Plekha6 (pleckstrin homology domain containing A6) - Rat Genome Database
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Gene: Plekha6 (pleckstrin homology domain containing A6) Rattus norvegicus
Analyze
Symbol: Plekha6
Name: pleckstrin homology domain containing A6
RGD ID: 1564395
Description: Orthologous to human PLEKHA6 (pleckstrin homology domain containing A6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC360842; pleckstrin homology domain containing, family A member 6; pleckstrin homology domain-containing family A member 6; RGD1564395; similar to Pleckstrin homology domain containing, family A member 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21344,614,740 - 44,754,951 (+)NCBI
Rnor_6.0 Ensembl1350,555,454 - 50,578,720 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01350,555,454 - 50,582,236 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01355,038,342 - 55,151,469 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01355,608,313 - 55,635,944 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41346,078,783 - 46,214,550 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1344,948,394 - 45,087,856 (+)NCBICelera
Cytogenetic Map13q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References


Genomics

Candidate Gene Status
Plekha6 is a candidate Gene for QTL Bp395
Comparative Map Data
Plekha6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21344,614,740 - 44,754,951 (+)NCBI
Rnor_6.0 Ensembl1350,555,454 - 50,578,720 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01350,555,454 - 50,582,236 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01355,038,342 - 55,151,469 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01355,608,313 - 55,635,944 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41346,078,783 - 46,214,550 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1344,948,394 - 45,087,856 (+)NCBICelera
Cytogenetic Map13q13NCBI
PLEKHA6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1204,218,853 - 204,377,665 (-)EnsemblGRCh38hg38GRCh38
GRCh381204,218,853 - 204,378,377 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371204,187,981 - 204,329,057 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361202,454,604 - 202,595,667 (-)NCBINCBI36hg18NCBI36
Build 341200,919,638 - 201,060,701NCBI
Celera1177,323,436 - 177,464,478 (-)NCBI
Cytogenetic Map1q32.1NCBI
HuRef1175,352,932 - 175,494,004 (-)NCBIHuRef
CHM1_11205,611,887 - 205,752,926 (-)NCBICHM1_1
Plekha6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391133,089,770 - 133,231,173 (+)NCBIGRCm39mm39
GRCm39 Ensembl1133,091,948 - 133,231,173 (+)Ensembl
GRCm381133,162,032 - 133,303,435 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1133,164,210 - 133,303,435 (+)EnsemblGRCm38mm10GRCm38
MGSCv371135,142,674 - 135,200,012 (+)NCBIGRCm37mm9NCBIm37
MGSCv361135,073,652 - 135,129,195 (+)NCBImm8
Celera1135,858,572 - 135,915,993 (+)NCBICelera
Cytogenetic Map1E4NCBI
Plekha6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540640,066,206 - 40,134,597 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540640,066,260 - 40,200,629 (-)NCBIChiLan1.0ChiLan1.0
PLEKHA6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11184,109,553 - 184,268,475 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1184,109,553 - 184,164,492 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01179,821,249 - 179,980,149 (-)NCBIMhudiblu_PPA_v0panPan3
PLEKHA6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl38799,918 - 838,835 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.138795,368 - 851,823 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Plekha6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936567430,383 - 564,429 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLEKHA6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl964,863,860 - 65,027,293 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1964,876,803 - 65,027,455 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2971,197,101 - 71,363,068 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PLEKHA6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12524,973,035 - 25,130,439 (+)NCBI
ChlSab1.1 Ensembl2525,000,340 - 25,130,573 (+)Ensembl
Plekha6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248076,653,383 - 6,784,287 (+)NCBI

Position Markers
D13Hmgc90  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01349,980,013 - 49,980,295NCBIRnor6.0
Rnor_6.01349,980,096 - 49,980,295NCBIRnor6.0
Rnor_5.01355,048,445 - 55,048,644UniSTSRnor5.0
Rnor_5.01355,048,362 - 55,048,644UniSTSRnor5.0
RGSC_v3.41346,088,424 - 46,088,623UniSTSRGSC3.4
Celera1344,958,127 - 44,958,195UniSTS
Cytogenetic Map13q13UniSTS
D13Hmgc84  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01349,994,708 - 49,994,961NCBIRnor6.0
Rnor_5.01355,063,057 - 55,063,310UniSTSRnor5.0
RGSC_v3.41346,103,036 - 46,103,289UniSTSRGSC3.4
Celera1344,972,608 - 44,972,861UniSTS
Cytogenetic Map13q13UniSTS
RH134546  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01350,555,494 - 50,555,678NCBIRnor6.0
Rnor_5.01355,608,353 - 55,608,537UniSTSRnor5.0
RGSC_v3.41346,218,710 - 46,218,894UniSTSRGSC3.4
Celera1345,087,632 - 45,087,816UniSTS
RH 3.4 Map13198.8UniSTS
Cytogenetic Map13q13UniSTS
RH143196  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01350,052,462 - 50,052,617NCBIRnor6.0
Rnor_5.01355,120,682 - 55,120,837UniSTSRnor5.0
RGSC_v3.41346,161,143 - 46,161,298UniSTSRGSC3.4
Celera1345,030,547 - 45,030,702UniSTS
RH 3.4 Map13182.8UniSTS
Cytogenetic Map13q13UniSTS
BF392626  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01350,049,822 - 50,049,927NCBIRnor6.0
Rnor_5.01355,118,241 - 55,118,346UniSTSRnor5.0
RGSC_v3.41346,158,334 - 46,158,439UniSTSRGSC3.4
Celera1345,027,915 - 45,028,020UniSTS
RH 3.4 Map13199.9UniSTS
Cytogenetic Map13q13UniSTS
AU046875  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01350,030,461 - 50,030,568NCBIRnor6.0
Rnor_5.01355,098,801 - 55,098,908UniSTSRnor5.0
RGSC_v3.41346,138,894 - 46,139,001UniSTSRGSC3.4
Celera1345,008,399 - 45,008,506UniSTS
Cytogenetic Map13q13UniSTS
RH141720  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01350,557,699 - 50,557,909NCBIRnor6.0
Rnor_5.01355,610,558 - 55,610,768UniSTSRnor5.0
RGSC_v3.41346,216,479 - 46,216,689UniSTSRGSC3.4
Celera1345,085,401 - 45,085,611UniSTS
Cytogenetic Map13q13UniSTS
BE119883  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01350,070,674 - 50,070,873NCBIRnor6.0
Rnor_5.01355,138,894 - 55,139,093UniSTSRnor5.0
RGSC_v3.41346,179,472 - 46,179,671UniSTSRGSC3.4
Celera1345,048,512 - 45,048,711UniSTS
RH 3.4 Map13173.4UniSTS
Cytogenetic Map13q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131409633059096330Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131409633059096330Rat
1300163Cardf1Cardiac cell morphology QTL 14.18aorta morphology trait (VT:0000272)artery lesion measurement (CMO:0000975)131444158250799665Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131444158251577031Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131981081464810814Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)132005247765052477Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132148248158537177Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132800833873008338Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132858445273584452Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132907693474076934Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132907693474076934Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133614753364868393Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133734634882346348Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133937292784372927Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)134231074486833540Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)134231074487310744Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)134250834587508345Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)134357571788575717Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
2303032Bp328Blood pressure QTL 328arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134644457050799665Rat
4145117Mcs27Mammary carcinoma susceptibility QTL 270.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)134877665553264877Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134905850767207219Rat
12879436Bp395Blood pressure QTL 395arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134999470851081193Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135026035750897964Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:228
Count of miRNA genes:84
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000046522, ENSRNOT00000060807
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 34 12 5 1 5 73 31 17 10
Low 9 45 36 18 36 8 11 1 4 24 1 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_039091291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091294 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091295 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091297 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091298 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091299 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091301 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091303 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091304 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091309 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_341118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005492446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000076153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1350,559,134 - 50,560,204 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1350,558,753 - 50,564,219 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077066
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1350,555,454 - 50,578,720 (-)Ensembl
RefSeq Acc Id: XM_006221473   ⟹   XP_006221535
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,092 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006221474   ⟹   XP_006221536
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,092 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006249816   ⟹   XP_006249878
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01350,555,454 - 50,582,235 (-)NCBI
Rnor_5.01355,608,313 - 55,635,944 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249818   ⟹   XP_006249880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01350,555,454 - 50,582,234 (-)NCBI
Rnor_5.01355,608,313 - 55,635,944 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017604601   ⟹   XP_017460090
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,091 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604602   ⟹   XP_017460091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,948,394 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604603   ⟹   XP_017460092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,091 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604604   ⟹   XP_017460093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,091 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604605   ⟹   XP_017460094
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,948,394 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604606   ⟹   XP_017460095
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,091 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604607   ⟹   XP_017460096
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,091 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604608   ⟹   XP_017460097
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,091 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604609   ⟹   XP_017460098
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,091 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604610   ⟹   XP_017460099
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1345,038,071 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604611   ⟹   XP_017460100
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1345,039,857 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604612   ⟹   XP_017460101
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,987,091 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604613   ⟹   XP_017460102
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1344,964,431 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604614   ⟹   XP_017460103
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1345,010,557 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604615   ⟹   XP_017460104
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1345,023,106 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604616   ⟹   XP_017460105
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1345,031,347 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017604617   ⟹   XP_017460106
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1345,054,503 - 45,087,856 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039091291   ⟹   XP_038947219
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,778 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091292   ⟹   XP_038947220
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,614,740 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091293   ⟹   XP_038947221
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,778 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091294   ⟹   XP_038947222
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,779 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091295   ⟹   XP_038947223
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,776 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091296   ⟹   XP_038947224
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,614,741 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091297   ⟹   XP_038947225
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,778 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091298   ⟹   XP_038947226
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,780 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091299   ⟹   XP_038947227
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,779 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091300   ⟹   XP_038947228
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,779 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091301   ⟹   XP_038947229
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,779 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091302   ⟹   XP_038947230
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,780 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091303   ⟹   XP_038947231
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,699,350 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091304   ⟹   XP_038947232
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,781 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091305   ⟹   XP_038947233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,774 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091306   ⟹   XP_038947234
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,781 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091307   ⟹   XP_038947235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,631,348 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091308   ⟹   XP_038947236
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,677,270 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091309   ⟹   XP_038947237
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,689,802 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091310   ⟹   XP_038947238
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,783 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_039091311   ⟹   XP_038947239
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,784 - 44,754,951 (+)NCBI
RefSeq Acc Id: XM_341118   ⟹   XP_341119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,721,260 - 44,754,951 (+)NCBI
Rnor_6.01350,555,454 - 50,582,236 (-)NCBI
Rnor_5.01355,608,313 - 55,635,944 (-)NCBI
RGSC_v3.41346,078,783 - 46,214,550 (+)RGD
Sequence:
RefSeq Acc Id: XR_005492444
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,774 - 44,754,951 (+)NCBI
RefSeq Acc Id: XR_005492445
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,774 - 44,754,951 (+)NCBI
RefSeq Acc Id: XR_005492446
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21344,653,773 - 44,754,951 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_341119   ⟸   XM_341118
- Peptide Label: isoform X20
- Sequence:
RefSeq Acc Id: XP_006221535   ⟸   XM_006221473
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_006221536   ⟸   XM_006221474
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_006249878   ⟸   XM_006249816
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006249880   ⟸   XM_006249818
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017460091   ⟸   XM_017604602
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017460094   ⟸   XM_017604605
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017460102   ⟸   XM_017604613
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: XP_017460090   ⟸   XM_017604601
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017460093   ⟸   XM_017604604
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017460097   ⟸   XM_017604608
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017460095   ⟸   XM_017604606
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017460096   ⟸   XM_017604607
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017460098   ⟸   XM_017604609
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017460101   ⟸   XM_017604612
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017460092   ⟸   XM_017604603
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017460103   ⟸   XM_017604614
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: XP_017460104   ⟸   XM_017604615
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: XP_017460105   ⟸   XM_017604616
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: XP_017460099   ⟸   XM_017604610
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_017460100   ⟸   XM_017604611
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017460106   ⟸   XM_017604617
- Peptide Label: isoform X19
- Sequence:
RefSeq Acc Id: XP_038947220   ⟸   XM_039091292
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038947224   ⟸   XM_039091296
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038947235   ⟸   XM_039091307
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038947233   ⟸   XM_039091305
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038947223   ⟸   XM_039091295
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038947219   ⟸   XM_039091291
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038947225   ⟸   XM_039091297
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038947221   ⟸   XM_039091293
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947228   ⟸   XM_039091300
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038947229   ⟸   XM_039091301
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038947227   ⟸   XM_039091299
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038947222   ⟸   XM_039091294
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038947226   ⟸   XM_039091298
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038947230   ⟸   XM_039091302
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038947232   ⟸   XM_039091304
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038947234   ⟸   XM_039091306
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038947238   ⟸   XM_039091310
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038947239   ⟸   XM_039091311
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038947236   ⟸   XM_039091308
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038947237   ⟸   XM_039091309
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038947231   ⟸   XM_039091303
- Peptide Label: isoform X13

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 (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 (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/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 (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)
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
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
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/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
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 (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
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
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
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
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
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 (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
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
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 (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 (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
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 (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 (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 (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
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 55625684 55625685 G A snv SR/JrHsd (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), SR/JrHsd (KNAW), SHR/NCrlPrin (KNAW), M520/N (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), BUF/N (KNAW), SHR/NHsd (KNAW)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 50564749 50564750 A G snv ACI/N (MCW), WKY/N (MCW), MR/N (MCW), Buf/N (MCW)
13 50572844 50572845 G A snv SHRSP/Gcrc (RGD), SR/JrHsd (RGD), SHR/NHsd (RGD), LL/MavRrrc (RGD), WKY/Gcrc (RGD), SR/JrHsd (MCW), LH/MavRrrc (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564395 AgrOrtholog
Ensembl Genes ENSRNOG00000002907 Ensembl, ENTREZGENE
NCBI Gene 360842 ENTREZGENE
PhenoGen Plekha6 PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Plekha6  pleckstrin homology domain containing A6  Plekha6  pleckstrin homology domain containing, family A member 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Plekha6  pleckstrin homology domain containing, family A member 6   Plekha6_predicted  pleckstrin homology domain containing, family A member 6 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Plekha6_predicted  pleckstrin homology domain containing, family A member 6 (predicted)  RGD1564395_predicted  similar to Pleckstrin homology domain containing, family A member 6 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1564395_predicted  similar to Pleckstrin homology domain containing, family A member 6 (predicted)  LOC360842  similar to Pleckstrin homology domain containing, family A member 6  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC360842  similar to Pleckstrin homology domain containing, family A member 6      Symbol and Name status set to provisional 70820 PROVISIONAL