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ATRX ATRX chromatin remodeler [ Homo sapiens (human) ]

Gene ID: 546, updated on 5-May-2024

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; AllianceGenome:HGNC:886
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
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Genomic context

See ATRX in Genome Data Viewer
Location:
Xq21.1
Exon count:
37
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (77504880..77786216, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (75942420..76223770, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (76760358..77041702, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene SPRY domain containing 7 pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:76642667-76643524 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:76643525-76644382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:76703913-76704414 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:76749658-76750240 Neighboring gene fibroblast growth factor 16 Neighboring gene NANOG hESC enhancer GRCh37_chrX:76757869-76758370 Neighboring gene fatty acid binding protein 5 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29780 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 Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC2094

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
 
enables ATP-dependent chromatin remodeler activity IEA
Inferred from Electronic Annotation
more info
 
enables DNA translocase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables chromo shadow domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables helicase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA damage response, signal transduction by p53 class mediator ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
 
involved_in Sertoli cell development IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to hydroxyurea ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in chromatin organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
involved_in chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in chromosome organization involved in meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in forebrain development IEA
Inferred from Electronic Annotation
more info
 
involved_in meiotic spindle organization IEA
Inferred from Electronic Annotation
more info
 
involved_in multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nucleosome assembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of nuclear cell cycle DNA replication ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of telomere maintenance ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in post-embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in protein localization to chromosome, telomeric region ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of DNA-templated transcription TAS
Traceable Author Statement
more info
PubMed 
involved_in replication fork processing IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in replication fork processing ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in seminiferous tubule development IEA
Inferred from Electronic Annotation
more info
 
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in subtelomeric heterochromatin formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in subtelomeric heterochromatin formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in PML body ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in chromosome, subtelomeric region IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with chromosome, telomeric region ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in chromosome, telomeric region ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in condensed chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
part_of heterochromatin TAS
Traceable Author Statement
more info
PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nuclear chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of pericentric heterochromatin IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of pericentric 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
NP_000480.3
NP_612114.2
XP_005262210.2
XP_005262211.2
XP_005262213.2
XP_005262214.2
XP_006724729.1
XP_006724731.1
XP_016885090.1
XP_016885093.1
XP_047298147.1
XP_054183252.1
XP_054183253.1
XP_054183254.1
XP_054183255.1
XP_054183256.1
XP_054183257.1
XP_054183258.1
XP_054183259.1
XP_054183260.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_000489.6NP_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)
    AC233293, AC233305, AL138743
    Consensus CDS
    CCDS14434.1
    UniProtKB/Swiss-Prot
    D3DTE2, P46100, P51068, Q15886, Q59FB5, Q59H31, Q5H9A2, Q5JWI4, Q7Z2J1, Q9H0Z1, Q9NTS3
    UniProtKB/TrEMBL
    A4LAA3
    Related
    ENSP00000362441.4, ENST00000373344.11
    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_138270.5NP_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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    77504880..77786216 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005262156.5XP_005262213.2  transcriptional regulator ATRX isoform X5

    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
  2. XM_005262157.6XP_005262214.2  transcriptional regulator ATRX isoform X7

    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
  3. XM_006724666.5XP_006724729.1  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
  4. XM_017029604.3XP_016885093.1  transcriptional regulator ATRX isoform X6

  5. XM_017029601.3XP_016885090.1  transcriptional regulator ATRX isoform X3

  6. XM_005262153.6XP_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
  7. XM_005262154.6XP_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
  8. XM_047442191.1XP_047298147.1  transcriptional regulator ATRX isoform X8

  9. XM_006724668.4XP_006724731.1  transcriptional regulator ATRX isoform X9

    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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    75942420..76223770 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327281.1XP_054183256.1  transcriptional regulator ATRX isoform X5

  2. XM_054327283.1XP_054183258.1  transcriptional regulator ATRX isoform X7

  3. XM_054327280.1XP_054183255.1  transcriptional regulator ATRX isoform X4

  4. XM_054327282.1XP_054183257.1  transcriptional regulator ATRX isoform X6

  5. XM_054327279.1XP_054183254.1  transcriptional regulator ATRX isoform X3

  6. XM_054327277.1XP_054183252.1  transcriptional regulator ATRX isoform X1

  7. XM_054327278.1XP_054183253.1  transcriptional regulator ATRX isoform X2

  8. XM_054327284.1XP_054183259.1  transcriptional regulator ATRX isoform X8

  9. XM_054327285.1XP_054183260.1  transcriptional regulator ATRX isoform X9

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.