Slit2 (slit guidance ligand 2) - Rat Genome Database

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Gene: Slit2 (slit guidance ligand 2) Rattus norvegicus
Analyze
Symbol: Slit2
Name: slit guidance ligand 2
RGD ID: 69310
Description: Enables heparan sulfate proteoglycan binding activity. Involved in several processes, including central nervous system development; negative regulation of inflammatory response; and negative regulation of monocyte chemotaxis. Located in plasma membrane. Biomarker of anti-basement membrane glomerulonephritis. Orthologous to human SLIT2 (slit guidance ligand 2); PARTICIPATES IN glypican signaling pathway; INTERACTS WITH (+)-pilocarpine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: slit (Drosophila) homolog 2; slit homolog 2 (Drosophila); slit homolog 2 protein; slit-2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21462,616,337 - 62,955,934 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1462,617,067 - 62,955,948 (-)Ensembl
Rnor_6.01466,831,848 - 67,171,491 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1466,831,848 - 67,170,361 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01466,864,065 - 67,202,691 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41467,546,283 - 67,891,840 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11467,624,799 - 67,894,206 (-)NCBI
Celera1461,665,582 - 62,001,006 (-)NCBICelera
Cytogenetic Map14q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-methylcholanthrene  (ISO)
3-Nitrobenzanthrone  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
7,12-dimethyltetraphene  (ISO)
acetaldehyde  (ISO)
acetamide  (EXP)
acrylamide  (EXP,ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
atrazine  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cyproconazole  (ISO)
cytarabine  (ISO)
deguelin  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
fenvalerate  (EXP)
flusilazole  (ISO)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
hexaconazole  (ISO)
L-methionine  (ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
mercury dibromide  (ISO)
methapyrilene  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
mifepristone  (EXP)
N-acetyl-1,4-benzoquinone imine  (ISO)
nickel sulfate  (ISO)
nitrofen  (EXP)
O-methyleugenol  (ISO)
oxaliplatin  (EXP)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
PD 0325901  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
pyrimidifen  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
temozolomide  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
thapsigargin  (ISO)
thifluzamide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (EXP)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aortic valve morphogenesis  (ISO)
apoptotic process involved in luteolysis  (IEA,ISO)
axon extension involved in axon guidance  (IEA,ISO)
axon guidance  (IBA,ISO)
axonogenesis  (ISO)
brain development  (IEP)
branching morphogenesis of an epithelial tube  (IEA,ISO)
cell differentiation  (IEA)
cell migration involved in sprouting angiogenesis  (IEA,ISO)
cell-cell adhesion  (ISO)
cellular response to heparin  (IEA,ISO)
cellular response to hormone stimulus  (IEA,ISO)
chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration  (ISO)
chemorepulsion involved in postnatal olfactory bulb interneuron migration  (IEA,ISO)
corticospinal neuron axon guidance through spinal cord  (IEA,ISO)
dorsal/ventral axon guidance  (ISO)
follicle-stimulating hormone signaling pathway  (IEA)
generation of neurons  (IEA)
in utero embryonic development  (ISO)
induction of negative chemotaxis  (IEA,ISO)
kidney development  (ISO)
mammary duct terminal end bud growth  (ISO)
mammary gland duct morphogenesis  (ISO)
metanephros development  (ISO)
motor neuron axon guidance  (IEA,ISO)
negative chemotaxis  (IBA,ISO)
negative regulation of actin filament polymerization  (IEA,ISO)
negative regulation of axon extension  (ISO)
negative regulation of catalytic activity  (IEA)
negative regulation of cell growth  (IBA,IEA,ISO)
negative regulation of cell migration  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of cellular response to growth factor stimulus  (IEA,ISO)
negative regulation of chemokine-mediated signaling pathway  (IEA,ISO)
negative regulation of endothelial cell migration  (IEA,ISO)
negative regulation of gene expression  (ISO)
negative regulation of inflammatory response  (IMP)
negative regulation of lamellipodium assembly  (IEA,ISO)
negative regulation of leukocyte chemotaxis  (ISO)
negative regulation of monocyte chemotaxis  (IDA)
negative regulation of mononuclear cell migration  (IEA,ISO)
negative regulation of neutrophil chemotaxis  (IEA,ISO)
negative regulation of protein phosphorylation  (IEA,ISO)
negative regulation of retinal ganglion cell axon guidance  (IEA,ISO)
negative regulation of small GTPase mediated signal transduction  (IEA,ISO)
negative regulation of smooth muscle cell chemotaxis  (IEA,ISO)
negative regulation of smooth muscle cell migration  (ISO)
negative regulation of vascular permeability  (IEA,ISO)
nervous system development  (IEA)
neuron projection morphogenesis  (ISO)
olfactory bulb development  (ISO)
positive regulation of apoptotic process  (IEA,ISO)
pulmonary valve morphogenesis  (ISO)
response to cortisol  (IEA,ISO)
response to nutrient levels  (IEP)
retinal ganglion cell axon guidance  (IBA,IEA,ISO)
Roundabout signaling pathway  (IEA,ISO)
spinal cord development  (IEP)
telencephalon cell migration  (ISO)
ureteric bud development  (IEA,ISO)
ventricular septum morphogenesis  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10197527   PMID:10864954   PMID:10975526   PMID:11309622   PMID:11375980   PMID:11748139   PMID:11804570   PMID:11804571   PMID:12097499   PMID:12879062   PMID:12954717   PMID:14605369  
PMID:14960623   PMID:15091338   PMID:15130495   PMID:15207848   PMID:15737744   PMID:16377904   PMID:16439476   PMID:16439689   PMID:16828733   PMID:16840550   PMID:16885222   PMID:17062560  
PMID:17848514   PMID:18345009   PMID:18566128   PMID:18755265   PMID:18829537   PMID:19005219   PMID:19033678   PMID:19056867   PMID:19351956   PMID:19498462   PMID:19759280   PMID:20153733  
PMID:21187345   PMID:22206666   PMID:22433866   PMID:22677040   PMID:23361995   PMID:23376485   PMID:24006456   PMID:25691540   PMID:26026792   PMID:26764532   PMID:27686659   PMID:27893610  
PMID:28260032   PMID:28973045   PMID:31964527  


Genomics

Comparative Map Data
Slit2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21462,616,337 - 62,955,934 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1462,617,067 - 62,955,948 (-)Ensembl
Rnor_6.01466,831,848 - 67,171,491 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1466,831,848 - 67,170,361 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01466,864,065 - 67,202,691 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41467,546,283 - 67,891,840 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11467,624,799 - 67,894,206 (-)NCBI
Celera1461,665,582 - 62,001,006 (-)NCBICelera
Cytogenetic Map14q11NCBI
SLIT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl420,251,905 - 20,620,561 (+)EnsemblGRCh38hg38GRCh38
GRCh38420,251,905 - 20,620,561 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37420,253,528 - 20,622,184 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36419,864,333 - 20,229,886 (+)NCBINCBI36hg18NCBI36
Build 34419,931,503 - 20,297,057NCBI
Celera420,712,350 - 21,077,291 (+)NCBI
Cytogenetic Map4p15.31NCBI
HuRef419,604,199 - 19,969,514 (+)NCBIHuRef
CHM1_1420,253,276 - 20,618,733 (+)NCBICHM1_1
Slit2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39548,138,633 - 48,465,077 (+)NCBIGRCm39mm39
GRCm39 Ensembl548,140,480 - 48,465,075 (+)Ensembl
GRCm38547,981,291 - 48,307,735 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl547,983,138 - 48,307,733 (+)EnsemblGRCm38mm10GRCm38
MGSCv37548,374,394 - 48,697,017 (+)NCBIGRCm37mm9NCBIm37
MGSCv36548,273,041 - 48,593,759 (+)NCBImm8
Celera545,381,658 - 45,708,133 (+)NCBICelera
Cytogenetic Map5B3NCBI
Slit2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554803,984,586 - 4,313,908 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554803,982,977 - 4,314,160 (-)NCBIChiLan1.0ChiLan1.0
SLIT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1419,946,369 - 20,314,656 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl420,158,952 - 20,314,656 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0414,654,448 - 15,023,708 (+)NCBIMhudiblu_PPA_v0panPan3
SLIT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1388,964,707 - 89,311,817 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl388,966,232 - 89,312,955 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha391,423,926 - 91,773,328 (-)NCBI
ROS_Cfam_1.0389,948,981 - 90,297,465 (-)NCBI
UMICH_Zoey_3.1389,094,518 - 89,443,898 (-)NCBI
UNSW_CanFamBas_1.0389,179,097 - 89,528,769 (-)NCBI
UU_Cfam_GSD_1.0389,562,948 - 89,912,569 (-)NCBI
Slit2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528554,409,516 - 54,746,912 (-)NCBI
SpeTri2.0NW_0049364778,111,212 - 8,448,567 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLIT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl814,756,619 - 15,149,510 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1814,758,426 - 15,149,515 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2814,998,769 - 15,257,500 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLIT2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12729,650,589 - 30,020,105 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2729,650,337 - 29,803,612 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604776,267,556 - 76,654,726 (-)NCBIVero_WHO_p1.0
Slit2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475511,470,810 - 11,819,800 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D14Got156  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21462,921,501 - 62,921,630 (+)MAPPERmRatBN7.2
Rnor_6.01467,136,878 - 67,137,006NCBIRnor6.0
Rnor_5.01467,168,120 - 67,168,248UniSTSRnor5.0
RGSC_v3.41467,858,616 - 67,858,744UniSTSRGSC3.4
Celera1461,967,928 - 61,968,056UniSTS
Cytogenetic Map14q11UniSTS
BE116869  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21462,912,713 - 62,912,877 (+)MAPPERmRatBN7.2
Rnor_6.01467,128,141 - 67,128,304NCBIRnor6.0
Rnor_5.01467,159,383 - 67,159,546UniSTSRnor5.0
RGSC_v3.41467,848,360 - 67,848,523UniSTSRGSC3.4
Celera1461,959,747 - 61,959,910UniSTS
RH 3.4 Map14475.6UniSTS
Cytogenetic Map14q11UniSTS
RH134686  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21462,617,915 - 62,618,105 (+)MAPPERmRatBN7.2
Rnor_6.01466,832,697 - 66,832,886NCBIRnor6.0
Rnor_5.01466,864,914 - 66,865,103UniSTSRnor5.0
RGSC_v3.41467,547,132 - 67,547,321UniSTSRGSC3.4
Celera1461,666,431 - 61,666,620UniSTS
RH 3.4 Map14478.1UniSTS
Cytogenetic Map14q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:577
Count of miRNA genes:279
Interacting mature miRNAs:355
Transcripts:ENSRNOT00000005477
Prediction methods:Microtar, Miranda, 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 20 60 35 27 11
Low 1 20 24 10 17 10 7 7 14 10 7
Below cutoff 2 3 32 30 2 30 1 4 4 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005477   ⟹   ENSRNOP00000005477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1462,617,067 - 62,954,577 (-)Ensembl
Rnor_6.0 Ensembl1466,831,848 - 67,170,361 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081601   ⟹   ENSRNOP00000075258
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1462,617,067 - 62,954,577 (-)Ensembl
Rnor_6.0 Ensembl1466,831,877 - 66,978,499 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098728   ⟹   ENSRNOP00000094520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1462,617,067 - 62,954,577 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101023   ⟹   ENSRNOP00000089142
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1462,618,940 - 62,955,948 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117062   ⟹   ENSRNOP00000096652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1462,787,996 - 62,955,948 (-)Ensembl
RefSeq Acc Id: NM_022632   ⟹   NP_072154
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21462,617,067 - 62,954,577 (-)NCBI
Rnor_6.01466,831,848 - 67,170,361 (-)NCBI
Rnor_5.01466,864,065 - 67,202,691 (-)NCBI
RGSC_v3.41467,546,283 - 67,891,840 (-)RGD
Celera1461,665,582 - 62,001,006 (-)RGD
Sequence:
RefSeq Acc Id: XM_017599275   ⟹   XP_017454764
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21462,616,337 - 62,955,934 (-)NCBI
Rnor_6.01466,831,849 - 67,171,491 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599276   ⟹   XP_017454765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21462,616,337 - 62,955,934 (-)NCBI
Rnor_6.01466,831,849 - 67,171,491 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599277   ⟹   XP_017454766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21462,616,337 - 62,955,934 (-)NCBI
Rnor_6.01466,831,849 - 67,171,491 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599278   ⟹   XP_017454767
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21462,616,337 - 62,955,934 (-)NCBI
Rnor_6.01466,831,849 - 67,171,491 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039092141   ⟹   XP_038948069
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21462,616,337 - 62,955,934 (-)NCBI
RefSeq Acc Id: XM_039092142   ⟹   XP_038948070
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21462,616,337 - 62,955,934 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_072154   ⟸   NM_022632
- Peptide Label: precursor
- UniProtKB: F1MA79 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454767   ⟸   XM_017599278
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017454766   ⟸   XM_017599277
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017454765   ⟸   XM_017599276
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017454764   ⟸   XM_017599275
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000075258   ⟸   ENSRNOT00000081601
RefSeq Acc Id: ENSRNOP00000005477   ⟸   ENSRNOT00000005477
RefSeq Acc Id: XP_038948069   ⟸   XM_039092141
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948070   ⟸   XM_039092142
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000094520   ⟸   ENSRNOT00000098728
RefSeq Acc Id: ENSRNOP00000089142   ⟸   ENSRNOT00000101023
RefSeq Acc Id: ENSRNOP00000096652   ⟸   ENSRNOT00000117062
Protein Domains
CTCK   EGF-like   LAM_G_DOMAIN   LRRCT   LRRNT

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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)
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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:69310 AgrOrtholog
Ensembl Genes ENSRNOG00000003840 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005477 UniProtKB/TrEMBL
  ENSRNOP00000075258 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005477 UniProtKB/TrEMBL
  ENSRNOT00000081601 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ConA-like_subgrp UniProtKB/TrEMBL
  Cys-rich_flank_reg_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cys_knot_C UniProtKB/TrEMBL
  EG-like_dom UniProtKB/TrEMBL
  EGF-like_Ca-bd UniProtKB/TrEMBL
  EGF-like_CS UniProtKB/TrEMBL
  EGF-type_Asp/Asn_hydroxyl_site UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/TrEMBL
  Fol_N UniProtKB/TrEMBL
  FSH_rcpt UniProtKB/Swiss-Prot
  Laminin_G UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:360272 UniProtKB/TrEMBL
NCBI Gene 360272 ENTREZGENE
Pfam EGF UniProtKB/TrEMBL
  hEGF UniProtKB/TrEMBL
  Laminin_G_1 UniProtKB/TrEMBL
  LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slit2 PhenoGen
PRINTS FSHRECEPTOR UniProtKB/Swiss-Prot
PROSITE ASX_HYDROXYL UniProtKB/TrEMBL
  CTCK_1 UniProtKB/TrEMBL
  CTCK_2 UniProtKB/TrEMBL
  EGF_1 UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/TrEMBL
  LRR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  FOLN UniProtKB/TrEMBL
  LamG UniProtKB/TrEMBL
  LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRRNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00041 UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
UniProt A0A0G2KA49_RAT UniProtKB/TrEMBL
  F1MA79 ENTREZGENE, UniProtKB/TrEMBL
  Q9WVC1 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-01 Slit2  slit guidance ligand 2  Slit2  slit homolog 2 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Slit2  slit homolog 2 (Drosophila)      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference