Cnot2 (CCR4-NOT transcription complex, subunit 2) - Rat Genome Database

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Gene: Cnot2 (CCR4-NOT transcription complex, subunit 2) Rattus norvegicus
Analyze
Symbol: Cnot2
Name: CCR4-NOT transcription complex, subunit 2
RGD ID: 1311672
Description: Predicted to enable transcription corepressor binding activity. Predicted to contribute to poly(A)-specific ribonuclease activity. Predicted to be involved in several processes, including negative regulation of cellular macromolecule biosynthetic process; negative regulation of intracellular estrogen receptor signaling pathway; and positive regulation of cytoplasmic mRNA processing body assembly. Predicted to be located in cytosol; nucleoplasm; and plasma membrane. Predicted to be part of CCR4-NOT core complex. Predicted to be active in P-body. Orthologous to human CNOT2 (CCR4-NOT transcription complex subunit 2); PARTICIPATES IN microRNA pathway; RNA degradation pathway; INTERACTS WITH 2,6-dinitrotoluene; bisphenol A; Brodifacoum.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CCR4-NOT transcription complex subunit 2; LOC299805
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
mRatBN7.2752,130,444 - 52,222,338 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl752,130,441 - 52,223,575 (-)Ensembl
Rnor_6.0759,526,105 - 59,617,307 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl759,527,124 - 59,587,385 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0759,537,579 - 59,628,786 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4755,823,982 - 55,880,812 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1755,844,724 - 55,901,542 (-)NCBI
Celera748,914,667 - 48,971,519 (-)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:14707134   PMID:16712523   PMID:16778766   PMID:19558367   PMID:19946888   PMID:21299754   PMID:22367759  


Genomics

Comparative Map Data
Cnot2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2752,130,444 - 52,222,338 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl752,130,441 - 52,223,575 (-)Ensembl
Rnor_6.0759,526,105 - 59,617,307 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl759,527,124 - 59,587,385 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0759,537,579 - 59,628,786 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4755,823,982 - 55,880,812 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1755,844,724 - 55,901,542 (-)NCBI
Celera748,914,667 - 48,971,519 (-)NCBICelera
Cytogenetic Map7q22NCBI
CNOT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1270,243,002 - 70,354,993 (+)EnsemblGRCh38hg38GRCh38
GRCh381270,242,993 - 70,354,993 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371270,636,798 - 70,748,773 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361268,923,044 - 69,035,040 (+)NCBINCBI36hg18NCBI36
Build 341268,923,488 - 69,033,960NCBI
Celera1270,300,448 - 70,412,447 (+)NCBI
Cytogenetic Map12q15NCBI
HuRef1267,686,934 - 67,798,932 (+)NCBIHuRef
CHM1_11270,606,077 - 70,718,081 (+)NCBICHM1_1
Cnot2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910116,321,065 - 116,418,891 (-)NCBIGRCm39mm39
GRCm39 Ensembl10116,321,066 - 116,417,416 (-)Ensembl
GRCm3810116,485,160 - 116,581,900 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10116,485,161 - 116,581,511 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710115,922,217 - 116,018,567 (-)NCBIGRCm37mm9NCBIm37
MGSCv3610115,889,276 - 115,985,621 (-)NCBImm8
Celera10118,426,741 - 118,523,052 (-)NCBICelera
Cytogenetic Map10D2NCBI
Cnot2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540510,451,414 - 10,547,229 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540510,451,414 - 10,547,229 (+)NCBIChiLan1.0ChiLan1.0
CNOT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11270,520,722 - 70,633,149 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1270,520,722 - 70,633,149 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01267,753,703 - 67,865,375 (+)NCBIMhudiblu_PPA_v0panPan3
CNOT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11012,057,269 - 12,174,405 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1012,009,762 - 12,172,427 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1011,995,863 - 12,112,451 (+)NCBI
ROS_Cfam_1.01012,188,879 - 12,305,324 (+)NCBI
UMICH_Zoey_3.11012,055,404 - 12,171,985 (+)NCBI
UNSW_CanFamBas_1.01012,302,721 - 12,419,265 (+)NCBI
UU_Cfam_GSD_1.01012,426,002 - 12,542,252 (+)NCBI
Cnot2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494546,069,715 - 46,170,762 (-)NCBI
SpeTri2.0NW_0049365457,938,934 - 8,040,409 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CNOT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl534,426,394 - 34,549,313 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1534,470,911 - 34,548,968 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2537,132,108 - 37,207,783 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CNOT2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11165,823,294 - 65,932,588 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1165,861,353 - 65,934,042 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037179,752,841 - 179,862,945 (-)NCBIVero_WHO_p1.0
Cnot2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475027,433,671 - 27,529,545 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH144030  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2752,138,261 - 52,138,425 (+)MAPPERmRatBN7.2
Rnor_6.0759,533,922 - 59,534,085NCBIRnor6.0
Rnor_5.0759,545,396 - 59,545,559UniSTSRnor5.0
RGSC_v3.4755,827,349 - 55,827,512UniSTSRGSC3.4
Celera748,918,034 - 48,918,197UniSTS
RH 3.4 Map7481.5UniSTS
Cytogenetic Map7q22UniSTS
RH140338  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2752,149,611 - 52,149,762 (+)MAPPERmRatBN7.2
Rnor_6.0759,545,272 - 59,545,422NCBIRnor6.0
Rnor_5.0759,556,746 - 59,556,896UniSTSRnor5.0
RGSC_v3.4755,838,699 - 55,838,849UniSTSRGSC3.4
Celera748,929,384 - 48,929,534UniSTS
RH 3.4 Map7503.6UniSTS
Cytogenetic Map7q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74110969256793354Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)74725178365728867Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:157
Count of miRNA genes:124
Interacting mature miRNAs:134
Transcripts:ENSRNOT00000066396
Prediction methods:Microtar, Miranda, Rnahybrid, 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 3 43 57 41 19 41 8 10 74 35 41 11 8
Low 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001011988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078720 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078730 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078731 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078732 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078733 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005486575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC136025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC136231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC087653 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000066396   ⟹   ENSRNOP00000061277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl752,134,908 - 52,191,729 (-)Ensembl
Rnor_6.0 Ensembl759,530,568 - 59,587,385 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000085836   ⟹   ENSRNOP00000075690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl752,131,074 - 52,221,608 (-)Ensembl
Rnor_6.0 Ensembl759,532,641 - 59,547,174 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091427   ⟹   ENSRNOP00000074023
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl752,136,860 - 52,221,617 (-)Ensembl
Rnor_6.0 Ensembl759,527,124 - 59,587,382 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100132   ⟹   ENSRNOP00000078367
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl752,130,594 - 52,221,611 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104908   ⟹   ENSRNOP00000084380
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl752,130,441 - 52,221,617 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114739   ⟹   ENSRNOP00000077944
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl752,130,443 - 52,221,617 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118688   ⟹   ENSRNOP00000095291
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl752,130,594 - 52,223,575 (-)Ensembl
RefSeq Acc Id: NM_001011988   ⟹   NP_001011988
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,134,895 - 52,191,729 (-)NCBI
Rnor_6.0759,530,555 - 59,587,385 (-)NCBI
Rnor_5.0759,537,579 - 59,628,786 (-)NCBI
RGSC_v3.4755,823,982 - 55,880,812 (-)RGD
Celera748,914,667 - 48,971,519 (-)RGD
Sequence:
RefSeq Acc Id: XM_006241363   ⟹   XP_006241425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,444 - 52,222,326 (-)NCBI
Rnor_6.0759,526,105 - 59,617,297 (-)NCBI
Rnor_5.0759,537,579 - 59,628,786 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241364   ⟹   XP_006241426
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,222,326 (-)NCBI
Rnor_6.0759,526,105 - 59,617,307 (-)NCBI
Rnor_5.0759,537,579 - 59,628,786 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241365   ⟹   XP_006241427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,221,608 (-)NCBI
Rnor_6.0759,526,105 - 59,617,307 (-)NCBI
Rnor_5.0759,537,579 - 59,628,786 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241367   ⟹   XP_006241429
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,222,326 (-)NCBI
Rnor_6.0759,526,105 - 59,617,307 (-)NCBI
Rnor_5.0759,537,579 - 59,628,786 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241369   ⟹   XP_006241431
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,222,327 (-)NCBI
Rnor_6.0759,526,105 - 59,617,297 (-)NCBI
Rnor_5.0759,537,579 - 59,628,786 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241370   ⟹   XP_006241432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,221,617 (-)NCBI
Rnor_6.0759,526,105 - 59,617,307 (-)NCBI
Rnor_5.0759,537,579 - 59,628,786 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594741   ⟹   XP_017450230
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,448 - 52,222,327 (-)NCBI
Rnor_6.0759,526,105 - 59,617,307 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078717   ⟹   XP_038934645
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,221,318 (-)NCBI
RefSeq Acc Id: XM_039078718   ⟹   XP_038934646
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,211,785 (-)NCBI
RefSeq Acc Id: XM_039078719   ⟹   XP_038934647
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,194,904 (-)NCBI
RefSeq Acc Id: XM_039078720   ⟹   XP_038934648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,222,326 (-)NCBI
RefSeq Acc Id: XM_039078722   ⟹   XP_038934650
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,191,726 (-)NCBI
RefSeq Acc Id: XM_039078723   ⟹   XP_038934651
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,222,326 (-)NCBI
RefSeq Acc Id: XM_039078724   ⟹   XP_038934652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,130,453 - 52,191,716 (-)NCBI
RefSeq Acc Id: XM_039078725   ⟹   XP_038934653
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,133,513 - 52,222,329 (-)NCBI
RefSeq Acc Id: XM_039078726   ⟹   XP_038934654
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,131,062 - 52,222,328 (-)NCBI
RefSeq Acc Id: XM_039078727   ⟹   XP_038934655
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,131,062 - 52,222,327 (-)NCBI
RefSeq Acc Id: XM_039078728   ⟹   XP_038934656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,131,062 - 52,222,328 (-)NCBI
RefSeq Acc Id: XM_039078730   ⟹   XP_038934658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,131,062 - 52,222,327 (-)NCBI
RefSeq Acc Id: XM_039078731   ⟹   XP_038934659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,131,062 - 52,222,328 (-)NCBI
RefSeq Acc Id: XM_039078732   ⟹   XP_038934660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,131,062 - 52,222,328 (-)NCBI
RefSeq Acc Id: XM_039078733   ⟹   XP_038934661
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,131,062 - 52,222,325 (-)NCBI
RefSeq Acc Id: XM_039078734   ⟹   XP_038934662
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,131,062 - 52,191,719 (-)NCBI
RefSeq Acc Id: XM_039078735   ⟹   XP_038934663
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,131,062 - 52,145,999 (-)NCBI
RefSeq Acc Id: XR_005486575
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,142,856 - 52,222,338 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001011988 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241425 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241426 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241427 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241429 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241431 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241432 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450230 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934645 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934646 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934647 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934648 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934650 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934651 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934652 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934653 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934654 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934655 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934656 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934658 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934659 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934660 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934661 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934662 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934663 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH87653 (Get FASTA)   NCBI Sequence Viewer  
  EDM16655 (Get FASTA)   NCBI Sequence Viewer  
  EDM16656 (Get FASTA)   NCBI Sequence Viewer  
  EDM16658 (Get FASTA)   NCBI Sequence Viewer  
  EDM16662 (Get FASTA)   NCBI Sequence Viewer  
  EDM16665 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001011988   ⟸   NM_001011988
- UniProtKB: Q5PPJ8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241431   ⟸   XM_006241369
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006241425   ⟸   XM_006241363
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006241432   ⟸   XM_006241370
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006241426   ⟸   XM_006241364
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K717 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241429   ⟸   XM_006241367
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006241427   ⟸   XM_006241365
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017450230   ⟸   XM_017594741
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: ENSRNOP00000074023   ⟸   ENSRNOT00000091427
RefSeq Acc Id: ENSRNOP00000061277   ⟸   ENSRNOT00000066396
RefSeq Acc Id: ENSRNOP00000075690   ⟸   ENSRNOT00000085836
RefSeq Acc Id: XP_038934648   ⟸   XM_039078720
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934651   ⟸   XM_039078723
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934645   ⟸   XM_039078717
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038934646   ⟸   XM_039078718
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038934647   ⟸   XM_039078719
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038934650   ⟸   XM_039078722
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934652   ⟸   XM_039078724
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934660   ⟸   XM_039078732
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038934656   ⟸   XM_039078728
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038934654   ⟸   XM_039078726
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038934659   ⟸   XM_039078731
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038934658   ⟸   XM_039078730
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038934655   ⟸   XM_039078727
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038934661   ⟸   XM_039078733
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038934662   ⟸   XM_039078734
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038934663   ⟸   XM_039078735
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038934653   ⟸   XM_039078725
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000084380   ⟸   ENSRNOT00000104908
RefSeq Acc Id: ENSRNOP00000095291   ⟸   ENSRNOT00000118688
RefSeq Acc Id: ENSRNOP00000077944   ⟸   ENSRNOT00000114739
RefSeq Acc Id: ENSRNOP00000078367   ⟸   ENSRNOT00000100132
Protein Domains
NOT2_3_5

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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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)
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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)
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:1311672 AgrOrtholog
Ensembl Genes ENSRNOG00000004909 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061277 UniProtKB/TrEMBL
  ENSRNOP00000074023 UniProtKB/TrEMBL
  ENSRNOP00000075690 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066396 UniProtKB/TrEMBL
  ENSRNOT00000085836 UniProtKB/TrEMBL
  ENSRNOT00000091427 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.1020 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7313082 IMAGE-MGC_LOAD
InterPro CCR4-NOT_su2/3/5_N_sf UniProtKB/TrEMBL
  NOT UniProtKB/TrEMBL
  Not2/3/5 UniProtKB/TrEMBL
KEGG Report rno:299805 UniProtKB/TrEMBL
MGC_CLONE MGC:105588 IMAGE-MGC_LOAD
NCBI Gene 299805 ENTREZGENE
PANTHER PTHR23326 UniProtKB/TrEMBL
Pfam NOT2_3_5 UniProtKB/TrEMBL
PhenoGen Cnot2 PhenoGen
UniProt A0A0G2K717 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2KB82_RAT UniProtKB/TrEMBL
  Q5PPJ8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Cnot2  CCR4-NOT transcription complex, subunit 2  Cnot2_predicted  CCR4-NOT transcription complex, subunit 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Cnot2_predicted  CCR4-NOT transcription complex, subunit 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED