Kitlg (KIT ligand) - Rat Genome Database

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Gene: Kitlg (KIT ligand) Rattus norvegicus
Analyze
Symbol: Kitlg
Name: KIT ligand
RGD ID: 3086
Description: Predicted to enable cytokine activity and stem cell factor receptor binding activity. Involved in ovarian follicle development and positive regulation of cell population proliferation. Predicted to be located in several cellular components, including extracellular space; filopodium; and lamellipodium. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 69 and familial progressive hyperpigmentation with or without hypopigmentation. Orthologous to human KITLG (KIT ligand); PARTICIPATES IN cytokine mediated signaling pathway; INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 1,2-dimethylhydrazine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: C-kit ligand; hematopoietic growth factor KL; Kitl; Kl1; Kl2; LOC60427; LOC60428; mast cell growth factor; Mgf; SCF; steel factor/kit ligand; stem cell factor; stem cell factor KL-1; stem cell factor KL-1 precursor; stem cell factor KL-2 precursor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2734,896,075 - 34,977,215 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl734,896,053 - 34,977,214 (+)Ensembl
Rnor_6.0742,269,784 - 42,351,054 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl742,269,784 - 42,351,054 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0742,302,651 - 42,383,921 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4737,714,157 - 37,795,722 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1737,734,427 - 37,804,538 (+)NCBI
Celera731,898,840 - 31,979,932 (+)NCBICelera
RH 3.4 Map7286.2RGD
Cytogenetic Map7q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-artemisinic acid  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1,4-benzoquinone  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-octadec-9-enoylglycero-3-phosphate  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4-diaminotoluene  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
all-trans-retinoic acid  (ISO)
allethrin  (EXP)
amiodarone  (ISO)
ammonium chloride  (EXP)
ammonium hexachloroplatinate  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
benzophenanthridine  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
butyric acid  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
ceric oxide  (ISO)
chloroprene  (EXP)
cholesterol  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
Cuprizon  (EXP)
cyclophosphamide  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
daidzein  (ISO)
daidzein 7-O-beta-D-glucoside  (ISO)
daunorubicin  (EXP)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
diethylstilbestrol  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
gadodiamide hydrate  (EXP)
gemcitabine  (ISO)
genistein  (ISO)
genistein 7-O-beta-D-glucoside  (ISO)
gentamycin  (EXP)
glycitein  (ISO)
glycitin  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hexamethylene diisocyanate  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
indometacin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
LY294002  (ISO)
melphalan  (ISO)
mercury dibromide  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (EXP)
N-methyl-N-nitrosourea  (ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
nitrofen  (EXP)
Nutlin-3  (ISO)
ochratoxin A  (EXP)
oxaliplatin  (EXP)
oxymetholone  (ISO)
ozone  (ISO)
p-menthan-3-ol  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phencyclidine  (ISO)
phenobarbital  (EXP,ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
pravastatin  (EXP,ISO)
quercetin  (EXP,ISO)
resveratrol  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
silver(1+) nitrate  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sunitinib  (ISO)
T-2 toxin  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
torcetrapib  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
wortmannin  (ISO)
zaragozic acid A  (EXP,ISO)
zearalenone  (ISO)
zinc atom  (ISO)
zinc protoporphyrin  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO,ISS)
cytoskeleton  (IEA)
extracellular region  (IEA)
extracellular space  (ISO)
filopodium  (IEA,ISO,ISS)
integral component of membrane  (IEA,ISO)
lamellipodium  (IEA,ISO,ISS)
plasma membrane  (IBA,IEA,ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1375116   PMID:1379243   PMID:1708771   PMID:2208278   PMID:7690439   PMID:9722506   PMID:10620616   PMID:10872802   PMID:11401406   PMID:11435472   PMID:12140361   PMID:12714518  
PMID:12951073   PMID:14525951   PMID:15039234   PMID:15947484   PMID:16427619   PMID:17107997   PMID:17581219   PMID:17848411   PMID:18087173   PMID:18087667   PMID:18448842   PMID:18469139  
PMID:18544282   PMID:18723513   PMID:19182706   PMID:19255573   PMID:21092510   PMID:21149635   PMID:21540074   PMID:21932404   PMID:22099173   PMID:22366471   PMID:22526758   PMID:22592456  
PMID:22850284   PMID:22931954   PMID:23745035   PMID:24068671   PMID:24228598   PMID:24825426   PMID:25420576   PMID:26522471   PMID:26742689   PMID:26862759   PMID:27707610   PMID:28801138  
PMID:30142893  


Genomics

Comparative Map Data
Kitlg
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2734,896,075 - 34,977,215 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl734,896,053 - 34,977,214 (+)Ensembl
Rnor_6.0742,269,784 - 42,351,054 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl742,269,784 - 42,351,054 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0742,302,651 - 42,383,921 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4737,714,157 - 37,795,722 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1737,734,427 - 37,804,538 (+)NCBI
Celera731,898,840 - 31,979,932 (+)NCBICelera
RH 3.4 Map7286.2RGD
Cytogenetic Map7q21NCBI
KITLG
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1288,492,793 - 88,580,851 (-)EnsemblGRCh38hg38GRCh38
GRCh381288,492,793 - 88,580,471 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371288,886,570 - 88,974,248 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361287,410,697 - 87,498,369 (-)NCBINCBI36hg18NCBI36
Build 341287,389,036 - 87,476,706NCBI
Celera1288,556,999 - 88,644,657 (-)NCBI
Cytogenetic Map12q21.32NCBI
HuRef1285,953,228 - 86,040,884 (-)NCBIHuRef
CHM1_11288,851,652 - 88,939,322 (-)NCBICHM1_1
Kitl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391099,851,477 - 99,936,278 (+)NCBIGRCm39mm39
GRCm39 Ensembl1099,851,492 - 99,936,278 (+)Ensembl
GRCm3810100,015,615 - 100,100,416 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10100,015,630 - 100,100,416 (+)EnsemblGRCm38mm10GRCm38
MGSCv371099,478,458 - 99,563,046 (+)NCBIGRCm37mm9NCBIm37
MGSCv361099,445,512 - 99,530,100 (+)NCBImm8
Celera10101,983,926 - 102,068,221 (+)NCBICelera
Cytogenetic Map10D1NCBI
cM Map1051.4NCBI
Kitlg
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540525,886,447 - 25,969,395 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540525,816,137 - 25,969,006 (-)NCBIChiLan1.0ChiLan1.0
KITLG
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11289,341,921 - 89,436,081 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1289,341,921 - 89,436,758 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01286,036,501 - 86,124,274 (-)NCBIMhudiblu_PPA_v0panPan3
KITLG
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11529,591,068 - 29,671,985 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1529,591,170 - 29,671,974 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1530,041,648 - 30,122,153 (-)NCBI
ROS_Cfam_1.01530,230,533 - 30,311,189 (-)NCBI
UMICH_Zoey_3.11529,545,261 - 29,626,200 (-)NCBI
UNSW_CanFamBas_1.01529,607,389 - 29,688,442 (-)NCBI
UU_Cfam_GSD_1.01529,890,288 - 29,970,909 (-)NCBI
Kitlg
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494530,584,662 - 30,669,431 (+)NCBI
SpeTri2.0NW_0049365075,566,144 - 5,650,412 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KITLG
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl594,017,384 - 94,110,216 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1594,016,992 - 94,110,219 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2598,745,850 - 98,834,052 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KITLG
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11183,856,149 - 83,943,095 (-)NCBI
ChlSab1.1 Ensembl1183,856,157 - 83,943,083 (-)Ensembl
Vero_WHO_p1.0NW_023666037161,319,600 - 161,407,409 (+)NCBI
Kitlg
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248377,456,116 - 7,541,764 (-)NCBI

Position Markers
D7Wox35  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2734,894,959 - 34,895,325 (+)MAPPERmRatBN7.2
Rnor_6.0742,268,669 - 42,269,034NCBIRnor6.0
Rnor_5.0742,301,536 - 42,301,901UniSTSRnor5.0
RGSC_v3.4737,713,042 - 37,713,407UniSTSRGSC3.4
Celera731,897,725 - 31,898,090UniSTS
Cytogenetic Map7q13UniSTS
RH94630  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2734,895,277 - 34,895,453 (+)MAPPERmRatBN7.2
Rnor_6.0742,268,987 - 42,269,162NCBIRnor6.0
Rnor_5.0742,301,854 - 42,302,029UniSTSRnor5.0
RGSC_v3.4737,713,360 - 37,713,535UniSTSRGSC3.4
Celera731,898,043 - 31,898,218UniSTS
RH 3.4 Map7286.2UniSTS
Cytogenetic Map7q13UniSTS
AA858739  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2734,976,844 - 34,976,994 (+)MAPPERmRatBN7.2
Rnor_6.0742,350,684 - 42,350,833NCBIRnor6.0
Rnor_5.0742,383,551 - 42,383,700UniSTSRnor5.0
RGSC_v3.4737,795,352 - 37,795,501UniSTSRGSC3.4
Celera731,979,562 - 31,979,711UniSTS
RH 3.4 Map7291.4UniSTS
Cytogenetic Map7q13UniSTS
RH137672  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2734,975,359 - 34,975,489 (+)MAPPERmRatBN7.2
Rnor_6.0742,349,199 - 42,349,328NCBIRnor6.0
Rnor_5.0742,382,066 - 42,382,195UniSTSRnor5.0
RGSC_v3.4737,793,867 - 37,793,996UniSTSRGSC3.4
Celera731,978,077 - 31,978,206UniSTS
Cytogenetic Map7q13UniSTS
MGF  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2734,957,638 - 34,958,490 (+)MAPPERmRatBN7.2
Rnor_6.0742,331,479 - 42,332,330NCBIRnor6.0
Rnor_5.0742,364,346 - 42,365,197UniSTSRnor5.0
RGSC_v3.4737,776,147 - 37,776,998UniSTSRGSC3.4
Celera731,960,353 - 31,961,204UniSTS
Cytogenetic Map7q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1031
Count of miRNA genes:279
Interacting mature miRNAs:354
Transcripts:ENSRNOT00000007231, ENSRNOT00000008471
Prediction methods:Microtar, Miranda
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 32 24 14 17 14 4 4 74 34 35 11 4
Low 11 32 26 2 26 4 7 1 6 4
Below cutoff 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007231   ⟹   ENSRNOP00000007231
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl742,269,784 - 42,351,054 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000008471   ⟹   ENSRNOP00000008471
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl734,896,053 - 34,977,214 (+)Ensembl
Rnor_6.0 Ensembl742,269,784 - 42,351,054 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085097   ⟹   ENSRNOP00000068846
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl742,304,534 - 42,339,598 (+)Ensembl
RefSeq Acc Id: NM_021843   ⟹   NP_068615
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2734,896,075 - 34,977,215 (+)NCBI
Rnor_6.0742,269,784 - 42,351,054 (+)NCBI
Rnor_5.0742,302,651 - 42,383,921 (+)NCBI
RGSC_v3.4737,714,157 - 37,795,722 (+)RGD
Celera731,898,840 - 31,979,932 (+)RGD
Sequence:
RefSeq Acc Id: NM_021844   ⟹   NP_068616
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2734,896,075 - 34,977,215 (+)NCBI
Rnor_6.0742,269,784 - 42,351,054 (+)NCBI
Rnor_5.0742,302,651 - 42,383,921 (+)NCBI
RGSC_v3.4737,714,157 - 37,795,722 (+)RGD
Celera731,898,840 - 31,979,932 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_068615   ⟸   NM_021843
- Peptide Label: isoform 1 precursor
- UniProtKB: P21581 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_068616   ⟸   NM_021844
- Peptide Label: isoform 2 precursor
- UniProtKB: Q54A14 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008471   ⟸   ENSRNOT00000008471
RefSeq Acc Id: ENSRNOP00000068846   ⟸   ENSRNOT00000085097
RefSeq Acc Id: ENSRNOP00000007231   ⟸   ENSRNOT00000007231

Transcriptome

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

Promoters
RGD ID:13695175
Promoter ID:EPDNEW_R5700
Type:single initiation site
Name:Kitlg_1
Description:KIT ligand
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0742,269,762 - 42,269,822EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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
BN/SsN (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
BN/SsN (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
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)
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
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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)
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
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)
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
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)
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
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)
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
SBH/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: 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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3086 AgrOrtholog
Ensembl Genes ENSRNOG00000005386 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007231 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000008471 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000068846 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007231 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000008471 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000085097 UniProtKB/TrEMBL
InterPro 4_helix_cytokine-like_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SCF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60427 UniProtKB/Swiss-Prot
NCBI Gene 60427 ENTREZGENE
PANTHER PTHR11574 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SCF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Kitlg PhenoGen
PIRSF SCF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47266 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JTU2_RAT UniProtKB/TrEMBL
  P21581 ENTREZGENE
  Q54A14 ENTREZGENE, UniProtKB/TrEMBL
  SCF_RAT UniProtKB/Swiss-Prot
UniProt Secondary A0A0A0MXU5 UniProtKB/TrEMBL
  Q9QWZ4 UniProtKB/Swiss-Prot
  Q9Z2E7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-11-17 Kitlg  KIT ligand  Kitl  kit ligand  Data Merged 737654 APPROVED
2004-12-14 Kitl  kit ligand      Symbol and Name status set to approved 1299863 APPROVED
2003-10-24 Kitl  kit ligand  LOC60428  stem cell factor KL-2 precursor  Data Merged 628472 PROVISIONAL
2003-10-24 Kitl  kit ligand  LOC60427  stem cell factor KL-1 precursor  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 PROVISIONAL
2003-04-09 Kitlg  KIT ligand  Mgf  Mast cell growth factor  Symbol and Name updated 629477 APPROVED
2002-06-10 Mgf  Mast cell growth factor      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization membrane-bound 1302207
gene_expression expressed in Seratoli cells 1298983
gene_expression expression in testis is by downregulated by effects of ghrelin, a regulator of cell proliferation 1302206
gene_function key signal in spermatogenesis and putative regulator of Leydig cell development 1302206
gene_function soluble growth factor that activates c-kit tyrosine kinase receptor 1302207
gene_function may affect vascular smooth muscle cells through an autocrine pathway 1302207
gene_regulation proximal promoter region is regulated by a cAMP-dependent pathway in Seratoli cells 1298983
gene_transcript promoter contains TATA, AP2 and Spl elements (-119 bp to +43) 1298983