ATRX ATRX chromatin remodeler [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: Xq21.1

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (77504880..77786216, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (75942420..76223770, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (76760358..77041702, complement)

Chromosome X - NC_000023.11 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: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of ATRX and DAXX in pancreatic neuroendocrine tumors: Association with recurrence risk, cellular phenotype, and heterogeneity.
Title: Loss of ATRX and DAXX in pancreatic neuroendocrine tumors: Association with recurrence risk, cellular phenotype, and heterogeneity.
The translocation activity of Rad54 reduces crossover outcomes during homologous recombination.
Title: The translocation activity of Rad54 reduces crossover outcomes during homologous recombination.
ATRX guards against aberrant differentiation in mesenchymal progenitor cells.
Title: ATRX guards against aberrant differentiation in mesenchymal progenitor cells.
Combined deletion of MEN1, ATRX and PTEN triggers development of high-grade pancreatic neuroendocrine tumors in mice.
Title: Combined deletion of MEN1, ATRX and PTEN triggers development of high-grade pancreatic neuroendocrine tumors in mice.
Multiparametric MRI and T2/FLAIR mismatch complements the World Health Organization 2021 classification for the diagnosis of IDH-mutant 1p/19q non-co-deleted/ATRX-mutant astrocytoma.
Title: Multiparametric MRI and T2/FLAIR mismatch complements the World Health Organization 2021 classification for the diagnosis of IDH-mutant 1p/19q non-co-deleted/ATRX-mutant astrocytoma.
DAXX promotes centromeric stability independently of ATRX by preventing the accumulation of R-loop-induced DNA double-stranded breaks.
Title: DAXX promotes centromeric stability independently of ATRX by preventing the accumulation of R-loop-induced DNA double-stranded breaks.
Integrated omics analyses clarifies ATRX copy number variant of uncertain significance.
Title: Integrated omics analyses clarifies ATRX copy number variant of uncertain significance.
ATRX is a predictive marker for endocrinotherapy and chemotherapy resistance in HER2-/HR+ breast cancer through the regulation of the AR, GLI3 and GATA2 transcriptional network.
Title: ATRX is a predictive marker for endocrinotherapy and chemotherapy resistance in HER2-/HR+ breast cancer through the regulation of the AR, GLI3 and GATA2 transcriptional network.
MYCN amplification, TERT rearrangements and ATRX mutations in neuroblastoma: clinicopathological correlates- an Indian perspective.
Title: MYCN amplification, TERT rearrangements and ATRX mutations in neuroblastoma: clinicopathological correlates- an Indian perspective.
Inhibition of p53 and ATRX increases telomeric recombination in primary fibroblasts.
Title: Inhibition of p53 and ATRX increases telomeric recombination in primary fibroblasts.

Submit: New GeneRIF Correction See all GeneRIFs (217)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Acquired hemoglobin H disease MedGen: C0585216 OMIM: 300448 GeneReviews: Not available	Compare labs
Alpha thalassemia-X-linked intellectual disability syndrome MedGen: C1845055 OMIM: 301040 GeneReviews: Alpha-Thalassemia X-Linked Intellectual Disability Syndrome	Compare labs
Intellectual disability-hypotonic facies syndrome, X-linked, 1 MedGen: C4759781 OMIM: 309580 GeneReviews: Alpha-Thalassemia X-Linked Intellectual Disability Syndrome	Compare labs

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH47714 (e-PCR)
- UniSTS:57350

DXS56 (e-PCR)
- UniSTS:99595

ATRX_1237 (e-PCR)
- UniSTS:277020

ATRX_v351 (e-PCR)
- UniSTS:277020

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

SHGC-112339 (e-PCR)
- UniSTS:168542

GDB:596193 (e-PCR)
- UniSTS:158050

GDB:596198 (e-PCR)
- UniSTS:158053

WI-21664 (e-PCR)
- UniSTS:77670

GDB:596204 (e-PCR)
- UniSTS:158057

GDB:596209 (e-PCR)
- UniSTS:158060

GDB:596212 (e-PCR)
- UniSTS:158061

GDB:596216 (e-PCR)
- UniSTS:158063

GDB:596219 (e-PCR)
- UniSTS:158064

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

GDB:596231 (e-PCR)
- UniSTS:158071

GDB:596234 (e-PCR)
- UniSTS:158072

GDB:596239 (e-PCR)
- UniSTS:158075

GDB:596244 (e-PCR)
- UniSTS:158076

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

GDB:596255 (e-PCR)
- UniSTS:158078

GDB:596258 (e-PCR)
- UniSTS:158079

GDB:596262 (e-PCR)
- UniSTS:158080

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

GDB:596281 (e-PCR)
- UniSTS:158084

GDB:596286 (e-PCR)
- UniSTS:158085

GDB:596290 (e-PCR)
- UniSTS:158086

GDB:596303 (e-PCR)
- UniSTS:158089

DXS6980E (e-PCR)
- UniSTS:99210

GDB:596309 (e-PCR)
- UniSTS:158091

DXS9779 (e-PCR)
- UniSTS:75921

STS-U72937 (e-PCR)
- UniSTS:71061

SHGC-6680 (e-PCR)
- UniSTS:15519

RH103658 (e-PCR)
- UniSTS:97983

NoName (e-PCR)
- UniSTS:99785

DXS56 (e-PCR)
- UniSTS:148171

DXS56 (e-PCR)
- UniSTS:148172

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
located_in 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
located_in pericentric heterochromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in pericentric heterochromatin	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: transcriptional regulator ATRX

Names: ATP-dependent helicase ATRX; X-linked helicase II; X-linked nuclear protein

NP_000480.3

EC 3.6.4.12

NP_612114.2

EC 3.6.4.12

XP_005262210.2

EC 3.6.4.12

XP_005262211.2

EC 3.6.4.12

XP_005262213.2

EC 3.6.4.12

XP_005262214.2

EC 3.6.4.12

XP_006724729.1

EC 3.6.4.12

XP_006724731.1

EC 3.6.4.12

XP_016885090.1

EC 3.6.4.12

XP_016885093.1

EC 3.6.4.12

XP_047298147.1

EC 3.6.4.12

XP_054183252.1

EC 3.6.4.12

XP_054183253.1

EC 3.6.4.12

XP_054183254.1

EC 3.6.4.12

XP_054183255.1

EC 3.6.4.12

XP_054183256.1

EC 3.6.4.12

XP_054183257.1

EC 3.6.4.12

XP_054183258.1

EC 3.6.4.12

XP_054183259.1

EC 3.6.4.12

XP_054183260.1

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.

Genomic

NG_008838.3 RefSeqGene

Range

5054..286392

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1153

mRNA and Protein(s)

NM_000489.6 → NP_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:1588 → 1750

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:2017 → 2163

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:167 → 270

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

pfam00176
Location:1563 → 1889

SNF2_N; SNF2 family N-terminal domain
NM_138270.5 → NP_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:1550 → 1712

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:1979 → 2125

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:129 → 232

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

pfam00176
Location:1525 → 1851

SNF2_N; SNF2 family N-terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

77504880..77786216 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (4) summary

cd00046
Location:1533 → 1695

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:1962 → 2108

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:112 → 215

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

pfam00176
Location:1508 → 1834

SNF2_N; SNF2 family N-terminal domain
XM_005262157.6 → XP_005262214.2 transcriptional regulator ATRX isoform X7

Conserved Domains (4) summary

cd00046
Location:1520 → 1682

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:1949 → 2095

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:128 → 231

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

pfam00176
Location:1495 → 1821

SNF2_N; SNF2 family N-terminal domain
XM_006724666.5 → XP_006724729.1 transcriptional regulator ATRX isoform X4

Conserved Domains (4) summary

cd00046
Location:1549 → 1711

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:1978 → 2124

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:128 → 231

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

pfam00176
Location:1524 → 1850

SNF2_N; SNF2 family N-terminal domain
XM_017029604.3 → XP_016885093.1 transcriptional regulator ATRX isoform X6
XM_017029601.3 → XP_016885090.1 transcriptional regulator ATRX isoform X3
XM_005262153.6 → XP_005262210.2 transcriptional regulator ATRX isoform X1

Conserved Domains (4) summary

cd00046
Location:1587 → 1749

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:2016 → 2162

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:166 → 269

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

pfam00176
Location:1562 → 1888

SNF2_N; SNF2 family N-terminal domain
XM_005262154.6 → XP_005262211.2 transcriptional regulator ATRX isoform X2

Conserved Domains (4) summary

cd00046
Location:1559 → 1721

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:1988 → 2134

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:167 → 270

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

pfam00176
Location:1534 → 1860

SNF2_N; SNF2 family N-terminal domain
XM_047442191.1 → XP_047298147.1 transcriptional regulator ATRX isoform X8
XM_006724668.4 → XP_006724731.1 transcriptional regulator ATRX isoform X9

Conserved Domains (3) summary

cd00046
Location:1588 → 1750

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:167 → 270

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

pfam00176
Location:1563 → 1869

SNF2_N; SNF2 family N-terminal domain

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

75942420..76223770 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054327281.1 → XP_054183256.1 transcriptional regulator ATRX isoform X5
XM_054327283.1 → XP_054183258.1 transcriptional regulator ATRX isoform X7
XM_054327280.1 → XP_054183255.1 transcriptional regulator ATRX isoform X4
XM_054327282.1 → XP_054183257.1 transcriptional regulator ATRX isoform X6
XM_054327279.1 → XP_054183254.1 transcriptional regulator ATRX isoform X3
XM_054327277.1 → XP_054183252.1 transcriptional regulator ATRX isoform X1
XM_054327278.1 → XP_054183253.1 transcriptional regulator ATRX isoform X2
XM_054327284.1 → XP_054183259.1 transcriptional regulator ATRX isoform X8
XM_054327285.1 → XP_054183260.1 transcriptional regulator ATRX isoform X9

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.