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ATRX ATRX chromatin remodeler [ Homo sapiens (human) ]

Gene ID: 546, updated on 18-Jun-2019

Summary

Official Symbol
ATRXprovided by HGNC
Official Full Name
ATRX chromatin remodelerprovided by HGNC
Primary source
HGNC:HGNC:886
See related
Ensembl:ENSG00000085224 MIM:300032
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
JMS; XH2; XNP; MRX52; RAD54; RAD54L; ZNF-HX
Summary
The protein encoded by this gene contains an ATPase/helicase domain, and thus it belongs to the SWI/SNF family of chromatin remodeling proteins. 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. Mutations in this gene are associated with X-linked syndromes exhibiting cognitive disabilities as well as 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. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2017]
Expression
Ubiquitous expression in brain (RPKM 12.1), endometrium (RPKM 9.2) and 25 other tissues See more
Orthologs

Genomic context

See ATRX in Genome Data Viewer
Location:
Xq21.1
Exon count:
38
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (77504878..77786235, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (76760356..77041755, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene SPRY domain containing 7 pseudogene 1 Neighboring gene fibroblast growth factor 16 Neighboring gene fatty acid binding protein 5 pseudogene 15 Neighboring gene RNA, U6 small nuclear 854, pseudogene Neighboring gene magnesium transporter 1 Neighboring gene RNA, 7SL, cytoplasmic 460, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Acquired hemoglobin H disease
MedGen: C0585216 OMIM: 300448 GeneReviews: Not available
not available
ATR-X syndrome not available
Mental retardation-hypotonic facies syndrome X-linked, 1
MedGen: C0796003 OMIM: 309580 GeneReviews: Not available
not available

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-07-31)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-31)

ClinGen Genome Curation PagePubMed

Pathways from BioSystems

  • Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
    Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC2094

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA helicase activity IEA
Inferred from Electronic Annotation
more info
 
DNA translocase activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
chromo shadow domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone binding IDA
Inferred from Direct Assay
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA damage response, signal transduction by p53 class mediator ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
 
DNA methylation TAS
Traceable Author Statement
more info
PubMed 
DNA repair IEA
Inferred from Electronic Annotation
more info
 
DNA replication-independent nucleosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Sertoli cell development IEA
Inferred from Electronic Annotation
more info
 
cellular response to hydroxyurea ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
chromosome organization involved in meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
forebrain development IEA
Inferred from Electronic Annotation
more info
 
meiotic spindle organization IEA
Inferred from Electronic Annotation
more info
 
multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of telomeric RNA transcription from RNA pol II promoter ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleosome assembly IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of nuclear cell cycle DNA replication ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of telomere maintenance ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of telomeric RNA transcription from RNA pol II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
post-embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
protein localization to chromosome, telomeric region ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of histone H3-K9 trimethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
replication fork processing ISS
Inferred from Sequence or Structural Similarity
more info
 
seminiferous tubule development IEA
Inferred from Electronic Annotation
more info
 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
PML body ISS
Inferred from Sequence or Structural Similarity
more info
 
condensed nuclear chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
nuclear body IDA
Inferred from Direct Assay
more info
 
nuclear chromosome, telomeric region ISS
Inferred from Sequence or Structural Similarity
more info
 
colocalizes_with nuclear chromosome, telomeric region ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear heterochromatin TAS
Traceable Author Statement
more info
PubMed 
nuclear pericentric heterochromatin IEA
Inferred from Electronic Annotation
more info
 
nuclear subtelomeric heterochromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus TAS
Traceable Author Statement
more info
PubMed 
pericentric heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
telomeric heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
transcriptional regulator ATRX
Names
ATP-dependent helicase ATRX
X-linked helicase II
X-linked nuclear protein
alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae)
NP_000480.3
NP_612114.2
XP_005262210.2
XP_005262211.2
XP_005262212.2
XP_005262213.2
XP_005262214.2
XP_006724729.1
XP_006724730.1
XP_006724731.1
XP_016885090.1
XP_016885091.1
XP_016885092.1
XP_016885093.1
XP_016885094.1
XP_016885095.1
XP_016885096.1
XP_016885097.1
XP_016885098.1
XP_016885099.1
XP_016885100.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008838.3 RefSeqGene

    Range
    5054..286392
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1153

mRNA and Protein(s)

  1. NM_000489.5NP_000480.3  transcriptional regulator ATRX isoform 1

    See identical proteins and their annotated locations for NP_000480.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AA732359, AB102641, AC233305, AK297183, U72937
    Consensus CDS
    CCDS14434.1
    UniProtKB/Swiss-Prot
    P46100
    UniProtKB/TrEMBL
    A4LAA3, B4DLW1
    Related
    ENSP00000362441.4, ENST00000373344.10
    Conserved Domains (4) summary
    cd00046
    Location:15881750
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:20172163
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd11726
    Location:167270
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:15631889
    SNF2_N; SNF2 family N-terminal domain
  2. NM_138270.4NP_612114.2  transcriptional regulator ATRX isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a segment within the coding region when compared to variant 1. The translation remains in-frame, and thus results in an isoform (2) that lacks an internal segment, as compared to isoform 1.
    Source sequence(s)
    AA732359, AB102641, AC233305, U72938
    Consensus CDS
    CCDS14435.1
    UniProtKB/Swiss-Prot
    P46100
    Related
    ENSP00000378967.3, ENST00000395603.7
    Conserved Domains (4) summary
    cd00046
    Location:15501712
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:19792125
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd11726
    Location:129232
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:15251851
    SNF2_N; SNF2 family N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    77504878..77786235 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029611.1XP_016885100.1  transcriptional regulator ATRX isoform X18

  2. XM_006724667.3XP_006724730.1  transcriptional regulator ATRX isoform X14

    Conserved Domains (4) summary
    cd00046
    Location:14951657
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:19242070
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd11726
    Location:74177
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:14701796
    SNF2_N; SNF2 family N-terminal domain
  3. XM_017029603.1XP_016885092.1  transcriptional regulator ATRX isoform X7

  4. XM_005262156.4XP_005262213.2  transcriptional regulator ATRX isoform X8

    Conserved Domains (4) summary
    cd00046
    Location:15331695
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:19622108
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd11726
    Location:112215
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:15081834
    SNF2_N; SNF2 family N-terminal domain
  5. XM_017029610.1XP_016885099.1  transcriptional regulator ATRX isoform X17

  6. XM_017029609.1XP_016885098.1  transcriptional regulator ATRX isoform X16

  7. XM_017029605.1XP_016885094.1  transcriptional regulator ATRX isoform X10

  8. XM_005262155.4XP_005262212.2  transcriptional regulator ATRX isoform X4

    Conserved Domains (4) summary
    cd00046
    Location:15491711
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:19782124
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd11726
    Location:128231
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:15241850
    SNF2_N; SNF2 family N-terminal domain
  9. XM_005262157.5XP_005262214.2  transcriptional regulator ATRX isoform X11

    Conserved Domains (4) summary
    cd00046
    Location:15201682
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:19492095
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd11726
    Location:128231
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:14951821
    SNF2_N; SNF2 family N-terminal domain
  10. XM_006724666.4XP_006724729.1  transcriptional regulator ATRX isoform X5

    Conserved Domains (4) summary
    cd00046
    Location:15491711
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:19782124
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd11726
    Location:128231
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:15241850
    SNF2_N; SNF2 family N-terminal domain
  11. XM_017029604.2XP_016885093.1  transcriptional regulator ATRX isoform X9

  12. XM_017029601.2XP_016885090.1  transcriptional regulator ATRX isoform X3

  13. XM_005262154.5XP_005262211.2  transcriptional regulator ATRX isoform X2

    Conserved Domains (4) summary
    cd00046
    Location:15591721
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:19882134
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd11726
    Location:167270
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:15341860
    SNF2_N; SNF2 family N-terminal domain
  14. XM_017029606.2XP_016885095.1  transcriptional regulator ATRX isoform X12

  15. XM_005262153.5XP_005262210.2  transcriptional regulator ATRX isoform X1

    Conserved Domains (4) summary
    cd00046
    Location:15871749
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00079
    Location:20162162
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    cd11726
    Location:166269
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:15621888
    SNF2_N; SNF2 family N-terminal domain
  16. XM_017029607.2XP_016885096.1  transcriptional regulator ATRX isoform X13

  17. XM_017029602.1XP_016885091.1  transcriptional regulator ATRX isoform X6

  18. XM_017029608.2XP_016885097.1  transcriptional regulator ATRX isoform X15

  19. XM_006724668.3XP_006724731.1  transcriptional regulator ATRX isoform X19

    Conserved Domains (3) summary
    cd00046
    Location:15881750
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd11726
    Location:167270
    ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    pfam00176
    Location:15631869
    SNF2_N; SNF2 family N-terminal domain

RNA

  1. XR_001755700.2 RNA Sequence

    Related
    ENST00000480283.5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_138271.1: Suppressed sequence

    Description
    NM_138271.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.
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