ Enzyme-SRS ]   3.6.4.12 [ IntEnz-EBI ]   3.6.4.12 [ PRIAM ]   3.6.4.12 [ BRENDA ]   3.6.4.12 [ KEGG ]   3.6.4.12 [ IUBMB ]
PhosPhoSitePlusP46100
Domaine pattern : Prosite (Expaxy)ADD (PS51533)    HELICASE_ATP_BIND_1 (PS51192)    HELICASE_CTER (PS51194)   
Domains : Interpro (EBI)ADD    Helicase_ATP-bd    Helicase_C    P-loop_NTPase    SNF2_N    Znf_FYVE_PHD    Znf_RING    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)Helicase_C (PF00271)    SNF2_N (PF00176)   
Domain families : Pfam (NCBI)pfam00271    pfam00176   
Domain families : Smart (EMBL)DEXDc (SM00487)  HELICc (SM00490)  RING (SM00184)  
DMDM Disease mutations546
Blocks (Seattle)ATRX
PDB (SRS)2JM1    2LBM    2LD1    3QL9    3QLA    3QLC    3QLN    4W5A   
PDB (PDBSum)2JM1    2LBM    2LD1    3QL9    3QLA    3QLC    3QLN    4W5A   
PDB (IMB)2JM1    2LBM    2LD1    3QL9    3QLA    3QLC    3QLN    4W5A   
PDB (RSDB)2JM1    2LBM    2LD1    3QL9    3QLA    3QLC    3QLN    4W5A   
Structural Biology KnowledgeBase2JM1    2LBM    2LD1    3QL9    3QLA    3QLC    3QLN    4W5A   
SCOP (Structural Classification of Proteins)2JM1    2LBM    2LD1    3QL9    3QLA    3QLC    3QLN    4W5A   
CATH (Classification of proteins structures)2JM1    2LBM    2LD1    3QL9    3QLA    3QLC    3QLN    4W5A   
Human Protein AtlasENSG00000085224
Peptide AtlasP46100
HPRD02069
IPIIPI00297633   IPI00883721   IPI00938010   IPI00845355   IPI00220109   IPI00940810   IPI00552321   IPI01025076   IPI00647789   
Protein Interaction databases
DIP (DOE-UCLA)P46100
IntAct (EBI)P46100
FunCoupENSG00000085224
BioGRIDATRX
IntegromeDBATRX
STRING (EMBL)ATRX
ZODIACATRX
Ontologies - Pathways
QuickGOP46100
Ontology : AmiGODNA binding  DNA helicase activity  chromatin binding  helicase activity  protein binding  ATP binding  nucleus  nuclear heterochromatin  DNA repair  DNA methylation  DNA recombination  nucleosome assembly  DNA replication-independent nucleosome assembly  chromatin remodeling  transcription, DNA-templated  regulation of transcription, DNA-templated  spermatogenesis  zinc ion binding  positive regulation of nuclear cell cycle DNA replication  DNA translocase activity  PML body  DNA damage response, signal transduction by p53 class mediator  forebrain development  replication fork processing  telomeric heterochromatin  positive regulation of telomere maintenance  DNA duplex unwinding  methylated histone binding  post-embryonic forelimb morphogenesis  multicellular organism growth  histone binding  positive regulation of transcription from RNA polymerase II promoter  Sertoli cell development  chromo shadow domain binding  SWI/SNF superfamily-type complex  seminiferous tubule development  cellular response to hydroxyurea  negative regulation of telomeric RNA transcription from RNA pol II promoter  
Ontology : EGO-EBIDNA binding  DNA helicase activity  chromatin binding  helicase activity  protein binding  ATP binding  nucleus  nuclear heterochromatin  DNA repair  DNA methylation  DNA recombination  nucleosome assembly  DNA replication-independent nucleosome assembly  chromatin remodeling  transcription, DNA-templated  regulation of transcription, DNA-templated  spermatogenesis  zinc ion binding  positive regulation of nuclear cell cycle DNA replication  DNA translocase activity  PML body  DNA damage response, signal transduction by p53 class mediator  forebrain development  replication fork processing  telomeric heterochromatin  positive regulation of telomere maintenance  DNA duplex unwinding  methylated histone binding  post-embryonic forelimb morphogenesis  multicellular organism growth  histone binding  positive regulation of transcription from RNA polymerase II promoter  Sertoli cell development  chromo shadow domain binding  SWI/SNF superfamily-type complex  seminiferous tubule development  cellular response to hydroxyurea  negative regulation of telomeric RNA transcription from RNA pol II promoter  
Protein Interaction DatabaseATRX
Atlas of Cancer Signalling NetworkATRX
Wikipedia pathwaysATRX
Orthology - Evolution
OrthoDB546
GeneTree (enSembl)ENSG00000085224
Phylogenetic Trees/Animal Genes : TreeFamATRX
Homologs : HomoloGeneATRX
Homology/Alignments : Family Browser (UCSC)ATRX
Gene fusions - Rearrangements
Fusion: TCGAATRX Xq21.1 BCL2 18q21.33 LGG
Fusion: TCGAATRX Xq21.1 ZNF304 19q13.43 LGG
Polymorphisms : SNP, variants
NCBI Variation ViewerATRX [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ATRX
dbVarATRX
ClinVarATRX
1000_GenomesATRX 
Exome Variant ServerATRX
Exome Aggregation Consortium (ExAC)ENSG00000085224
SNP (GeneSNP Utah)ATRX
SNP : HGBaseATRX
Genetic variants : HAPMAPATRX
Genomic Variants (DGV)ATRX [DGVbeta]
Mutations
ICGC Data PortalATRX 
TCGA Data PortalATRX 
Tumor PortalATRX
TCGA Copy Number PortalATRX
Cancer Gene: CensusATRX 
Somatic Mutations in Cancer : COSMICATRX 
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)The Globin Gene Server
BioMutasearch ATRX
DgiDB (Drug Gene Interaction Database)ATRX
DoCM (Curated mutations)ATRX (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ATRX (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)X:76760356-77041755
CONAN: Copy Number AnalysisATRX 
Mutations and Diseases : HGMDATRX
OMIM300448    300504    301040    309580   
MedgenATRX
NextProtP46100 [Medical]
TSGene546
GENETestsATRX
Huge Navigator ATRX [HugePedia]  ATRX [HugeCancerGEM]
snp3D : Map Gene to Disease546
BioCentury BCIQATRX
General knowledge
Chemical/Protein Interactions : CTD546
Chemical/Pharm GKB GenePA25179
Clinical trialATRX
Other databases
Probes
Litterature
PubMed155 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineATRX
GoPubMedATRX
iHOPATRX
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Jan 16 18:11:33 CET 2016

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