Atxn2 (ataxin 2) - Rat Genome Database

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Gene: Atxn2 (ataxin 2) Rattus norvegicus
Analyze
Symbol: Atxn2
Name: ataxin 2
RGD ID: 1306637
Description: Predicted to enable RNA binding activity; epidermal growth factor receptor binding activity; and protein C-terminus binding activity. Predicted to be involved in P-body assembly; negative regulation of receptor internalization; and stress granule assembly. Predicted to act upstream of or within several processes, including homeostasis of number of cells; neuromuscular process; and neuron differentiation. Predicted to be located in cytosol; perinuclear region of cytoplasm; and trans-Golgi network. Predicted to be part of polysome. Predicted to be active in cytoplasmic stress granule. Human ortholog(s) of this gene implicated in late onset Parkinson's disease and spinocerebellar ataxia type 2. Orthologous to human ATXN2 (ataxin 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: ataxin-2; LOC288663; Sca2; spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)
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
mRatBN7.21234,754,132 - 34,851,175 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1234,754,137 - 34,851,479 (-)Ensembl
Rnor_6.01240,264,601 - 40,335,637 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1240,266,662 - 40,332,612 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01242,137,228 - 42,206,238 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41235,962,308 - 36,009,114 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11235,822,590 - 35,875,779 (-)NCBI
Celera1236,417,282 - 36,487,757 (-)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:9668173   PMID:10814712   PMID:10973246   PMID:11471052   PMID:12477932   PMID:12812977   PMID:15663938   PMID:16023918   PMID:16293225   PMID:16835262   PMID:17097639   PMID:17392519  
PMID:18602463   PMID:19946888   PMID:22658674   PMID:22681889   PMID:25002582   PMID:30361391  


Genomics

Comparative Map Data
Atxn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21234,754,132 - 34,851,175 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1234,754,137 - 34,851,479 (-)Ensembl
Rnor_6.01240,264,601 - 40,335,637 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1240,266,662 - 40,332,612 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01242,137,228 - 42,206,238 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41235,962,308 - 36,009,114 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11235,822,590 - 35,875,779 (-)NCBI
Celera1236,417,282 - 36,487,757 (-)NCBICelera
Cytogenetic Map12q16NCBI
ATXN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12111,443,485 - 111,599,676 (-)EnsemblGRCh38hg38GRCh38
GRCh3812111,452,214 - 111,599,673 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712111,890,018 - 112,037,477 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612110,374,401 - 110,521,863 (-)NCBINCBI36hg18NCBI36
Build 3412110,352,737 - 110,500,200NCBI
Celera12111,516,452 - 111,663,853 (-)NCBI
Cytogenetic Map12q24.12NCBI
HuRef12108,904,559 - 109,051,670 (-)NCBIHuRef
CHM1_112111,857,982 - 112,005,420 (-)NCBICHM1_1
Atxn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395121,849,672 - 121,954,372 (+)NCBIGRCm39mm39
GRCm39 Ensembl5121,849,400 - 121,954,556 (+)Ensembl
GRCm385121,711,609 - 121,814,950 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5121,711,337 - 121,816,493 (+)EnsemblGRCm38mm10GRCm38
MGSCv375122,161,618 - 122,264,959 (+)NCBIGRCm37mm9NCBIm37
MGSCv365121,972,226 - 122,075,325 (+)NCBImm8
Celera5118,835,912 - 118,905,112 (+)NCBICelera
Cytogenetic Map5FNCBI
Atxn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554828,101,917 - 8,216,219 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554828,101,410 - 8,187,815 (-)NCBIChiLan1.0ChiLan1.0
ATXN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112112,419,337 - 112,565,096 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12112,419,337 - 112,566,360 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v012109,024,620 - 109,174,135 (-)NCBIMhudiblu_PPA_v0panPan3
ATXN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1269,073,667 - 9,188,429 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl269,073,809 - 9,188,414 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha269,236,242 - 9,351,196 (-)NCBI
ROS_Cfam_1.0269,333,114 - 9,448,244 (-)NCBI
ROS_Cfam_1.0 Ensembl269,333,120 - 9,448,072 (-)Ensembl
UMICH_Zoey_3.1269,289,083 - 9,404,017 (-)NCBI
UNSW_CanFamBas_1.0269,351,063 - 9,466,629 (-)NCBI
UU_Cfam_GSD_1.0269,304,823 - 9,419,816 (-)NCBI
Atxn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118155,291,141 - 155,351,949 (+)NCBI
SpeTri2.0NW_0049365584,127,477 - 4,188,307 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATXN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1432,656,558 - 32,771,813 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11432,656,537 - 32,772,082 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21434,652,086 - 34,767,878 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATXN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111106,704,532 - 106,860,450 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl11106,705,127 - 106,859,337 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037138,238,814 - 138,393,492 (+)NCBIVero_WHO_p1.0
Atxn2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474720,603,319 - 20,728,346 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D12Rat101  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21234,818,802 - 34,818,908 (+)MAPPERmRatBN7.2
Rnor_6.01240,331,109 - 40,331,214NCBIRnor6.0
Rnor_5.01242,202,084 - 42,202,189UniSTSRnor5.0
Celera1236,483,229 - 36,483,334UniSTS
FHH x ACI Map1234.96RGD
FHH x ACI Map1234.96UniSTS
Cytogenetic Map12q16UniSTS
AW544490  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21234,754,538 - 34,754,662 (+)MAPPERmRatBN7.2
Rnor_6.01240,266,680 - 40,266,803NCBIRnor6.0
Rnor_5.01242,137,637 - 42,137,760UniSTSRnor5.0
RGSC_v3.41235,959,369 - 35,959,492UniSTSRGSC3.4
Celera1236,419,361 - 36,419,484UniSTS
Cytogenetic Map12q16UniSTS
RH137509  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21234,761,961 - 34,762,178 (+)MAPPERmRatBN7.2
mRatBN7.21211,470,103 - 11,470,644 (+)MAPPERmRatBN7.2
Rnor_6.01213,523,743 - 13,524,283NCBIRnor6.0
Rnor_6.01240,274,101 - 40,274,317NCBIRnor6.0
Rnor_5.01215,562,742 - 15,563,282UniSTSRnor5.0
Rnor_5.01242,145,058 - 42,145,274UniSTSRnor5.0
RGSC_v3.41235,966,790 - 35,967,006UniSTSRGSC3.4
RGSC_v3.41211,865,825 - 11,866,365UniSTSRGSC3.4
Celera1236,426,782 - 36,426,998UniSTS
Celera1213,264,657 - 13,265,197UniSTS
RH 3.4 Map12616.2UniSTS
Cytogenetic Map12q16UniSTS
Cytogenetic Map12p11UniSTS
MARC_2373-2374:991932707:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21234,754,450 - 34,755,580 (+)MAPPERmRatBN7.2
Rnor_6.01240,266,592 - 40,267,721NCBIRnor6.0
Rnor_5.01242,137,549 - 42,138,678UniSTSRnor5.0
RGSC_v3.41235,959,281 - 35,960,410UniSTSRGSC3.4
Celera1236,419,273 - 36,420,402UniSTS
Cytogenetic Map12q16UniSTS
MARC_17487-17488:1030377680:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21234,788,633 - 34,790,159 (+)MAPPERmRatBN7.2
Rnor_6.01240,300,685 - 40,302,210NCBIRnor6.0
Rnor_5.01242,171,642 - 42,173,167UniSTSRnor5.0
RGSC_v3.41235,993,631 - 35,995,156UniSTSRGSC3.4
Celera1236,453,502 - 36,455,027UniSTS
Cytogenetic Map12q16UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961088935682913Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121983578938193007Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat
70169Eae13Experimental allergic encephalomyelitis QTL 130.032nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)122413920236638073Rat
1556747Calcic1Intracellular calcium level QTL 13.6platelet calcium amount (VT:0010500)platelet intracellular calcium level (CMO:0000922)122806443340130419Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)122806443345899022Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)122806443346669029Rat
1331787Rf41Renal function QTL 412.998kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)122806455740218380Rat
631829Alc6Alcohol consumption QTL 64.7consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)122860752637691617Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123210317445899022Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:652
Count of miRNA genes:191
Interacting mature miRNAs:212
Transcripts:ENSRNOT00000001691, ENSRNOT00000040587, ENSRNOT00000045666
Prediction methods:Microtar, Miranda, 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 35 56 40 19 40 1 4 73 34 40 11 1
Low 8 1 1 1 7 7 1 1 1 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_008760469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760500 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769282 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598524 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598527 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598530 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598532 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604496 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090142 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090143 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090144 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090155 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039090158 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001840679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC091406 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC168999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230562 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000001691   ⟹   ENSRNOP00000001691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1234,754,137 - 34,851,479 (-)Ensembl
Rnor_6.0 Ensembl1240,266,662 - 40,332,612 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108093   ⟹   ENSRNOP00000089697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1234,754,185 - 34,851,479 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115112   ⟹   ENSRNOP00000079599
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1234,754,137 - 34,823,560 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115534   ⟹   ENSRNOP00000095616
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1234,754,137 - 34,851,479 (-)Ensembl
RefSeq Acc Id: XM_039090141   ⟹   XP_038946069
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090142   ⟹   XP_038946070
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090143   ⟹   XP_038946071
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090144   ⟹   XP_038946072
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,849,227 (-)NCBI
RefSeq Acc Id: XM_039090146   ⟹   XP_038946074
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090147   ⟹   XP_038946075
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090148   ⟹   XP_038946076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090149   ⟹   XP_038946077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,849,224 (-)NCBI
RefSeq Acc Id: XM_039090150   ⟹   XP_038946078
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090151   ⟹   XP_038946079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090152   ⟹   XP_038946080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090153   ⟹   XP_038946081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,849,224 (-)NCBI
RefSeq Acc Id: XM_039090154   ⟹   XP_038946082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090155   ⟹   XP_038946083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090157   ⟹   XP_038946085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,763,370 - 34,851,175 (-)NCBI
RefSeq Acc Id: XM_039090158   ⟹   XP_038946086
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21234,754,132 - 34,847,862 (-)NCBI
Reference Sequences
RefSeq Acc Id: ENSRNOP00000001691   ⟸   ENSRNOT00000001691
RefSeq Acc Id: XP_038946083   ⟸   XM_039090155
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038946071   ⟸   XM_039090143
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038946078   ⟸   XM_039090150
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038946080   ⟸   XM_039090152
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038946075   ⟸   XM_039090147
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038946070   ⟸   XM_039090142
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946079   ⟸   XM_039090151
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038946074   ⟸   XM_039090146
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038946082   ⟸   XM_039090154
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038946076   ⟸   XM_039090148
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038946069   ⟸   XM_039090141
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946072   ⟸   XM_039090144
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038946077   ⟸   XM_039090149
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038946081   ⟸   XM_039090153
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038946086   ⟸   XM_039090158
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038946085   ⟸   XM_039090157
- Peptide Label: isoform X15
RefSeq Acc Id: ENSRNOP00000095616   ⟸   ENSRNOT00000115534
RefSeq Acc Id: ENSRNOP00000089697   ⟸   ENSRNOT00000108093
RefSeq Acc Id: ENSRNOP00000079599   ⟸   ENSRNOT00000115112
Protein Domains
LsmAD

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)
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
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)
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
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)
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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)
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)
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
LEXF3/Stm (2020)
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
LEXF4/Stm (2020)
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
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)
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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/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
LN/MavRrrcAek (2020)
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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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: 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)
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:1306637 AgrOrtholog
Ensembl Genes ENSRNOG00000001256 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001691 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000079599 ENTREZGENE
  ENSRNOP00000089697 ENTREZGENE
  ENSRNOP00000095616 ENTREZGENE
Ensembl Transcript ENSRNOT00000001691 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000108093 ENTREZGENE
  ENSRNOT00000115112 ENTREZGENE
  ENSRNOT00000115534 ENTREZGENE
InterPro Ataxin-2_C UniProtKB/TrEMBL
  ATXN2 UniProtKB/TrEMBL
  LSM_dom UniProtKB/TrEMBL
  LsmAD_domain UniProtKB/TrEMBL
  SM_dom_ATX UniProtKB/TrEMBL
NCBI Gene 288663 ENTREZGENE
PANTHER PTHR12854:SF11 UniProtKB/TrEMBL
Pfam LsmAD UniProtKB/TrEMBL
  PAM2 UniProtKB/TrEMBL
  SM-ATX UniProtKB/TrEMBL
PhenoGen Atxn2 PhenoGen
SMART LsmAD UniProtKB/TrEMBL
Superfamily-SCOP Sm_like_riboprot UniProtKB/TrEMBL
UniProt B5DFB6_RAT UniProtKB/TrEMBL
  F1M049_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Atxn2  ataxin 2   Atxn2_predicted  ataxin 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Atxn2_predicted  ataxin 2 (predicted)  Sca2_predicted  spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2) (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Sca2_predicted  spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2) (predicted)      Symbol and Name status set to approved 70820 APPROVED