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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ATRX Gene

protein-coding   GIFtS: 65
GCID: GC0XM076760

alpha thalassemia/mental retardation syndrome X-linked

(Previous names: alpha thalassemia/mental retardation syndrome X-linked...)
(Previous symbols: RAD54, JMS)
 Explore 49 diseases affiliated with
ATRX via
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our new
 Human Malady Compendium 
Biological research products
for ATRX    

Aliases
for ATRX gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Alpha Thalassemia/Mental Retardation Syndrome X-Linked1 2     Juberg-Marsidi Syndrome1
XH21 2 3 5     ATR22
XNP1 2 3 5     ZNF-HX2
JMS1 2     Alpha Thalassemia/Mental Retardation Syndrome X-Linked (RAD54 Homolog, S.
Cerevisiae)2
RAD541 2     DNA Dependent ATPase And Helicase2
RAD54L2 3     Helicase 2, X-Linked2
ATP-Dependent Helicase ATRX2 3     RAD54 Homolog2
X-Linked Helicase II2 3     Transcriptional Regulator ATRX2
X-Linked Nuclear Protein2 3     Zinc Finger Helicase2
MRXHF12 5     EC 3.6.4.123
SFM12 5     Znf-HX3
SHS2 5     EC 3.6.18
Alpha Thalassemia/Mental Retardation Syndrome X-Linked (RAD54 (S. Cerevisiae)
Homolog)1
     

External Ids:    HGNC: 8861   Entrez Gene: 5462   Ensembl: ENSG000000852247   OMIM: 3000325   UniProtKB: P461003   

Export aliases for ATRX gene to outside databases

Previous GC identifers: GC0XM072306 GC0XM073722 GC0XM074802 GC0XM075518 GC0XM075519 GC0XM076567 GC0XM070349


Summaries
for ATRX gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for ATRX:
The protein encoded by this gene contains an ATPase/helicase domain, and thus it belongs to the SWI/SNF family of
chromatin remodeling proteins. The mutations of this gene are associated with an X-linked mental retardation (XLMR)
syndrome most often accompanied by alpha-thalassemia (ATRX) syndrome. These mutations have been shown to cause diverse
changes in the pattern of DNA methylation, which may provide a link between chromatin remodeling, DNA methylation, and
gene expression in developmental processes. This protein is found to undergo cell cycle-dependent phosphorylation,
which regulates its nuclear matrix and chromatin association, and suggests its involvement in the gene regulation at
interphase and chromosomal segregation in mitosis. Multiple alternatively spliced transcript variants encoding
distinct isoforms have been reported. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: ATRX_HUMAN, P46100
Function: Could be a global transcriptional regulator. Modifies gene expression by affecting chromatin. May be involved
in brain development and facial morphogenesis

Gene Wiki entry for ATRX


Genomic Views
for ATRX gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.1  NT_011651.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ATRX gene promoter:
         AML1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): ATRX promoter sequence
   Search SABiosciences Chromatin IP Primers for ATRX

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ATRX


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq21.1   Ensembl cytogenetic band:  Xq21.1   HGNC cytogenetic band: Xq21.1

ATRX Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ATRX gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM076760:  view genomic region     (about GC identifiers)

Start:
 76,760,356 bp from pter      End:
 77,041,719 bp from pter
Size:
 281,364 bases      Orientation:
 minus strand

Proteins
for ATRX gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: ATRX_HUMAN, P46100 (See protein sequence)
Recommended Name: Transcriptional regulator ATRX  
Size: 2492 amino acids; 282586 Da
Subunit: Probably binds EZH2. Binds annexin V in a calcium and phosphatidylcholine/phosphatidylserine-dependent manner
(By similarity). Interacts directly with CBX5 via the PxVxL motif
Subcellular location: Nucleus. Note=Associated with pericentromeric heterochromatin during interphase and mitosis,
probably by interacting with HP1
Sequence caution: Sequence=AAA20872.1; Type=Miscellaneous discrepancy; Note=Many frameshifts and conflits;
Sequence=AAC50069.1; Type=Frameshift; Positions=Several; Sequence=BAD92165.1; Type=Erroneous initiation;
Note=Translation N-terminally shortened;
6/7 PDB 3D structures from and Proteopedia for ATRX (see all 7):
2JM1 (3D)        2LBM (3D)        2LD1 (3D)        3QL9 (3D)        3QLA (3D)        3QLC (3D)    
Secondary accessions: D3DTE2 P51068 Q15886 Q59FB5 Q59H31 Q5H9A2 Q5JWI4 Q7Z2J1 Q9H0Z1 Q9NTS3
Alternative splicing: 6 isoforms:  P46100-1   P46100-2   P46100-3   P46100-4   P46100-5   P46100-6   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ATRX: NX_P46100

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P46100

    • 4/69 DME Specific Peptides for ATRX (P46100) (see all 69)
     LVFSQSL  TGTPLQN  FDASWNP  SGSVTYS 

    ATRX Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_000480.2  NP_612114.1  

    ENSEMBL proteins: 
     ENSP00000362441   ENSP00000378967   ENSP00000383663   ENSP00000362438  

    Human Recombinant Protein Products: 
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    Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
    Browse OriGene Protein Over-expression Lysates
    OriGene Custom Protein Services for ATRX 
    GenScript Custom Purified and Recombinant Proteins Services for ATRX
    Novus Biologicals ATRX Proteins
    Novus Biologicals ATRX Lysate
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Uscn Proteins for ATRX

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000228nuclear chromosome ----
    GO:0000792heterochromatin ----
    GO:0005634nucleus TAS7874112
    GO:0005720nuclear heterochromatin TAS10570185


    ATRX for ontologies           About GeneDecksing



    ATRX Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of ATRX
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    OriGene Antibodies: ATRX
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    Novus Biologicals ATRX Antibodies
    Abcam antibodies for ATRX 
    Uscn Antibodies for ATRX
    ThermoFisher Antibody for ATRX

    Assay Products for ATRX: 
    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Immunoassay Development
    Browse OriGene Fluorogenic Cell Assay Kits
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    GenScript Custom Assay Services for ATRX
    Browse Enzo Life Sciences for kits & assays
    Uscn ELISAs and CLIAs for ATRX

    Protein Domains /
    Families
    for ATRX gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    ATRX for domains           About GeneDecksing

    5/7 InterPro domains/families (see all 7):
     IPR001841 Znf_RING
     IPR000330 SNF2_N
     IPR013083 Znf_RING/FYVE/PHD
     IPR014001 Helicase_ATP-bd
     IPR025766 ADD

    Graphical View of Domain Structure for InterPro Entry P46100

    ProtoNet protein and cluster: P46100

    1 Blocks protein family: IPB000330 SNF2 related domain

    UniProtKB/Swiss-Prot: ATRX_HUMAN, P46100
    Domain: Contains one Pro-Xaa-Val-Xaa-Leu (PxVxL) motif, which is required for interaction with chromoshadow domains.
    This motif requires additional residues -7, -6, +4 and +5 of the central Val which contact the chromoshadow domain
    Similarity: Belongs to the SNF2/RAD54 helicase family
    Similarity: Contains 1 ADD domain
    Similarity: Contains 1 GATA-type zinc finger
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain
    Similarity: Contains 1 PHD-type zinc finger


    Function
    for ATRX gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: ATRX_HUMAN, P46100
    Function: Could be a global transcriptional regulator. Modifies gene expression by affecting chromatin. May be involved
    in brain development and facial morphogenesis
    Catalytic activity: ATP + H(2)O = ADP + phosphate

    Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.121

    miRNA
    Products:            		miRTarBase miRNAs that target ATRX:
    hsa-mir-30a (MIRT005165)

    OriGene 3'-UTR Clone (see all 2): ATRX
    Browse MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat ATRX
    8/88 QIAGEN miScript miRNA Assays for microRNAs that regulate ATRX (see all 88):
    hsa-miR-323-3p hsa-miR-300 hsa-miR-3653 hsa-miR-761 hsa-miR-92b hsa-miR-130b hsa-miR-374b* hsa-miR-27a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for ATRX (see all 7)
    OriGene shRNA RFP: ATRX
    OriGene siRNA: ATRX
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat ATRX

    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for ATRX

    Clone
    Products:             		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for ATRX (see all 3)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for ATRX (see all 3)
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector (see all 2): ATRX (NM_000489)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for ATRX
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat ATRX 

    Cell Line
    Products:             		GenScript Custom overexpressing Cell Line Services for ATRX
    Search LifeMap BioReagents cell lines for ATRX

    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ATRX

    Gene Ontology (GO): 5/8 molecular function terms (GO ID links to tree view) (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003678DNA helicase activity TAS7697714
    GO:0003682chromatin binding IEA--
    GO:0004386helicase activity TAS7874112
    GO:0005515protein binding IPI12953102


    ATRX for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for ATRX:
     Increased cell death in HCC-19 

    Animal Models:
         10 MGI mutant phenotypes (inferred from 6 alleles) (MGI details for Atrx):
     behavior/neurological  cardiovascular system  cellular  embryogenesis  growth/size 
     homeostasis/metabolism  mortality/aging  nervous system  reproductive system  vision/eye 

    ATRX for phenotypes           About GeneDecksing


    Pathways & Interactions
    for ATRX gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for ATRX

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/598 Interacting proteins for ATRX (P461001, 2, 3 ENSP000003624414) via UniProtKB, MINT, STRING, and/or I2D (see all 598)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H3AP684313, ENSP000003502754I2D: score=1 STRING: ENSP00000350275
    HIST1H3BP684313I2D: score=1 
    HIST1H3CP684313I2D: score=1 
    HIST1H3DP684313I2D: score=1 
    HIST1H3EP684313I2D: score=1 
    About this table

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006281DNA repair IEA--
    GO:0006306DNA methylation TAS10742099
    GO:0006310DNA recombination TAS7697714
    GO:0006355regulation of transcription, DNA-dependent TAS7697714
    GO:0030900forebrain development IEA--


    ATRX for ontologies           About GeneDecksing



    Drugs & Compounds
    for ATRX gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    ATRX for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ATRX

    10/125 HMDB Compounds for ATRX (see all 125)    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    PS(14:0/14:0)Phosphatidylserine(14:0/14:0) (see all 7)----
    PS(14:0/14:1(9Z))Phosphatidylserine(14:0/14:1n5) (see all 13)----
    PS(14:0/16:0)1-myristoyl-2-palmitoyl-sn-glycero-3-phosphoserine (see all 7)----
    PS(14:0/16:1(9Z))PS(14:0/16:1n7) (see all 13)----
    PS(14:0/18:0)Phosphatidylserine(32:0) (see all 7)----
    PS(14:0/18:1(9Z))PSer(14:0/18:1n9) (see all 13)----
    PS(14:0/18:2(9Z,12Z))PS(14:0/18:2) (see all 13)----
    PS(14:0/18:3(9Z,12Z,15Z))Phosphatidylserine(14:0/18:3) (see all 14)----
    PS(14:0/20:3(8Z,11Z,14Z))PSer(14:0/20:3) (see all 14)----
    3 Novoseek chemical compound relationships for ATRX gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    atp 32.1 7 15653683 (2), 10209103 (1), 19017809 (1), 16818238 (1) (see all 6)
    zinc 19.3 8 10857753 (2), 10699177 (1), 10995512 (1), 17609377 (1) (see all 6)
    cytosine 11.2 1 15120073 (1)

    Search CenterWatch for drugs/clinical trials and news about ATRX 

    Transcripts
    for ATRX gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for ATRX gene (3 alternative transcripts): 
    NM_000489.3  NM_138270.2  NM_138271.1  

    Unigene Cluster for ATRX:

    Alpha thalassemia/mental retardation syndrome X-linked
    Hs.533526  [show with all ESTs]
    Unigene Representative Sequence: NM_000489
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000373344(uc004ecp.4 uc010nlx.1 uc010nly.1) ENST00000395603(uc004ecq.4 uc004ecr.2)
    ENST00000480283(uc004eco.4) ENST00000479487 ENST00000400866 ENST00000460639
    ENST00000493470 ENST00000373341

    miRNA
    Products:             		 OriGene 3'-UTR Clone (see all 2): ATRX
    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat ATRX
    8/88 QIAGEN miScript miRNA Assays for microRNAs that regulate ATRX (see all 88):
    hsa-miR-323-3p hsa-miR-300 hsa-miR-3653 hsa-miR-761 hsa-miR-92b hsa-miR-130b hsa-miR-374b* hsa-miR-27a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:             		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for ATRX (see all 7)
    OriGene shRNA RFP: ATRX
    OriGene siRNA: ATRX
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat ATRX
    Clone
    Products:             		 OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for ATRX (see all 3)
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    GenScript: all cDNA clones in your preferred vector (see all 2): ATRX (NM_000489)
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    Primer
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    Browse OriGene validated miRNA SYBR primer pairs
    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat ATRX
      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ATRX
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat ATRX

    Additional cDNA sequence: 

    AB102641.1 AB208928.1 AB209545.1 AK293241.1 AK295107.1 AK296959.1 AK297183.1 AK307791.1 
    AK308419.1 BC002521.2 BT007188.1 BX647222.1 L33812.1 L33813.1 U09820.1 U72936.2 
    U72937.2 U72938.2 

    22 DOTS entries:

    DT.75188922  DT.100797559  DT.95207537  DT.99950475  DT.95207550  DT.100736904  DT.121314392  DT.97845877 
    DT.121314448  DT.92442528  DT.92442532  DT.121314396  DT.121314430  DT.121314453  DT.121314456  DT.423143 
    DT.75111679  DT.92442504  DT.95332718  DT.99998422  DT.121314440  DT.95245849 

    24/375 AceView cDNA sequences (see all 375):

    U72936 BG619429 BE206496 AI813887 CK724945 CB133947 AI273172 AA406426 
    CA392870 AA488113 AI922880 BU431755 AI754123 BU193209 BE501775 BM479663 
    BE884374 AI858806 BM668434 AA806986 BQ008335 BQ778428 AA971532 AA719092 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for ATRX (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19a · 19b
    SP1:                                                                                                                                                
    SP2:                                                                                                                                                
    SP3:                                                                                                                                                
    SP4:                                                                                                                                                
    SP5:                                                                                                                                                


    ECgene alternative splicing isoforms for ATRX

    Expression
    for ATRX gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    ATRX expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCAGAACCAT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    ATRX expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    KidneyCap MesenchymeCap Mesenchyme CellsKidney
    KidneyS-shaped BodyKidney
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See ATRX Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ATRX

    SOURCE GeneReport for Unigene cluster: Hs.533526

    UniProtKB/Swiss-Prot: ATRX_HUMAN, P46100
    Tissue specificity: Ubiquitous

        SABiosciences Expression via Pathway-Focused PCR Arrays including ATRX: 
              DNA Damage Signaling Pathway in human mouse rat
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    Orthologs
    for ATRX gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for ATRX gene from 6/26 species (see all 26)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves ATRX1 alpha thalassemia/mental retardation syndrome X-linked 76.1(n)
    76.2(a)    		   422331  XM_420305.3  XP_420305.3 
    lizard
    (Anolis carolinensis)    		 Reptilia ATRX6
    		 --
    		 69(a)
    		 1 ↔ 1
    		 GL343420.1(789292-834301)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.191432 Xenopus laevis transcribed sequence with moderate similarity more 79.4(n)    BX843733.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii zgc662232 hypothetical protein MGC66223 75.68(n)   393626  BC057486.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta XNP1 , 3 DNA helicase3
    CG4548-PA1    		 47(a)3
    47.95(n)1
    43.22(a)1    		   430801  NM_170228.21  NP_733107.11 
    worm
    (Caenorhabditis elegans)    		 Secernentea xnp-11 , 3 Protein XNP-11 45(a)3
    51.38(n)1
    42.61(a)1    		   I(4666147-4671715)3
    1720771  NM_001025787.11  NP_001020958.11 


    ENSEMBL Gene Tree for ATRX (if available)
    TreeFam Gene Tree for ATRX (if available) 

    Paralogs
    for ATRX gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ATRX gene
    RAD54L22  RAD54L2  
    7 SIMAP similar genes for ATRX using alignment to 8 protein entries:     ATRX_HUMAN (see all proteins):
    RAD54L2    SHPRH    ERCC6    SRCAP    SMARCA4    BTAF1
    SMARCA1

    ATRX for paralogs           About GeneDecksing



    Genomic Variants
    for ATRX gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/2513 NCBI SNPs in ATRX are shown (see all 2513)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr X posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs454397991,2
    		C,F,pathogenic76856021(-) CAATAA/GTAGTG 8 N S mis16Minor allele frequency- G:0.01NS NA 4728
    rs1863779041,2
    		--76759863(+) TCTCTC/TAATAG 2 -- ds50010--------
    rs1908291621,2
    		--76760000(+) ATATGC/GTGTAT 2 -- ds50010--------
    rs38308911,2
    		C,F--76760407(+) AATGTTGT/-GAAGA 4 -- ut315Minor allele frequency- -:0.04NS 140
    rs1999599341,2
    		C,--76760407(+) TAAAA-/TGTTGTGA 2 -- ut310--------
    rs2019881781,2
    		--76760890(+) TGACT-/TAAAA 
                TGAGT     		2 -- ut310--------
    rs1834055991,2
    		--76760970(+) CACACA/GTGGAC 2 -- ut310--------
    rs1884670011,2
    		--76761058(+) ACTTCA/GTGACC 2 -- ut310--------
    rs1912644481,2
    		--76761940(+) GACCAC/TGTTGA 2 -- ut310--------
    rs66235131,2
    		C,F,--76762191(+) AGGGGC/TGTGGA 2 -- ut31 ese36Minor allele frequency- T:0.04NS WA 190

    HapMap Linkage Disequilibrium report for ATRX (76760356 - 77010356 bp, first 250kb of ATRX)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for ATRX: --
    Human Gene Mutation Database (HGMD): ATRX

    Locus Specific Mutation Databases (LSDB): ATRX

    4 SABiosciences Cancer Mutation PCR Assays for ATRX:
    Cosmic IdAA Change
    13840p.K971E
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    85983p.L192F
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing ATRX
    DNA2.0 Custom Variant and Variant Library Synthesis for ATRX

    Disorders / Diseases
    for ATRX gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    ATRX for disorders           About GeneDecksing

    OMIM gene information: 300032   
    OMIM disorders: 301040  300448  309580  
    UniProtKB/Swiss-Prot: ATRX_HUMAN, P46100
  • Defects in ATRX are the cause of alpha-thalassemia mental retardation syndrome X-linked (ATRX) [MIM:301040].
    • ATR-X is an X-linked disorder comprising severe psychomotor retardation, facial dysmorphism, urogenital abnormalities,
    and alpha-thalassemia. An essential phenotypic trait are hemoglobin H erythrocyte inclusions
  • Defects in ATRX are the cause of mental retardation syndromic X-linked with hypotonic facies syndrome type 1
    • (MRXSHF1) [MIM:309580]; also called Carpenter-Waziri syndrome (CWS), Juberg-Marsidi syndrome (JMS),
    Smith-Fineman-Myers syndrome type 1 (SFM1). Clinical features include severe mental retardation, dysmorphic facies,
    and a highly skewed X-inactivation pattern in carrier women. Other more variable features include hypogonadism,
    deafness, renal anomalies, and mild skeletal defects
  • Defects in ATRX are a cause of alpha-thalassemia myelodysplasia syndrome (ATMDS) [MIM:300448]. In this
    • disorder, alpha-thalassemia occurs as an acquired abnormality in association with a multilineage myelodysplasia

    20/49 diseases for ATRX (see all 49):    About MalaCards
    alpha-thalassemia/mental retardation syndrome    alpha thalassemia    juberg-marsidi syndrome    thalassemia
    mental retardation-hypotonic facies syndrome, x-linked    mental retardation syndrome    alpha-thalassemia myelodysplasia syndrome    alpha-thalassemia myelodysplasia syndrome, somatic
    smith-fineman-myers syndrome    chudley-lowry syndrome    myelodysplasia syndrome    mental retardation, x-linked
    short stature    gonadal dysgenesis    spastic diplegia    sex reversal
    mental retardation epilepsy    autism spectrum disorder    faces syndrome    x inactivation

    2 diseases from the University of Copenhagen DISEASES database for ATRX:
    Thalassemia     Intellectual disability

    10/17 Novoseek disease relationships for ATRX gene (see all 17)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    atr-x syndrome 98.5 24 8968741 (2), 16266892 (2), 10872473 (1), 10398234 (1) (see all 17)
    juberg-marsidi syndrome 90.4 4 11449489 (1), 8630485 (1)
    alpha-thalassemia 88.4 17 8644709 (3), 9043863 (2), 10398234 (1), 16480427 (1) (see all 10)
    mental retardation 83.1 59 8644709 (3), 19291773 (3), 17296936 (3), 12673795 (2) (see all 32)
    severe mental retardation 71.3 3 10742099 (1), 12673795 (1)
    thalassemia 67.6 13 14592816 (2), 11449489 (1), 14729260 (1), 8644709 (1) (see all 7)
    promyelocytic leukemia 59.6 3 14729260 (1), 12953102 (1), 17957225 (1)
    genitourinary anomaly 55.2 4 10742099 (1), 15350606 (1), 16813605 (1)
    myelodysplastic syndromes 52.6 6 14592816 (2), 16480427 (1), 19157545 (1), 18409179 (1)
    mild mental retardation 51.7 1 10632111 (1)

    GeneTests: ATRX
    Alpha-Thalassemia X-Linked Mental Retardation Syndrome

    Human Genome Epidemiology (HuGE) Navigator: ATRX (1 document)

    Export disorders for ATRX gene to outside databases

    Publications
    for ATRX gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for ATRX gene, integrated from 9 sources (see all 216):
    (articles sorted by number of sources associating them with ATRX)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and characterization of a new human Xq13 gene, encoding a putative helicase. (PubMed id 7874112)1, 2, 3, 9 Stayton C.L.... Consalez G.G. (1994)
    2. XNP mutation in a large family with Juberg-Marsidi syndrome. (PubMed id 8630485)1, 2, 3, 9 Villard L.... Lyonnet S. (1996)
    3. Localization of a putative transcriptional regulator (ATRX) at pericentromeric heterochromatin and the short arms of acrocentric chromosomes. (PubMed id 10570185)1, 2, 9 McDowell T.L.... Higgs D.R. (1999)
    4. Structural consequences of disease-causing mutations in the ATRX-DNMT3-DNMT3L (ADD) domain of the chromatin-associated protein ATRX. (PubMed id 17609377)1, 2, 9 Argentaro A....Rhodes D. (2007)
    5. Specific interaction between the XNP/ATR-X gene product and the SET domain of the human EZH2 protein. (PubMed id 9499421)1, 2, 9 Cardoso C....Colleaux L. (1998)
    6. ATRX encodes a novel member of the SNF2 family of proteins: mutations point to a common mechanism underlying the ATR-X syndrome. (PubMed id 8968741)1, 2, 9 Picketts D.J....Gibbons R.J. (1996)
    7. A point mutation in the XNP gene, associated with an ATR-X phenotype without alpha-thalassemia. (PubMed id 9043863)1, 2, 9 Villard L.... Fontes M. (1996)
    8. Molecular genetic study of Japanese patients with X-linked alpha- thalassemia/mental retardation syndrome (ATR-X). (PubMed id 10995512)1, 2, 9 Wada T.... Saitoh S. (2000)
    9. Carpenter-Waziri syndrome results from a mutation in XNP. (PubMed id 10398237)1, 2, 9 Abidi F....Curtis M. (1999)
    10. Determination of the genomic structure of the XNP/ATRX gene encoding a potential zinc finger helicase. (PubMed id 9244431)1, 2, 9 Villard L.... Fontes M. (1997)

    External Searches for ATRX gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing ATRX gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 546 HGNC: 886 AceView: ATRX Ensembl:ENSG00000085224 euGenes: HUgn546
    ECgene: ATRX H-InvDB: ATRX

    Other Databases showing ATRX gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing ATRX gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for ATRX Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for ATRX Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ATRX

    Intellectual Property
    for ATRX gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for ATRX gene:
    Search GeneIP for patents involving ATRX

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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