Atxn1 (ataxin 1) - Rat Genome Database

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Gene: Atxn1 (ataxin 1) Rattus norvegicus
Analyze
Symbol: Atxn1
Name: ataxin 1
RGD ID: 3624
Description: Predicted to enable several functions, including identical protein binding activity; protein C-terminus binding activity; and single-stranded RNA binding activity. Predicted to be involved in several processes, including learning or memory; negative regulation of transcription by RNA polymerase II; and social behavior. Predicted to act upstream of or within several processes, including negative regulation of insulin-like growth factor receptor signaling pathway; positive regulation of glial cell proliferation; and visual learning. Predicted to be located in cytosol; nuclear inclusion body; and nuclear lumen. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 1. Orthologous to human ATXN1 (ataxin 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ataxin-1; RNSCA1; Sca1; spinocerebellar ataxia 1; spinocerebellar ataxia 1 homolog (human); Spinocerebellar ataxia type 1; spinocerebellar ataxia type 1 protein homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21718,737,491 - 19,142,360 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1718,737,533 - 19,142,360 (+)Ensembl
Rnor_6.01719,160,986 - 19,533,814 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1719,249,952 - 19,533,814 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01721,184,036 - 21,473,347 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01721,544,083 - 21,559,271 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41724,719,383 - 25,138,270 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13103,267,365 - 103,268,238 (+)NCBI
Celera1718,442,710 - 18,844,739 (+)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
(S)-colchicine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cadmium dichloride  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloroacetaldehyde  (ISO)
chromium(6+)  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
cocaine  (EXP)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
daunorubicin  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
Enterolactone  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
fonofos  (ISO)
glyphosate  (EXP)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
ibuprofen  (ISO)
ifosfamide  (ISO)
lead diacetate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (ISO)
nickel sulfate  (ISO)
O-methyleugenol  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
parathion  (ISO)
pentanal  (ISO)
permethrin  (EXP)
phenobarbital  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium fluoride  (ISO)
succimer  (ISO)
sunitinib  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
trichostatin A  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cellular_component  (ND)
cytoplasm  (ISO,ISS)
cytosol  (IEA,ISO)
nuclear inclusion body  (ISO,ISS)
nuclear matrix  (ISO,ISS)
nucleolus  (IEA,ISO)
nucleoplasm  (ISO,ISS)
nucleus  (IBA,ISO,ISS)
postsynapse  (IEA)
protein-containing complex  (ISO)

Molecular Function

References

Additional References at PubMed
PMID:7647801   PMID:9097953   PMID:9353120   PMID:9651231   PMID:11001934   PMID:11136710   PMID:12757932   PMID:15016912   PMID:15514462   PMID:15615787   PMID:15893665   PMID:16713569  
PMID:17545040   PMID:17557114   PMID:18216249   PMID:18337722   PMID:19208651   PMID:20531390   PMID:20628574   PMID:22014525   PMID:25416956   PMID:28288114   PMID:31375326  


Genomics

Comparative Map Data
Atxn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21718,737,491 - 19,142,360 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1718,737,533 - 19,142,360 (+)Ensembl
Rnor_6.01719,160,986 - 19,533,814 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1719,249,952 - 19,533,814 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01721,184,036 - 21,473,347 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01721,544,083 - 21,559,271 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41724,719,383 - 25,138,270 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13103,267,365 - 103,268,238 (+)NCBI
Celera1718,442,710 - 18,844,739 (+)NCBICelera
Cytogenetic Map17p14NCBI
ATXN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl616,299,112 - 16,761,491 (-)EnsemblGRCh38hg38GRCh38
GRCh38616,299,112 - 16,761,490 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37616,299,343 - 16,761,721 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36616,407,322 - 16,869,700 (-)NCBINCBI36hg18NCBI36
Build 34616,407,322 - 16,869,700NCBI
Celera617,537,162 - 17,999,561 (-)NCBI
Cytogenetic Map6p22.3NCBI
HuRef616,246,641 - 16,707,370 (-)NCBIHuRef
CHM1_1616,301,995 - 16,764,390 (-)NCBICHM1_1
Atxn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391345,703,231 - 46,118,467 (-)NCBIGRCm39mm39
GRCm39 Ensembl1345,703,231 - 46,118,484 (-)Ensembl
GRCm381345,549,755 - 45,964,991 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1345,549,755 - 45,965,008 (-)EnsemblGRCm38mm10GRCm38
MGSCv371345,650,262 - 46,060,345 (-)NCBIGRCm37mm9NCBIm37
MGSCv361345,565,865 - 45,975,948 (-)NCBImm8
Celera1346,630,758 - 47,041,580 (-)NCBICelera
Cytogenetic Map13A5NCBI
cM Map1321.98NCBI
Atxn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554839,536,261 - 9,552,321 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554839,159,877 - 9,559,453 (+)NCBIChiLan1.0ChiLan1.0
ATXN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1616,519,331 - 16,978,090 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl616,526,563 - 16,548,566 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0616,155,049 - 16,952,827 (-)NCBIMhudiblu_PPA_v0panPan3
ATXN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13515,458,498 - 15,863,829 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3515,452,135 - 15,649,747 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3515,407,327 - 15,813,549 (-)NCBI
ROS_Cfam_1.03515,554,267 - 15,960,589 (-)NCBI
UMICH_Zoey_3.13515,378,364 - 15,779,653 (-)NCBI
UNSW_CanFamBas_1.03515,430,962 - 15,836,082 (-)NCBI
UU_Cfam_GSD_1.03516,757,017 - 17,163,739 (-)NCBI
Atxn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049469,209,716 - 9,230,696 (+)NCBI
SpeTri2.0NW_0049365522,498,711 - 2,521,225 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATXN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl712,300,999 - 12,720,718 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1712,299,938 - 12,730,850 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2712,896,238 - 13,321,905 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATXN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11755,810,621 - 55,832,565 (+)NCBI
ChlSab1.1 Ensembl1755,810,279 - 55,832,472 (+)Ensembl
Vero_WHO_p1.0NW_02366604416,382,231 - 16,840,941 (-)NCBI
Atxn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247569,770,261 - 10,167,560 (+)NCBI

Position Markers
D17Wox16  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21719,141,577 - 19,141,833 (+)MAPPERmRatBN7.2
Rnor_6.01719,533,032 - 19,533,287NCBIRnor6.0
Rnor_5.01721,558,489 - 21,558,744UniSTSRnor5.0
RGSC_v3.41725,137,488 - 25,137,743UniSTSRGSC3.4
Celera1718,843,957 - 18,844,212UniSTS
Cytogenetic Map17p13UniSTS
RH132155  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1718,466,824 - 18,467,021UniSTS
RH 3.4 Map17201.6UniSTS
Cytogenetic Map17p13UniSTS
RH133713  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21718,735,609 - 18,735,811 (-)MAPPERmRatBN7.2
Rnor_6.01716,749,555 - 16,749,756NCBIRnor6.0
Rnor_5.01718,801,090 - 18,801,291UniSTSRnor5.0
RGSC_v3.41724,717,130 - 24,717,331UniSTSRGSC3.4
Celera1718,440,788 - 18,440,989UniSTS
RH 3.4 Map17201.2UniSTS
Cytogenetic Map17p13UniSTS
BF386213  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21719,036,069 - 19,036,212 (+)MAPPERmRatBN7.2
Rnor_6.01719,450,734 - 19,450,876NCBIRnor6.0
Rnor_5.01721,475,126 - 21,475,268UniSTSRnor5.0
RGSC_v3.41725,026,336 - 25,026,478UniSTSRGSC3.4
Celera1718,738,615 - 18,738,757UniSTS
RH 3.4 Map17250.6UniSTS
Cytogenetic Map17p13UniSTS
BE106629  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21718,896,287 - 18,896,438 (+)MAPPERmRatBN7.2
Rnor_6.01719,311,586 - 19,311,736NCBIRnor6.0
Rnor_5.01721,336,084 - 21,336,234UniSTSRnor5.0
RGSC_v3.41724,885,277 - 24,885,427UniSTSRGSC3.4
Celera1718,598,660 - 18,598,810UniSTS
RH 3.4 Map17212.8UniSTS
Cytogenetic Map17p13UniSTS
RH138268  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21718,922,968 - 18,923,147 (+)MAPPERmRatBN7.2
Rnor_6.01719,338,262 - 19,338,440NCBIRnor6.0
Rnor_5.01721,363,014 - 21,363,192UniSTSRnor5.0
RGSC_v3.41724,910,919 - 24,911,097UniSTSRGSC3.4
Celera1718,625,945 - 18,626,123UniSTS
RH 3.4 Map17201.1UniSTS
Cytogenetic Map17p13UniSTS
AI502631  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21718,850,240 - 18,850,427 (+)MAPPERmRatBN7.2
Rnor_6.01719,250,051 - 19,250,237NCBIRnor6.0
Rnor_5.01721,272,917 - 21,273,103UniSTSRnor5.0
RGSC_v3.41724,819,776 - 24,819,962UniSTSRGSC3.4
Celera1718,554,213 - 18,554,399UniSTS
RH 3.4 Map17214.2UniSTS
Cytogenetic Map17p13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17429913021293263Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat
1549900Iddm20Insulin dependent diabetes mellitus QTL 203.7pancreas integrity trait (VT:0010560)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)171398677321975515Rat
1331720Rf43Renal function QTL 432.881kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)171533061323017269Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:199
Count of miRNA genes:135
Interacting mature miRNAs:165
Transcripts:ENSRNOT00000023140
Prediction methods:Miranda, Pita, Targetscan
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 2 9 10 3 3 41 8 7 11 3
Low 3 41 48 41 9 41 5 8 33 27 33 5
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000023140   ⟹   ENSRNOP00000023140
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1718,737,533 - 19,142,360 (+)Ensembl
Rnor_6.0 Ensembl1719,249,952 - 19,533,814 (+)Ensembl
RefSeq Acc Id: NM_012726   ⟹   NP_036858
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,533 - 19,142,360 (+)NCBI
Rnor_6.01719,160,986 - 19,533,814 (+)NCBI
Rnor_5.01721,184,036 - 21,473,347 (+)NCBI
Rnor_5.01721,544,083 - 21,559,271 (+)NCBI
RGSC_v3.41724,719,383 - 25,138,270 (+)RGD
Celera1718,442,710 - 18,844,739 (+)RGD
Sequence:
RefSeq Acc Id: XM_039095351   ⟹   XP_038951279
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,496 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095352   ⟹   XP_038951280
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,494 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095353   ⟹   XP_038951281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,491 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095354   ⟹   XP_038951282
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,492 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095355   ⟹   XP_038951283
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,493 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095356   ⟹   XP_038951284
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,738,884 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095357   ⟹   XP_038951285
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,739,412 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095359   ⟹   XP_038951287
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,739,098 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095360   ⟹   XP_038951288
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,914 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095361   ⟹   XP_038951289
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,741,927 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095362   ⟹   XP_038951290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,497 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095363   ⟹   XP_038951291
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,492 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095364   ⟹   XP_038951292
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,737,491 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095365   ⟹   XP_038951293
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,746,619 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095366   ⟹   XP_038951294
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,746,619 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095367   ⟹   XP_038951295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,849,931 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095368   ⟹   XP_038951296
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,797,679 - 19,141,676 (+)NCBI
RefSeq Acc Id: XM_039095369   ⟹   XP_038951297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21718,883,338 - 19,141,676 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036858   ⟸   NM_012726
- UniProtKB: Q63540 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023140   ⟸   ENSRNOT00000023140
RefSeq Acc Id: XP_038951281   ⟸   XM_039095353
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951292   ⟸   XM_039095364
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951282   ⟸   XM_039095354
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951291   ⟸   XM_039095363
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951283   ⟸   XM_039095355
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951280   ⟸   XM_039095352
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951279   ⟸   XM_039095351
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951290   ⟸   XM_039095362
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951288   ⟸   XM_039095360
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951284   ⟸   XM_039095356
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951287   ⟸   XM_039095359
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951285   ⟸   XM_039095357
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951289   ⟸   XM_039095361
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951294   ⟸   XM_039095366
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951293   ⟸   XM_039095365
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951296   ⟸   XM_039095368
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951295   ⟸   XM_039095367
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951297   ⟸   XM_039095369
- Peptide Label: isoform X1
Protein Domains
AXH

Transcriptome

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


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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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:3624 AgrOrtholog
Ensembl Genes ENSRNOG00000016998 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000023140 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000023140 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro ATAXIN1-like UniProtKB/Swiss-Prot
  Ataxin_AXH_dom UniProtKB/Swiss-Prot
  Ataxin_AXH_dom_sf UniProtKB/Swiss-Prot
  ATXN1 UniProtKB/Swiss-Prot
KEGG Report rno:25049 UniProtKB/Swiss-Prot
NCBI Gene 25049 ENTREZGENE
PANTHER PTHR13392 UniProtKB/Swiss-Prot
  PTHR13392:SF5 UniProtKB/Swiss-Prot
Pfam AXH UniProtKB/Swiss-Prot
PhenoGen Atxn1 PhenoGen
PROSITE AXH UniProtKB/Swiss-Prot
SMART AXH UniProtKB/Swiss-Prot
Superfamily-SCOP SSF102031 UniProtKB/Swiss-Prot
TIGR TC207283
UniProt ATX1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Atxn1  ataxin 1  Sca1  spinocerebellar ataxia 1 homolog (human)  Symbol and Name updated 1299863 APPROVED
2002-06-10 Sca1  Spinocerebellar ataxia type 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the pyramidal cell layer of the hippocampus and in cerebellar Purkinje cells 729738