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    ATRX ATRX chromatin remodeler [ Homo sapiens (human) ]

    Gene ID: 546, updated on 17-Jun-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    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.