Kalrn (kalirin, RhoGEF kinase) - Rat Genome Database

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Gene: Kalrn (kalirin, RhoGEF kinase) Rattus norvegicus
Analyze
Symbol: Kalrn
Name: kalirin, RhoGEF kinase
RGD ID: 621865
Description: Enables enzyme binding activity. Involved in several processes, including NMDA selective glutamate receptor signaling pathway; modification of postsynaptic actin cytoskeleton; and neurotransmitter receptor localization to postsynaptic specialization membrane. Located in several cellular components, including glutamatergic synapse; neuronal cell body; and postsynaptic density. Is active in presynapse. Orthologous to human KALRN (kalirin RhoGEF kinase); PARTICIPATES IN ephrin - ephrin receptor bidirectional signaling axis; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cyclin B1; Duo; Hapip; huntingtin-associated protein interacting protein (duo); huntingtin-associated protein-interacting protein; kalirin; P-CIP10; PAM COOH-terminal interactor protein 10; serine/threonine kinase with Dbl- and pleckstrin homology domain; serine/threonine-protein kinase with Dbl- and pleckstrin homology domain
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
mRatBN7.21166,198,155 - 66,803,166 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1166,198,173 - 66,797,610 (+)Ensembl
Rnor_6.01169,484,293 - 70,025,682 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1169,484,293 - 70,025,633 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01172,575,016 - 73,115,328 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41168,124,348 - 68,611,336 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11168,205,034 - 68,668,925 (+)NCBI
Celera1165,708,953 - 66,248,259 (+)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrobenzenesulfonic acid  (ISO)
2,6-dinitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
chlordecone  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
diarsenic trioxide  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
genistein  (ISO)
glyphosate  (EXP)
graphite  (EXP)
hydrogen peroxide  (ISO)
kainic acid  (EXP)
lead diacetate  (ISO)
leflunomide  (ISO)
melphalan  (ISO)
methapyrilene  (ISO)
methotrexate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nitrofen  (EXP)
paracetamol  (ISO)
PCB138  (ISO)
permethrin  (EXP)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
pirinixic acid  (EXP,ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sulindac sulfide  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
triadimefon  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult locomotory behavior  (IEA,ISO)
axon guidance  (IEA)
axonogenesis  (IDA)
behavioral fear response  (ISO)
behavioral response to cocaine  (ISO)
behavioral response to formalin induced pain  (ISO)
central nervous system development  (IEA)
habituation  (IEA,ISO)
intracellular signal transduction  (IBA,IDA)
lactation  (IEA,ISO)
maternal behavior  (IEA,ISO)
maternal process involved in parturition  (IEA,ISO)
memory  (IEA,ISO)
modification of postsynaptic actin cytoskeleton  (IMP)
negative regulation of growth hormone secretion  (IEA,ISO)
nervous system development  (IDA)
neuromuscular junction development  (IEA,ISO)
neurotransmitter receptor localization to postsynaptic specialization membrane  (IMP)
NMDA selective glutamate receptor signaling pathway  (IMP)
positive regulation of dendritic spine development  (ISO)
positive regulation of dendritic spine morphogenesis  (IEA,ISO)
positive regulation of GTPase activity  (IEA,ISO)
positive regulation of long-term synaptic potentiation  (ISO)
protein phosphorylation  (IEA)
regulation of dendrite development  (IDA)
regulation of modification of postsynaptic actin cytoskeleton  (IDA,IMP)
regulation of neuronal synaptic plasticity  (ISO)
regulation of neurotransmitter receptor localization to postsynaptic specialization membrane  (IDA,IMP)
regulation of protein localization to plasma membrane  (ISO)
regulation of synaptic transmission, glutamatergic  (ISO)
response to mechanical stimulus  (ISO)
Rho protein signal transduction  (ISO)
smooth muscle cell migration  (ISO)
smooth muscle cell proliferation  (ISO)
social behavior  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9915831   PMID:10692441   PMID:10974569   PMID:12546821   PMID:14742910   PMID:15923627   PMID:16644733   PMID:18585704   PMID:18625710   PMID:18628310   PMID:19020030   PMID:19056867  
PMID:19625617   PMID:19889983   PMID:20333733   PMID:21880917   PMID:22458534   PMID:22738176   PMID:23116210   PMID:23288169   PMID:23516288   PMID:23742124   PMID:23825406   PMID:25146373  
PMID:25378388   PMID:25865668   PMID:26921771   PMID:27989699   PMID:28418645   PMID:30053369   PMID:30565792   PMID:30875016   PMID:32203420   PMID:32375403  


Genomics

Comparative Map Data
Kalrn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21166,198,155 - 66,803,166 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1166,198,173 - 66,797,610 (+)Ensembl
Rnor_6.01169,484,293 - 70,025,682 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1169,484,293 - 70,025,633 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01172,575,016 - 73,115,328 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41168,124,348 - 68,611,336 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11168,205,034 - 68,668,925 (+)NCBI
Celera1165,708,953 - 66,248,259 (+)NCBICelera
Cytogenetic Map11q22NCBI
KALRN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3124,033,369 - 124,726,325 (+)EnsemblGRCh38hg38GRCh38
GRCh383124,033,341 - 124,726,325 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373123,813,554 - 124,445,172 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363125,296,275 - 125,922,726 (+)NCBINCBI36hg18NCBI36
Celera3122,221,230 - 122,847,210 (+)NCBI
Cytogenetic Map3q21.1-q21.2NCBI
HuRef3121,187,838 - 121,814,322 (+)NCBIHuRef
CHM1_13123,776,558 - 124,403,021 (+)NCBICHM1_1
Kalrn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391633,789,443 - 34,393,647 (-)NCBIGRCm39mm39
GRCm39 Ensembl1633,789,443 - 34,393,902 (-)Ensembl
GRCm381633,969,073 - 34,573,277 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1633,969,073 - 34,573,532 (-)EnsemblGRCm38mm10GRCm38
MGSCv371633,969,159 - 34,514,113 (-)NCBIGRCm37mm9NCBIm37
MGSCv361633,892,682 - 34,433,795 (-)NCBImm8
Celera1634,453,093 - 34,990,407 (-)NCBICelera
Cytogenetic Map16B3NCBI
Kalrn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542723,184,739 - 23,816,811 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542723,184,751 - 23,823,128 (+)NCBIChiLan1.0ChiLan1.0
KALRN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13128,098,363 - 128,722,156 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3128,225,413 - 128,720,441 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03121,138,136 - 121,828,723 (+)NCBIMhudiblu_PPA_v0panPan3
KALRN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13327,161,403 - 27,752,891 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3327,161,504 - 27,746,497 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3327,117,706 - 27,776,818 (+)NCBI
ROS_Cfam_1.03327,329,328 - 27,797,773 (+)NCBI
UMICH_Zoey_3.13327,125,464 - 27,784,937 (+)NCBI
UNSW_CanFamBas_1.03327,169,910 - 27,829,241 (+)NCBI
UU_Cfam_GSD_1.03327,786,940 - 28,447,934 (+)NCBI
Kalrn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602126,658,106 - 127,230,908 (-)NCBI
SpeTri2.0NW_004936725749,382 - 1,020,702 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KALRN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12256,106,677 - 56,820,004 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2256,151,819 - 56,754,538 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041109,573,807 - 110,217,834 (+)NCBIVero_WHO_p1.0
Kalrn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473154,934 - 756,707 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D11Mgh3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21166,422,148 - 66,422,316 (+)MAPPERmRatBN7.2
Rnor_6.01169,649,708 - 69,649,875NCBIRnor6.0
Rnor_5.01172,739,687 - 72,739,854UniSTSRnor5.0
RGSC_v3.41168,234,781 - 68,234,949RGDRGSC3.4
RGSC_v3.41168,234,782 - 68,234,949UniSTSRGSC3.4
RGSC_v3.11168,292,371 - 68,292,538RGD
Celera1165,874,140 - 65,874,287UniSTS
RH 3.4 Map11411.0UniSTS
RH 3.4 Map11411.0RGD
Cytogenetic Map11q22UniSTS
D11Arb4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21166,422,141 - 66,422,377 (+)MAPPERmRatBN7.2
Rnor_6.01169,649,701 - 69,649,936NCBIRnor6.0
Rnor_5.01172,739,680 - 72,739,915UniSTSRnor5.0
RGSC_v3.41168,234,774 - 68,235,010RGDRGSC3.4
RGSC_v3.41168,234,775 - 68,235,010UniSTSRGSC3.4
RGSC_v3.11168,292,364 - 68,292,599RGD
Celera1165,874,133 - 65,874,348UniSTS
RH 3.4 Map11416.8UniSTS
RH 3.4 Map11416.8RGD
RH 2.0 Map11147.1RGD
SHRSP x BN Map1129.8399RGD
Cytogenetic Map11q22UniSTS
D11Got53  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21166,414,395 - 66,414,504 (+)MAPPERmRatBN7.2
Rnor_6.01169,641,939 - 69,642,047NCBIRnor6.0
Rnor_5.01172,731,918 - 72,732,026UniSTSRnor5.0
RGSC_v3.41168,227,012 - 68,227,121RGDRGSC3.4
RGSC_v3.41168,227,013 - 68,227,121UniSTSRGSC3.4
RGSC_v3.11168,284,602 - 68,284,710RGD
Celera1165,866,395 - 65,866,495UniSTS
RH 3.4 Map11416.9UniSTS
RH 3.4 Map11416.9RGD
RH 2.0 Map11147.0RGD
Cytogenetic Map11q22UniSTS
BE102756  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map11423.8UniSTS
Cytogenetic Map11q22UniSTS
RH137364  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21166,762,510 - 66,762,678 (+)MAPPERmRatBN7.2
Rnor_6.01169,990,587 - 69,990,754NCBIRnor6.0
Rnor_5.01173,080,299 - 73,080,466UniSTSRnor5.0
RGSC_v3.41168,575,790 - 68,575,957UniSTSRGSC3.4
Celera1166,213,376 - 66,213,543UniSTS
RH 3.4 Map11410.0UniSTS
Cytogenetic Map11q22UniSTS
BE110052  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21166,550,775 - 66,550,986 (+)MAPPERmRatBN7.2
Rnor_6.01169,778,868 - 69,779,078NCBIRnor6.0
Rnor_5.01172,868,257 - 72,868,467UniSTSRnor5.0
RGSC_v3.41168,363,209 - 68,363,419UniSTSRGSC3.4
Celera1166,001,487 - 66,001,697UniSTS
RH 3.4 Map11413.6UniSTS
Cytogenetic Map11q22UniSTS
BF396995  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21166,584,216 - 66,584,428 (+)MAPPERmRatBN7.2
Rnor_6.01169,812,304 - 69,812,515NCBIRnor6.0
Rnor_5.01172,901,599 - 72,901,810UniSTSRnor5.0
RGSC_v3.41168,396,645 - 68,396,856UniSTSRGSC3.4
Celera1166,034,975 - 66,035,186UniSTS
RH 3.4 Map11415.4UniSTS
Cytogenetic Map11q22UniSTS
AU046621  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01172,583,938 - 72,584,303NCBIRnor5.0
RGSC_v3.41168,082,751 - 68,083,111UniSTSRGSC3.4
Celera1165,717,382 - 65,717,746UniSTS
Cytogenetic Map11q22UniSTS
RH137626  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21166,797,618 - 66,797,774 (+)MAPPERmRatBN7.2
Rnor_6.01170,025,691 - 70,025,846NCBIRnor6.0
Rnor_5.01173,115,337 - 73,115,492UniSTSRnor5.0
RGSC_v3.41168,611,345 - 68,611,500UniSTSRGSC3.4
Celera1166,248,268 - 66,248,423UniSTS
Cytogenetic Map11q22UniSTS
RH138291  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21166,698,064 - 66,698,218 (+)MAPPERmRatBN7.2
Rnor_6.01169,926,149 - 69,926,302NCBIRnor6.0
Rnor_5.01173,015,452 - 73,015,605UniSTSRnor5.0
RGSC_v3.41168,511,288 - 68,511,441UniSTSRGSC3.4
Celera1166,148,872 - 66,149,025UniSTS
RH 3.4 Map11420.8UniSTS
Cytogenetic Map11q22UniSTS
AU049016  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21166,739,774 - 66,740,015 (+)MAPPERmRatBN7.2
mRatBN7.21166,739,924 - 66,740,015 (+)MAPPERmRatBN7.2
Rnor_6.01169,968,003 - 69,968,093NCBIRnor6.0
Rnor_6.01169,967,853 - 69,968,093NCBIRnor6.0
Rnor_5.01173,057,717 - 73,057,807UniSTSRnor5.0
Rnor_5.01173,057,567 - 73,057,807UniSTSRnor5.0
RGSC_v3.41168,552,992 - 68,553,232UniSTSRGSC3.4
RGSC_v3.41168,553,142 - 68,553,232UniSTSRGSC3.4
Celera1166,190,796 - 66,190,886UniSTS
Celera1166,190,646 - 66,190,886UniSTS
Cytogenetic Map11q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116611332182169223Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:202
Count of miRNA genes:136
Interacting mature miRNAs:149
Transcripts:ENSRNOT00000002324, ENSRNOT00000016340, ENSRNOT00000049292
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 2 6 6 4 6 66 20 18 3
Low 3 41 51 35 15 35 8 11 8 15 23 8 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_032062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088648 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088649 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088650 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088653 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088654 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088656 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088657 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088658 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC133403 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF046121 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF229255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF230644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF232668 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF232669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY621095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LS482391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U88156 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U88157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U94189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000016340   ⟹   ENSRNOP00000016340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1166,198,173 - 66,628,157 (+)Ensembl
Rnor_6.0 Ensembl1169,739,384 - 69,856,241 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000049292   ⟹   ENSRNOP00000039072
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1166,254,969 - 66,797,610 (+)Ensembl
Rnor_6.0 Ensembl1169,484,293 - 70,025,633 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098731   ⟹   ENSRNOP00000078050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1166,254,969 - 66,797,610 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101686   ⟹   ENSRNOP00000097769
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1166,688,941 - 66,797,589 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112350   ⟹   ENSRNOP00000084630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1166,616,200 - 66,760,639 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114138   ⟹   ENSRNOP00000089775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1166,198,173 - 66,797,610 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117056   ⟹   ENSRNOP00000094025
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1166,254,810 - 66,797,610 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118953   ⟹   ENSRNOP00000084297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1166,254,682 - 66,797,610 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119829   ⟹   ENSRNOP00000083298
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1166,688,941 - 66,765,434 (+)Ensembl
RefSeq Acc Id: NM_032062   ⟹   NP_114451
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,254,969 - 66,797,610 (+)NCBI
Rnor_6.01169,484,293 - 70,025,682 (+)NCBI
Rnor_5.01172,575,016 - 73,115,328 (+)NCBI
RGSC_v3.41168,124,348 - 68,611,336 (+)RGD
Celera1165,708,953 - 66,248,259 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088638   ⟹   XP_038944566
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,541 - 66,803,166 (+)NCBI
RefSeq Acc Id: XM_039088639   ⟹   XP_038944567
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,541 - 66,803,166 (+)NCBI
RefSeq Acc Id: XM_039088640   ⟹   XP_038944568
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,541 - 66,803,166 (+)NCBI
RefSeq Acc Id: XM_039088641   ⟹   XP_038944569
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,254,969 - 66,797,564 (+)NCBI
RefSeq Acc Id: XM_039088642   ⟹   XP_038944570
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,198,520 - 66,797,564 (+)NCBI
RefSeq Acc Id: XM_039088643   ⟹   XP_038944571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,254,969 - 66,797,564 (+)NCBI
RefSeq Acc Id: XM_039088644   ⟹   XP_038944572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,541 - 66,797,564 (+)NCBI
RefSeq Acc Id: XM_039088645   ⟹   XP_038944573
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,541 - 66,803,166 (+)NCBI
RefSeq Acc Id: XM_039088646   ⟹   XP_038944574
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,541 - 66,803,166 (+)NCBI
RefSeq Acc Id: XM_039088647   ⟹   XP_038944575
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,541 - 66,803,166 (+)NCBI
RefSeq Acc Id: XM_039088648   ⟹   XP_038944576
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,311,425 - 66,797,602 (+)NCBI
RefSeq Acc Id: XM_039088649   ⟹   XP_038944577
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,542 - 66,803,166 (+)NCBI
RefSeq Acc Id: XM_039088650   ⟹   XP_038944578
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,541 - 66,803,166 (+)NCBI
RefSeq Acc Id: XM_039088651   ⟹   XP_038944579
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,544 - 66,770,216 (+)NCBI
RefSeq Acc Id: XM_039088652   ⟹   XP_038944580
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,545 - 66,761,497 (+)NCBI
RefSeq Acc Id: XM_039088653   ⟹   XP_038944581
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,545 - 66,761,497 (+)NCBI
RefSeq Acc Id: XM_039088654   ⟹   XP_038944582
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,545 - 66,760,639 (+)NCBI
RefSeq Acc Id: XM_039088655   ⟹   XP_038944583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,545 - 66,760,966 (+)NCBI
RefSeq Acc Id: XM_039088656   ⟹   XP_038944584
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,311,425 - 66,761,474 (+)NCBI
RefSeq Acc Id: XM_039088657   ⟹   XP_038944585
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,511,317 - 66,803,166 (+)NCBI
RefSeq Acc Id: XM_039088658   ⟹   XP_038944586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,198,155 - 66,736,072 (+)NCBI
RefSeq Acc Id: XM_039088659   ⟹   XP_038944587
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,542 - 66,702,923 (+)NCBI
RefSeq Acc Id: XM_039088660   ⟹   XP_038944588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,543 - 66,629,551 (+)NCBI
RefSeq Acc Id: XM_039088661   ⟹   XP_038944589
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,198,156 - 66,629,551 (+)NCBI
RefSeq Acc Id: XM_039088662   ⟹   XP_038944590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,543 - 66,629,551 (+)NCBI
RefSeq Acc Id: XM_039088663   ⟹   XP_038944591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,543 - 66,629,551 (+)NCBI
RefSeq Acc Id: XM_039088664   ⟹   XP_038944592
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,198,156 - 66,629,551 (+)NCBI
RefSeq Acc Id: XM_039088665   ⟹   XP_038944593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,543 - 66,629,551 (+)NCBI
RefSeq Acc Id: XM_039088666   ⟹   XP_038944594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,543 - 66,629,551 (+)NCBI
RefSeq Acc Id: XM_039088667   ⟹   XP_038944595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21166,251,543 - 66,629,551 (+)NCBI
Protein Sequences
Protein RefSeqs NP_114451 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944566 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944567 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944568 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944569 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944570 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944571 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944572 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944573 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944574 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944575 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944576 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944577 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944578 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944579 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944580 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944581 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944582 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944583 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944584 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944585 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944586 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944587 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944588 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944589 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944590 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944591 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944592 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944593 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944594 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944595 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB66366 (Get FASTA)   NCBI Sequence Viewer  
  AAB66367 (Get FASTA)   NCBI Sequence Viewer  
  AAC03057 (Get FASTA)   NCBI Sequence Viewer  
  AAC15790 (Get FASTA)   NCBI Sequence Viewer  
  AAF66014 (Get FASTA)   NCBI Sequence Viewer  
  AAF66018 (Get FASTA)   NCBI Sequence Viewer  
  AAF66019 (Get FASTA)   NCBI Sequence Viewer  
  AAF69144 (Get FASTA)   NCBI Sequence Viewer  
  AAT39517 (Get FASTA)   NCBI Sequence Viewer  
  EDM11342 (Get FASTA)   NCBI Sequence Viewer  
  EDM11343 (Get FASTA)   NCBI Sequence Viewer  
  EDM11344 (Get FASTA)   NCBI Sequence Viewer  
  EDM11345 (Get FASTA)   NCBI Sequence Viewer  
  EDM11346 (Get FASTA)   NCBI Sequence Viewer  
  EDM11347 (Get FASTA)   NCBI Sequence Viewer  
  EDM11348 (Get FASTA)   NCBI Sequence Viewer  
  EDM11349 (Get FASTA)   NCBI Sequence Viewer  
  P97924 (Get FASTA)   NCBI Sequence Viewer  
  SPT35768 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_114451   ⟸   NM_032062
- UniProtKB: P97924 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016340   ⟸   ENSRNOT00000016340
RefSeq Acc Id: ENSRNOP00000039072   ⟸   ENSRNOT00000049292
RefSeq Acc Id: XP_038944586   ⟸   XM_039088658
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038944589   ⟸   XM_039088661
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038944592   ⟸   XM_039088664
- Peptide Label: isoform X27
RefSeq Acc Id: XP_038944570   ⟸   XM_039088642
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038944566   ⟸   XM_039088638
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944574   ⟸   XM_039088646
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038944567   ⟸   XM_039088639
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944568   ⟸   XM_039088640
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944578   ⟸   XM_039088650
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038944573   ⟸   XM_039088645
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038944575   ⟸   XM_039088647
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038944572   ⟸   XM_039088644
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038944577   ⟸   XM_039088649
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038944587   ⟸   XM_039088659
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038944588   ⟸   XM_039088660
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038944591   ⟸   XM_039088663
- Peptide Label: isoform X26
RefSeq Acc Id: XP_038944594   ⟸   XM_039088666
- Peptide Label: isoform X29
RefSeq Acc Id: XP_038944595   ⟸   XM_039088667
- Peptide Label: isoform X30
RefSeq Acc Id: XP_038944590   ⟸   XM_039088662
- Peptide Label: isoform X25
RefSeq Acc Id: XP_038944593   ⟸   XM_039088665
- Peptide Label: isoform X28
RefSeq Acc Id: XP_038944579   ⟸   XM_039088651
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038944581   ⟸   XM_039088653
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038944580   ⟸   XM_039088652
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038944583   ⟸   XM_039088655
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038944582   ⟸   XM_039088654
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038944569   ⟸   XM_039088641
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038944571   ⟸   XM_039088643
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038944576   ⟸   XM_039088648
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038944584   ⟸   XM_039088656
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038944585   ⟸   XM_039088657
- Peptide Label: isoform X20
RefSeq Acc Id: ENSRNOP00000084297   ⟸   ENSRNOT00000118953
RefSeq Acc Id: ENSRNOP00000078050   ⟸   ENSRNOT00000098731
RefSeq Acc Id: ENSRNOP00000094025   ⟸   ENSRNOT00000117056
RefSeq Acc Id: ENSRNOP00000084630   ⟸   ENSRNOT00000112350
RefSeq Acc Id: ENSRNOP00000097769   ⟸   ENSRNOT00000101686
RefSeq Acc Id: ENSRNOP00000083298   ⟸   ENSRNOT00000119829
RefSeq Acc Id: ENSRNOP00000089775   ⟸   ENSRNOT00000114138
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NRrrc (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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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
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)
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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: 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)
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/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: 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)
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
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:621865 AgrOrtholog
Ensembl Genes ENSRNOG00000001706 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016340 UniProtKB/Swiss-Prot
  ENSRNOP00000039072 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016340 UniProtKB/Swiss-Prot
  ENSRNOT00000049292 UniProtKB/TrEMBL
Gene3D-CATH 1.20.900.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.525.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CRAL-TRIO_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRAL-TRIO_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DBL_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DH-domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kalirin/TRIO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spectrin/alpha-actinin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spectrin_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84009 UniProtKB/Swiss-Prot
NCBI Gene 84009 ENTREZGENE
PANTHER PTHR22826:SF104 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CRAL_TRIO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRAL_TRIO_2 UniProtKB/TrEMBL
  fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00169 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RhoGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spectrin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Kalrn PhenoGen
PROSITE CRAL_TRIO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DH_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RhoGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  S_TKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SEC14 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00233 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPEC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48065 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50044 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52087 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A2X0SFF1_RAT UniProtKB/TrEMBL
  F1LZV1_RAT UniProtKB/TrEMBL
  KALRN_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O70135 UniProtKB/Swiss-Prot
  Q6IV51 UniProtKB/Swiss-Prot
  Q9JIF1 UniProtKB/Swiss-Prot
  Q9JIF2 UniProtKB/Swiss-Prot
  Q9JIG0 UniProtKB/Swiss-Prot
  Q9JIH3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-03-14 Kalrn  kalirin, RhoGEF kinase  Hapip  huntingtin-associated protein interacting protein (duo)  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2002-08-07 Hapip  huntingtin-associated protein interacting protein (duo)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains dual Rho GTPase guanine nucleotide exchange factor (GEF) domains that interact with Rac1 and RhoA 628431
gene_expression expressed mainly in the nervous system 628431
gene_physical_interaction binds to the cytoplasmic domain of peptidylglycine alpha-amidating monooxygenase (PAM), a membrane protein mediating neuropeptide biosynthesis 628431
gene_process participates in regulation of neuronal fiber extension and pathfinding during development 628431
gene_process initiates new axons and axonal outgrowth via RhoG-mediated mechanisms 628431