Atrx (ATRX, chromatin remodeler) - Rat Genome Database

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Gene: Atrx (ATRX, chromatin remodeler) Rattus norvegicus
Analyze
Symbol: Atrx
Name: ATRX, chromatin remodeler
RGD ID: 619795
Description: 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 cellular response to hydroxyurea; chromatin remodeling; and positive regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within several processes, including male gonad development; meiotic spindle organization; and post-embryonic forelimb morphogenesis. Predicted to be located in chromosomal region and nuclear lumen. Predicted to be part of pericentric heterochromatin. 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); INTERACTS WITH (+)-pilocarpine; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: alpha thalassemia/mental retardation syndrome X-linked; alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae); alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S.cerevisiae); alpha thalassemia/mental retardation syndrome X-linked homolog; alpha thalassemia/mental retardation syndrome X-linked homolog (human); ATP-dependent helicase ATRX; helicase II; LOC103690008; pABP-2; transcriptional regulator ATRX; transcriptional regulator ATRX-like; X-linked nuclear protein; Xnp
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X70,850,981 - 70,997,330 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX70,850,981 - 70,997,330 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX72,359,919 - 72,506,253 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X75,860,229 - 76,006,565 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X73,423,392 - 73,569,729 (-)NCBIRnor_WKY
Rnor_6.0X76,820,110 - 76,979,155 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX76,820,329 - 76,979,115 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 EnsemblX76,692,970 - 76,708,878 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X77,469,497 - 77,515,204 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0X55,943,493 - 56,101,756 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X93,903,794 - 94,051,337 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X94,034,366 - 94,057,029 (-)NCBI
CeleraX72,164,814 - 72,309,854 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
adenoid cystic carcinoma  (ISO)
adrenocortical carcinoma  (ISO)
alpha thalassemia-X-linked intellectual disability syndrome  (ISO)
alpha-thalassemia myelodysplasia syndrome  (ISO)
anaplastic astrocytoma  (ISO)
atypical teratoid rhabdoid tumor  (ISO)
autistic disorder  (ISO)
bone osteosarcoma  (ISO)
brachydactyly  (ISO)
Craniofacial Abnormalities  (ISO)
cryptorchidism  (ISO)
Developmental Disabilities  (ISO)
Developmental Disease  (ISO)
disorder of sexual development  (ISO)
Dwarfism  (ISO)
Gastro-Enteropancreatic Neuroendocrine Tumor  (ISO)
genetic disease  (ISO)
glioblastoma  (ISO)
Growth Disorders  (ISO)
high grade glioma  (ISO)
Huntington's disease  (ISO)
intellectual disability  (ISO)
islet cell tumor  (ISO)
lung adenocarcinoma  (ISO)
Lung Carcinoid Tumors  (ISO)
lung small cell carcinoma  (ISO)
lung squamous cell carcinoma  (ISO)
malignant astrocytoma  (ISO)
melanoma  (ISO)
Menkes disease  (ISO)
microcephaly  (ISO)
Muscle Hypotonia  (ISO)
myelodysplastic syndrome  (ISO)
Nervous System Malformations  (ISO)
neuroblastoma  (ISO)
Neurodevelopmental Disorders  (ISO)
neuroendocrine tumor  (ISO)
oligodendroglioma  (ISO)
osteosarcoma  (ISO)
pancreatic cancer  (ISO)
penile disease  (ISO)
sarcoma  (ISO)
schizophrenia  (ISO)
stomach cancer  (ISO)
syndromic X-linked intellectual disability Lubs type  (ISO)
syndromic X-linked intellectual disability Siderius type  (ISO)
thoracic disease  (ISO)
X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia  (ISO)
X-Linked Intellectual Developmental Disorders  (ISO)
X-linked mental retardation-hypotonic facies syndrome-1  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-dexrazoxane  (ISO)
(+)-pilocarpine  (EXP)
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
17beta-estradiol  (EXP)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,4,7,8-Pentachlorodibenzofuran  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4-vinylcyclohexene dioxide  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
Brevetoxin B  (ISO)
Brodifacoum  (EXP)
butanal  (ISO)
caffeine  (ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
clobetasol  (ISO)
clorgyline  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
coumarin  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
cypermethrin  (ISO)
deoxynivalenol  (ISO)
diazinon  (EXP,ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (ISO)
Enterolactone  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (EXP)
fulvestrant  (ISO)
geldanamycin  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
idarubicin  (ISO)
irinotecan  (ISO)
ivermectin  (ISO)
josamycin  (ISO)
menadione  (ISO)
methoxychlor  (ISO)
methylparaben  (ISO)
miconazole  (ISO)
mitomycin C  (ISO)
morphine  (ISO)
N-ethyl-N-nitrosourea  (EXP)
naphthalene  (EXP)
nicotine  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
parathion  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenethyl isothiocyanate  (EXP)
phenobarbital  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
succimer  (ISO)
sunitinib  (ISO)
tamibarotene  (ISO)
terbufos  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
theophylline  (ISO)
thimerosal  (ISO)
topotecan  (EXP)
torcetrapib  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. The alternative lengthening of telomere phenotype is significantly associated with loss of ATRX expression in high-grade pediatric and adult astrocytomas: a multi-institutional study of 214 astrocytomas. Abedalthagafi M, etal., Mod Pathol. 2013 Nov;26(11):1425-32. doi: 10.1038/modpathol.2013.90. Epub 2013 Jun 14.
2. Alpha-thalassemia intellectual disability: variable phenotypic expression among males with a recurrent nonsense mutation - c.109C>T (p.R37X). Basehore MJ, etal., Clin Genet. 2014 May 7. doi: 10.1111/cge.12420.
3. Novel ATRX gene damaging missense mutation c.6740A>C segregates with profound to severe intellectual deficiency without alpha thalassaemia. Bouazzi H, etal., Indian J Med Res. 2016 Jan;143(1):43-8. doi: 10.4103/0971-5916.178589.
4. Expression and prognostic impact of alpha thalassemia/mental retardation X-linked and death domain-associated protein in human lung cancer. Buentzel J, etal., Medicine (Baltimore). 2019 Aug;98(31):e16712. doi: 10.1097/MD.0000000000016712.
5. ATRX mRNA expression combined with IDH1/2 mutational status and Ki-67 expression refines the molecular classification of astrocytic tumors: evidence from the whole transcriptome sequencing of 169 samples samples. Cai J, etal., Oncotarget. 2014 May 15;5(9):2551-61.
6. Immunohistochemical Analysis of ATRX, IDH1 and p53 in Glioblastoma and Their Correlations with Patient Survival. Chaurasia A, etal., J Korean Med Sci. 2016 Aug;31(8):1208-14. doi: 10.3346/jkms.2016.31.8.1208. Epub 2016 May 30.
7. Genomic alterations of plasma cell-free DNAs in small cell lung cancer and their clinical relevance. Du M, etal., Lung Cancer. 2018 Jun;120:113-121. doi: 10.1016/j.lungcan.2018.04.008. Epub 2018 Apr 12.
8. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. A nonsense mutation of the ATRX gene causing mild mental retardation and epilepsy. Guerrini R, etal., Ann Neurol. 2000 Jan;47(1):117-21.
10. Whole-exome sequencing identifies ATRX mutation as a key molecular determinant in lower-grade glioma. Kannan K, etal., Oncotarget. 2012 Oct;3(10):1194-203.
11. Telomere length abnormalities and telomerase RNA component expression in gastroenteropancreatic neuroendocrine tumors. Kim HS, etal., Anticancer Res. 2015 Jun;35(6):3501-10.
12. Mutations of codon 2085 in the helicase domain of ATRX are recurrent and cause ATRX syndrome. Lacoste C, etal., Clin Genet. 2013 Dec 1. doi: 10.1111/cge.12319.
13. ATRX induction by mutant huntingtin via Cdx2 modulates heterochromatin condensation and pathology in Huntington's disease. Lee J, etal., Cell Death Differ. 2012 Jul;19(7):1109-16. doi: 10.1038/cdd.2011.196. Epub 2012 Jan 13.
14. Comprehensive screening of alternative lengthening of telomeres phenotype and loss of ATRX expression in sarcomas. Liau JY, etal., Mod Pathol. 2015 Dec;28(12):1545-54. doi: 10.1038/modpathol.2015.114. Epub 2015 Oct 2.
15. [Mutation analysis for a Chinese family featuring X-linked alpha thalassemia/mental retardation syndrome]. Lin SB, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2013 Dec;30(6):654-8. doi: 10.3760/cma.j.issn.1003-9406.2013.06.004.
16. Loss of DAXX and ATRX are associated with chromosome instability and reduced survival of patients with pancreatic neuroendocrine tumors. Marinoni I, etal., Gastroenterology. 2014 Feb;146(2):453-60.e5. doi: 10.1053/j.gastro.2013.10.020. Epub 2013 Oct 19.
17. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
18. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Molecular cloning and characterization of annexin V-binding proteins with highly hydrophilic peptide structure. Ohsawa K, etal., J Neurochem 1996 Jul;67(1):89-97.
20. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
21. Online Mendelian Inheritance in Man, OMIM (TM). Online Mendelian Inheritance in Man, OMIM (TM).
22. Decreased expression of the chromatin remodeler ATRX associates with melanoma progression. Qadeer ZA, etal., J Invest Dermatol. 2014 Jun;134(6):1768-72. doi: 10.1038/jid.2014.45. Epub 2014 Jan 27.
23. GOA pipeline RGD automated data pipeline
24. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
26. Comprehensive gene review and curation RGD comprehensive gene curation
27. Targeted loss of the ATR-X syndrome protein in the limb mesenchyme of mice causes brachydactyly. Solomon LA, etal., Hum Mol Genet. 2013 Dec 15;22(24):5015-25. doi: 10.1093/hmg/ddt351. Epub 2013 Jul 25.
28. Sleeping Beauty transposon mutagenesis identifies genes that cooperate with mutant Smad4 in gastric cancer development. Takeda H, etal., Proc Natl Acad Sci U S A. 2016 Apr 5;113(14):E2057-65. doi: 10.1073/pnas.1603223113. Epub 2016 Mar 22.
29. Localization of the chromatin remodelling protein, ATRX in the adult testis. Tang P, etal., J Reprod Dev. 2011 Jun;57(3):317-21. Epub 2009 May 15.
30. Loss of ATRX expression predicts worse prognosis in pulmonary carcinoid tumors. Terra Md SBSP, etal., Hum Pathol. 2019 Dec;94:78-85. doi: 10.1016/j.humpath.2019.08.022. Epub 2019 Sep 6.
31. XNP mutation in a large family with Juberg-Marsidi syndrome. Villard L, etal., Nat Genet. 1996 Apr;12(4):359-60.
32. Expanding phenotype of XNP mutations: mild to moderate mental retardation. Yntema HG, etal., Am J Med Genet. 2002 Jul 1;110(3):243-7.
Additional References at PubMed
PMID:11555636   PMID:12477932   PMID:12953102   PMID:14519686   PMID:15242786   PMID:15252119   PMID:15522233   PMID:15668733   PMID:15882967   PMID:17296936   PMID:20110566   PMID:20211137  
PMID:20651253   PMID:21421568   PMID:21427128   PMID:22391447   PMID:23444137   PMID:24386478   PMID:24651726   PMID:26055325   PMID:26159997   PMID:26373281   PMID:27029610  


Genomics

Comparative Map Data
Atrx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X70,850,981 - 70,997,330 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX70,850,981 - 70,997,330 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX72,359,919 - 72,506,253 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X75,860,229 - 76,006,565 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X73,423,392 - 73,569,729 (-)NCBIRnor_WKY
Rnor_6.0X76,820,110 - 76,979,155 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX76,820,329 - 76,979,115 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 EnsemblX76,692,970 - 76,708,878 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X77,469,497 - 77,515,204 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0X55,943,493 - 56,101,756 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X93,903,794 - 94,051,337 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X94,034,366 - 94,057,029 (-)NCBI
CeleraX72,164,814 - 72,309,854 (-)NCBICelera
Cytogenetic MapXq22NCBI
ATRX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X77,504,880 - 77,786,216 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX77,504,880 - 77,786,233 (-)EnsemblGRCh38hg38GRCh38
GRCh37X76,760,358 - 77,041,702 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X76,647,012 - 76,928,375 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX77,001,253 - 77,282,613 (-)NCBICelera
Cytogenetic MapXq21.1NCBI
HuRefX70,349,443 - 70,629,029 (-)NCBIHuRef
CHM1_1X76,653,073 - 76,934,420 (-)NCBICHM1_1
T2T-CHM13v2.0X75,942,420 - 76,223,770 (-)NCBIT2T-CHM13v2.0
Atrx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X104,841,221 - 104,972,978 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX104,841,221 - 104,973,009 (-)EnsemblGRCm39 Ensembl
GRCm38X105,797,615 - 105,929,372 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX105,797,615 - 105,929,403 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X102,992,954 - 103,124,711 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X102,002,872 - 102,132,061 (-)NCBIMGSCv36mm8
CeleraX92,651,743 - 92,783,324 (-)NCBICelera
Cytogenetic MapXDNCBI
cM MapX47.26NCBI
Atrx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955557947,167 - 1,252,724 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955557947,368 - 1,252,701 (-)NCBIChiLan1.0ChiLan1.0
ATRX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1X77,085,587 - 77,372,212 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X66,682,968 - 66,969,421 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X76,795,574 - 77,083,486 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX76,795,574 - 77,083,486 (-)Ensemblpanpan1.1panPan2
ATRX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X59,772,067 - 60,107,016 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX59,774,585 - 60,106,980 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX50,787,446 - 51,120,278 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X61,011,471 - 61,270,437 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX61,011,677 - 61,270,443 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X58,719,357 - 59,051,934 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X60,325,606 - 60,661,270 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X59,917,163 - 60,249,816 (-)NCBIUU_Cfam_GSD_1.0
Atrx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X42,229,198 - 42,451,804 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366832,495,959 - 2,718,620 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049366832,496,307 - 2,718,539 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATRX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX61,584,848 - 61,872,287 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X61,584,028 - 61,872,341 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X70,390,618 - 70,509,341 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATRX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X66,449,830 - 66,737,220 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX66,448,449 - 66,737,164 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606714,772,636 - 15,066,083 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Atrx
216 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:120
Count of miRNA genes:99
Interacting mature miRNAs:100
Transcripts:ENSRNOT00000042751, ENSRNOT00000045534
Prediction methods:Microtar, Miranda, Pita, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat

Markers in Region
DXMgh10  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X70,871,973 - 70,872,106 (+)MAPPERmRatBN7.2
Rnor_6.0X76,841,244 - 76,841,376NCBIRnor6.0
Rnor_5.0X55,964,627 - 55,964,759UniSTSRnor5.0
RGSC_v3.4X93,924,589 - 93,924,722RGDRGSC3.4
RGSC_v3.4X93,924,590 - 93,924,722UniSTSRGSC3.4
RGSC_v3.1X93,998,022 - 93,998,155RGD
CeleraX72,185,808 - 72,185,937UniSTS
Cytogenetic MapXq31UniSTS
RH142511  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X70,899,773 - 70,899,880 (+)MAPPERmRatBN7.2
Rnor_6.0X76,869,042 - 76,869,148NCBIRnor6.0
Rnor_5.0X55,992,425 - 55,992,531UniSTSRnor5.0
RGSC_v3.4X93,952,390 - 93,952,496UniSTSRGSC3.4
CeleraX72,213,604 - 72,213,710UniSTS
Cytogenetic MapXq31UniSTS
MARC_6759-6760:992007400:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X70,912,436 - 70,912,996 (+)MAPPERmRatBN7.2
Rnor_6.0X76,881,270 - 76,881,829NCBIRnor6.0
Rnor_6.0X76,666,051 - 76,666,610NCBIRnor6.0
Rnor_5.0X56,004,653 - 56,005,212UniSTSRnor5.0
Rnor_5.0X77,472,343 - 77,472,902UniSTSRnor5.0
RGSC_v3.4X93,965,086 - 93,965,645UniSTSRGSC3.4
CeleraX72,226,236 - 72,226,795UniSTS
Cytogenetic MapXq31UniSTS
GDB:596250  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X70,855,127 - 70,856,601 (+)MAPPERmRatBN7.2
Rnor_6.0X76,824,257 - 76,825,730NCBIRnor6.0
Rnor_5.0X55,947,640 - 55,949,113UniSTSRnor5.0
RGSC_v3.4X93,907,744 - 93,909,217UniSTSRGSC3.4
CeleraX72,168,961 - 72,170,434UniSTS
Cytogenetic MapXq31UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 39 36 20 19 20 8 9 74 35 34 11 8
Low 4 21 21 21 2 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001105757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588265 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588270 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588271 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017588274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099459 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099461 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099462 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099465 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099466 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC169005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D64059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000045534   ⟹   ENSRNOP00000051120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX76,692,970 - 76,708,878 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078997   ⟹   ENSRNOP00000071468
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX70,939,675 - 70,996,592 (-)Ensembl
Rnor_6.0 EnsemblX76,908,189 - 76,924,362 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086752
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX76,857,656 - 76,865,244 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087977   ⟹   ENSRNOP00000070457
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX70,850,981 - 70,956,139 (-)Ensembl
Rnor_6.0 EnsemblX76,823,010 - 76,925,195 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX76,890,272 - 76,899,366 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091284
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX70,850,981 - 70,997,330 (-)Ensembl
Rnor_6.0 EnsemblX76,820,329 - 76,979,115 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095781   ⟹   ENSRNOP00000087702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX70,850,981 - 70,997,330 (-)Ensembl
RefSeq Acc Id: NM_001105757   ⟹   NP_001099227
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,850,981 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099458   ⟹   XP_038955386
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,850,981 - 70,996,607 (-)NCBI
RefSeq Acc Id: XM_039099459   ⟹   XP_038955387
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,996,607 (-)NCBI
RefSeq Acc Id: XM_039099460   ⟹   XP_038955388
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,996,607 (-)NCBI
RefSeq Acc Id: XM_039099461   ⟹   XP_038955389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,996,607 (-)NCBI
RefSeq Acc Id: XM_039099462   ⟹   XP_038955390
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099464   ⟹   XP_038955392
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099465   ⟹   XP_038955393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099466   ⟹   XP_038955394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099467   ⟹   XP_038955395
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099468   ⟹   XP_038955396
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099469   ⟹   XP_038955397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099470   ⟹   XP_038955398
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099471   ⟹   XP_038955399
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,298 (-)NCBI
RefSeq Acc Id: XM_039099472   ⟹   XP_038955400
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099473   ⟹   XP_038955401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099474   ⟹   XP_038955402
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,853,881 - 70,997,330 (-)NCBI
RefSeq Acc Id: XM_039099475   ⟹   XP_038955403
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X70,883,232 - 70,996,607 (-)NCBI
Reference Sequences
RefSeq Acc Id: ENSRNOP00000051120   ⟸   ENSRNOT00000045534
RefSeq Acc Id: ENSRNOP00000070457   ⟸   ENSRNOT00000087977
RefSeq Acc Id: ENSRNOP00000071468   ⟸   ENSRNOT00000078997
RefSeq Acc Id: NP_001099227   ⟸   NM_001105757
- UniProtKB: A0A8I6GFB1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955386   ⟸   XM_039099458
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955402   ⟸   XM_039099474
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038955401   ⟸   XM_039099473
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038955390   ⟸   XM_039099462
- Peptide Label: isoform X5
- UniProtKB: A0A8I6A4N1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955397   ⟸   XM_039099469
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038955398   ⟸   XM_039099470
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038955396   ⟸   XM_039099468
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038955400   ⟸   XM_039099472
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038955392   ⟸   XM_039099464
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038955394   ⟸   XM_039099466
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038955395   ⟸   XM_039099467
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038955393   ⟸   XM_039099465
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038955399   ⟸   XM_039099471
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038955389   ⟸   XM_039099461
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955388   ⟸   XM_039099460
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955387   ⟸   XM_039099459
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955403   ⟸   XM_039099475
- Peptide Label: isoform X10
RefSeq Acc Id: ENSRNOP00000087702   ⟸   ENSRNOT00000095781
Protein Domains
Helicase ATP-binding   Helicase C-terminal   PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P70486-F1-model_v2 AlphaFold P70486 1-527 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701901
Promoter ID:EPDNEW_R12421
Type:initiation region
Name:Atrx_1
Description:ATRX, chromatin remodeler
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X76,979,115 - 76,979,175EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619795 AgrOrtholog
BioCyc Gene G2FUF-1932 BioCyc
Ensembl Genes ENSRNOG00000046897 Ensembl
  ENSRNOG00000056703 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070457.2 UniProtKB/TrEMBL
  ENSRNOP00000071468.2 UniProtKB/TrEMBL
  ENSRNOP00000087612 ENTREZGENE
  ENSRNOP00000087612.1 UniProtKB/TrEMBL
  ENSRNOP00000087702 ENTREZGENE
  ENSRNOP00000087702.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078997.2 UniProtKB/TrEMBL
  ENSRNOT00000087977.2 UniProtKB/TrEMBL
  ENSRNOT00000091284 ENTREZGENE
  ENSRNOT00000091284.2 UniProtKB/TrEMBL
  ENSRNOT00000095781 ENTREZGENE
  ENSRNOT00000095781.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
  3.40.50.10810 UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/TrEMBL
  SWI2/SNF2 ATPases, N-terminal domain UniProtKB/TrEMBL
InterPro ADD UniProtKB/TrEMBL
  ADD_ATRX UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  SNF2-like_sf UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene 246284 ENTREZGENE
PANTHER TRANSCRIPTIONAL REGULATOR ATRX UniProtKB/Swiss-Prot
  TRANSCRIPTIONAL REGULATOR ATRX UniProtKB/Swiss-Prot
  TRANSCRIPTIONAL REGULATOR ATRX UniProtKB/TrEMBL
  TRANSCRIPTIONAL REGULATOR ATRX UniProtKB/TrEMBL
Pfam ADD_ATRX UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  SNF2_N UniProtKB/TrEMBL
PhenoGen Atrx PhenoGen
PROSITE ADD UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
SMART DEXDc UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
  SSF57903 UniProtKB/TrEMBL
UniProt A0A0G2JXZ3_RAT UniProtKB/TrEMBL
  A0A0G2K0J1_RAT UniProtKB/TrEMBL
  A0A8I6A4N1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GFB1 ENTREZGENE, UniProtKB/TrEMBL
  ATRX_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Atrx  ATRX, chromatin remodeler  LOC103690008  transcriptional regulator ATRX-like  Data Merged 737654 PROVISIONAL
2016-06-01 Atrx  ATRX, chromatin remodeler  Atrx  alpha thalassemia/mental retardation syndrome X-linked  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103690008  transcriptional regulator ATRX-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2011-07-28 Atrx  alpha thalassemia/mental retardation syndrome X-linked  Atrx  alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Atrx  alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae)  Atrx  alpha thalassemia/mental retardation syndrome X-linked homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Atrx  alpha thalassemia/mental retardation syndrome X-linked homolog (human)    alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S.cerevisiae)  Name updated 1299863 APPROVED
2002-08-07 Atrx  alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S.cerevisiae)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology high homology with human X-linked Helicase2 (XH2) 631943