Atrx ATRX, chromatin remodeler [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Atrxprovided by RGD
Full Name: ATRX, chromatin remodelerprovided by RGD
Primary source: RGD:619795
See related: Ensembl:ENSRNOG00000056703 AllianceGenome:RGD:619795
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Xnp
Summary: Predicted to enable several functions, including DNA translocase activity; chromo shadow domain binding activity; and methylated histone binding activity. Predicted to be involved in several processes, including chromatin assembly; regulation of chromosome organization; and regulation of telomeric RNA transcription from RNA pol II promoter. Predicted to act upstream of or within several processes, including male gonad development; meiotic spindle organization; and post-embryonic forelimb morphogenesis. Located in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in X-linked mental retardation-hypotonic facies syndrome-1; alpha thalassemia-X-linked intellectual disability syndrome; alpha-thalassemia myelodysplasia syndrome; high grade glioma; and lung small cell carcinoma. Orthologous to human ATRX (ATRX chromatin remodeler). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 224.2), Brain (RPKM 211.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: Xq22

Exon count:: 40

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (74916548..75062880, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (70850981..70997330, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (76820110..76979155, complement)

Chromosome X - NC_086039.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LncRNA PWRN2 promotes polycystic ovary syndrome progression via epigenetically reducing ATRX by recruiting LSD1.
Title: LncRNA PWRN2 promotes polycystic ovary syndrome progression via epigenetically reducing ATRX by recruiting LSD1.
ATRX is present in adult human and rat testis and is expressed in the somatic cells; Sertoli, Leydig, and peritubular myoid cells, and also in germ cells; spermatogonia and early meiotic spermatocytes.
Title: Localization of the chromatin remodelling protein, ATRX in the adult testis.

Submit: New GeneRIF Correction

General gene information

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Markers

dxmgh10 (e-PCR)
- UniSTS:120585

RH142511 (e-PCR)
- UniSTS:231758

MARC_6759-6760:992007400:1 (e-PCR)
- UniSTS:231262

GDB:596225 (e-PCR)
- UniSTS:158067

GDB:596250 (e-PCR)
- UniSTS:158077

GDB:596276 (e-PCR)
- UniSTS:158082

Gene Ontology Provided by RGD

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	IEA Inferred from Electronic Annotation more info
enables DNA translocase activity	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromo shadow domain binding	IEA Inferred from Electronic Annotation more info
enables chromo shadow domain binding	ISO Inferred from Sequence Orthology more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
involved_in DNA damage response, signal transduction by p53 class mediator	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of_or_within Sertoli cell development	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in cellular response to hydroxyurea	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hydroxyurea	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hydroxyurea	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin organization	ISO Inferred from Sequence Orthology more info
involved_in chromatin organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromosome organization involved in meiotic cell cycle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chromosome organization involved in meiotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in forebrain development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within forebrain development	ISO Inferred from Sequence Orthology more info
involved_in meiotic spindle organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within meiotic spindle organization	ISO Inferred from Sequence Orthology more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of macromolecule metabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric	ISO Inferred from Sequence Orthology more info
involved_in nucleosome assembly	IEA Inferred from Electronic Annotation more info
involved_in nucleosome assembly	ISO Inferred from Sequence Orthology more info
involved_in nucleosome assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of nuclear cell cycle DNA replication	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of nuclear cell cycle DNA replication	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of telomere maintenance	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in post-embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-embryonic forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in protein localization to chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
involved_in protein localization to chromosome, telomeric region	ISO Inferred from Sequence Orthology more info
involved_in replication fork processing	IEA Inferred from Electronic Annotation more info
involved_in replication fork processing	ISO Inferred from Sequence Orthology 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
acts_upstream_of_or_within seminiferous tubule development	ISO Inferred from Sequence Orthology more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info
involved_in subtelomeric heterochromatin formation	IEA Inferred from Electronic Annotation more info
involved_in subtelomeric heterochromatin formation	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in PML body	IEA Inferred from Electronic Annotation more info
located_in PML body	ISO Inferred from Sequence Orthology more info
located_in chromosome, subtelomeric region	IEA Inferred from Electronic Annotation more info
located_in chromosome, subtelomeric region	ISO Inferred from Sequence Orthology more info
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
located_in chromosome, telomeric region	ISO Inferred from Sequence Orthology 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
located_in condensed chromosome, centromeric region	ISO Inferred from Sequence Orthology more info
part_of heterochromatin	ISO Inferred from Sequence Orthology more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nuclear chromosome	IEA Inferred from Electronic Annotation more info
located_in nuclear chromosome	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of pericentric heterochromatin	IEA Inferred from Electronic Annotation more info
part_of pericentric heterochromatin	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: transcriptional regulator ATRX

Names: ATP-dependent helicase ATRX; X-linked nuclear protein; helicase II; pABP-2; transcriptional regulator ATRX-like

NP_001099227.2

EC 3.6.4.12

XP_038955386.1

EC 3.6.4.12

XP_038955387.1

EC 3.6.4.12

XP_038955388.1

EC 3.6.4.12

XP_038955389.1

EC 3.6.4.12

XP_038955390.1

EC 3.6.4.12

XP_038955392.1

EC 3.6.4.12

XP_038955393.1

EC 3.6.4.12

XP_038955394.1

EC 3.6.4.12

XP_038955395.1

EC 3.6.4.12

XP_038955396.1

EC 3.6.4.12

XP_038955397.1

EC 3.6.4.12

XP_038955398.1

EC 3.6.4.12

XP_038955399.1

EC 3.6.4.12

XP_038955400.1

EC 3.6.4.12

XP_038955401.1

EC 3.6.4.12

XP_038955403.1

EC 3.6.4.12

XP_063135850.1

EC 3.6.4.12

XP_063135852.1

EC 3.6.4.12

XP_063135853.1

EC 3.6.4.12

XP_063135854.1

EC 3.6.4.12

XP_063135856.1

EC 3.6.4.12

XP_063135857.1

EC 3.6.4.12

XP_063135858.1

EC 3.6.4.12

XP_063135859.1

EC 3.6.4.12

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_001105757.2 → NP_001099227.2 transcriptional regulator ATRX

Status: VALIDATED

Source sequence(s)

JAXUCZ010000021

UniProtKB/TrEMBL

A0A0G2JXZ3, A0A8I6GFB1

Related

ENSRNOP00000087612.1, ENSRNOT00000091284.2

Conserved Domains (3) summary

COG0553
Location:1513 → 2164

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:166 → 269

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1538 → 1781

DEXHc_ATRX; DEXH-box helicase domain of ATRX

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086039.1 Reference GRCr8

Range

74916548..75062880 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063279780.1 → XP_063135850.1 transcriptional regulator ATRX isoform X3
XM_039099473.2 → XP_038955401.1 transcriptional regulator ATRX isoform X10

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1458 → 2109

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:111 → 214

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1483 → 1726

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099471.2 → XP_038955399.1 transcriptional regulator ATRX isoform X8

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1474 → 2125

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:127 → 230

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1499 → 1742

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099462.2 → XP_038955390.1 transcriptional regulator ATRX isoform X6

UniProtKB/TrEMBL

A0A0G2JXZ3, A0A8I6A4N1

Related

ENSRNOP00000087702.1

Conserved Domains (3) summary

COG0553
Location:1475 → 2126

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:128 → 231

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1500 → 1743

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099469.2 → XP_038955397.1 transcriptional regulator ATRX isoform X7

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1474 → 2125

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:127 → 230

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1499 → 1742

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_063279786.1 → XP_063135856.1 transcriptional regulator ATRX isoform X10
XM_039099470.2 → XP_038955398.1 transcriptional regulator ATRX isoform X7

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1474 → 2125

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:127 → 230

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1499 → 1742

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099468.2 → XP_038955396.1 transcriptional regulator ATRX isoform X7

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1474 → 2125

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:127 → 230

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1499 → 1742

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099472.2 → XP_038955400.1 transcriptional regulator ATRX isoform X10

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1458 → 2109

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:111 → 214

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1483 → 1726

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099464.2 → XP_038955392.1 transcriptional regulator ATRX isoform X7

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1474 → 2125

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:127 → 230

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1499 → 1742

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099466.2 → XP_038955394.1 transcriptional regulator ATRX isoform X7

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1474 → 2125

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:127 → 230

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1499 → 1742

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_063279784.1 → XP_063135854.1 transcriptional regulator ATRX isoform X10
XM_039099467.2 → XP_038955395.1 transcriptional regulator ATRX isoform X7

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1474 → 2125

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:127 → 230

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1499 → 1742

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099465.2 → XP_038955393.1 transcriptional regulator ATRX isoform X7

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1474 → 2125

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:127 → 230

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1499 → 1742

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_063279787.1 → XP_063135857.1 transcriptional regulator ATRX isoform X11
XM_063279782.1 → XP_063135852.1 transcriptional regulator ATRX isoform X7
XM_063279788.1 → XP_063135858.1 transcriptional regulator ATRX isoform X12
XM_063279783.1 → XP_063135853.1 transcriptional regulator ATRX isoform X9
XM_039099458.2 → XP_038955386.1 transcriptional regulator ATRX isoform X1

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1523 → 2174

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:176 → 279

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1548 → 1791

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099461.2 → XP_038955389.1 transcriptional regulator ATRX isoform X5

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1484 → 2135

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:137 → 240

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1509 → 1752

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099460.2 → XP_038955388.1 transcriptional regulator ATRX isoform X4

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1485 → 2136

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:138 → 241

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1510 → 1753

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_039099459.2 → XP_038955387.1 transcriptional regulator ATRX isoform X2

UniProtKB/TrEMBL

A0A0G2JXZ3

Conserved Domains (3) summary

COG0553
Location:1522 → 2173

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd11726
Location:175 → 278

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1547 → 1790

DEXHc_ATRX; DEXH-box helicase domain of ATRX
XM_063279789.1 → XP_063135859.1 transcriptional regulator ATRX isoform X14
XM_039099475.2 → XP_038955403.1 transcriptional regulator ATRX isoform X13

Conserved Domains (2) summary

cd11726
Location:176 → 279

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

cd18068
Location:1548 → 1791

DEXHc_ATRX; DEXH-box helicase domain of ATRX