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 chromatin organization; 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); INTERACTS WITH (+)-pilocarpine; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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; LOW QUALITY PROTEIN: transcriptional regulator ATRX; 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 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX70,850,981 - 70,997,330 (-)Ensembl
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_5.0X55,943,493 - 56,101,756 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0X77,469,497 - 77,515,204 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X93,903,794 - 94,051,337 (-)NCBIRGSC3.4rn4RGSC3.4
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


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  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (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)
carbon nanotube  (ISO)
chloroprene  (EXP)
clobetasol  (ISO)
clorgyline  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
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)
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 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
1. Abedalthagafi M, etal., Mod Pathol. 2013 Nov;26(11):1425-32. doi: 10.1038/modpathol.2013.90. Epub 2013 Jun 14.
2. Basehore MJ, etal., Clin Genet. 2014 May 7. doi: 10.1111/cge.12420.
3. Bouazzi H, etal., Indian J Med Res. 2016 Jan;143(1):43-8. doi: 10.4103/0971-5916.178589.
4. Buentzel J, etal., Medicine (Baltimore). 2019 Aug;98(31):e16712. doi: 10.1097/MD.0000000000016712.
5. Cai J, etal., Oncotarget. 2014 May 15;5(9):2551-61.
6. 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. Du M, etal., Lung Cancer. 2018 Jun;120:113-121. doi: 10.1016/j.lungcan.2018.04.008. Epub 2018 Apr 12.
8. Guerrini R, etal., Ann Neurol. 2000 Jan;47(1):117-21.
9. Kannan K, etal., Oncotarget. 2012 Oct;3(10):1194-203.
10. Kim HS, etal., Anticancer Res. 2015 Jun;35(6):3501-10.
11. Lacoste C, etal., Clin Genet. 2013 Dec 1. doi: 10.1111/cge.12319.
12. Lee J, etal., Cell Death Differ. 2012 Jul;19(7):1109-16. doi: 10.1038/cdd.2011.196. Epub 2012 Jan 13.
13. Liau JY, etal., Mod Pathol. 2015 Dec;28(12):1545-54. doi: 10.1038/modpathol.2015.114. Epub 2015 Oct 2.
14. 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.
15. Marinoni I, etal., Gastroenterology. 2014 Feb;146(2):453-60.e5. doi: 10.1053/j.gastro.2013.10.020. Epub 2013 Oct 19.
16. MGD data from the GO Consortium
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. Ohsawa K, etal., J Neurochem 1996 Jul;67(1):89-97.
19. OMIM Disease Annotation Pipeline
20. Online Mendelian Inheritance in Man, OMIM (TM).
21. Qadeer ZA, etal., J Invest Dermatol. 2014 Jun;134(6):1768-72. doi: 10.1038/jid.2014.45. Epub 2014 Jan 27.
22. RGD automated data pipeline
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. RGD comprehensive gene curation
26. Solomon LA, etal., Hum Mol Genet. 2013 Dec 15;22(24):5015-25. doi: 10.1093/hmg/ddt351. Epub 2013 Jul 25.
27. Tang P, etal., J Reprod Dev. 2011 Jun;57(3):317-21. Epub 2009 May 15.
28. Terra Md SBSP, etal., Hum Pathol. 2019 Dec;94:78-85. doi: 10.1016/j.humpath.2019.08.022. Epub 2019 Sep 6.
29. Villard L, etal., Nat Genet. 1996 Apr;12(4):359-60.
30. 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 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX70,850,981 - 70,997,330 (-)Ensembl
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_5.0X55,943,493 - 56,101,756 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0X77,469,497 - 77,515,204 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X93,903,794 - 94,051,337 (-)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 EnsemblX77,504,880 - 77,786,233 (-)EnsemblGRCh38hg38GRCh38
GRCh38X77,504,880 - 77,786,235 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X76,760,358 - 77,041,702 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X76,647,012 - 76,928,375 (-)NCBINCBI36hg18NCBI36
CeleraX77,001,253 - 77,282,613 (-)NCBI
Cytogenetic MapXq21.1NCBI
HuRefX70,349,443 - 70,629,029 (-)NCBIHuRef
CHM1_1X76,653,073 - 76,934,420 (-)NCBICHM1_1
Atrx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X104,841,221 - 104,972,978 (-)NCBIGRCm39mm39
GRCm39 EnsemblX104,841,221 - 104,973,009 (-)Ensembl
GRCm38X105,797,615 - 105,929,372 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX105,797,615 - 105,929,403 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X102,992,954 - 103,124,711 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X102,002,872 - 102,132,061 (-)NCBImm8
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
PanPan1.1X76,795,574 - 77,083,486 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX76,795,574 - 77,083,486 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X66,682,968 - 66,969,421 (-)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.0X61,011,471 - 61,270,437 (-)NCBI
UMICH_Zoey_3.1X58,719,357 - 59,051,934 (-)NCBI
UNSW_CanFamBas_1.0X60,325,606 - 60,661,270 (-)NCBI
UU_Cfam_GSD_1.0X59,917,163 - 60,249,816 (-)NCBI
Atrx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X42,229,198 - 42,451,804 (+)NCBI
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 - 61,872,288 (-)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 (-)NCBI
ChlSab1.1 EnsemblX66,448,449 - 66,737,164 (-)Ensembl
Vero_WHO_p1.0NW_02366606714,772,636 - 15,066,083 (+)NCBI

Position Markers
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


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

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.


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
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
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
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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619795 AgrOrtholog
Ensembl Genes ENSRNOG00000046897 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000056703 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000051120 UniProtKB/TrEMBL
  ENSRNOP00000070457 UniProtKB/TrEMBL
  ENSRNOP00000071468 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045534 UniProtKB/TrEMBL
  ENSRNOT00000078997 UniProtKB/TrEMBL
  ENSRNOT00000087977 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
  3.40.50.10810 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
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
  ATRX_RAT UniProtKB/Swiss-Prot
  D3ZZM6_RAT UniProtKB/TrEMBL
  P70486 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