Robo1 (roundabout guidance receptor 1) - Rat Genome Database

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Gene: Robo1 (roundabout guidance receptor 1) Rattus norvegicus
Analyze
Symbol: Robo1
Name: roundabout guidance receptor 1
RGD ID: 61941
Description: Enables axon guidance receptor activity. Involved in axon midline choice point recognition; regulation of dendrite morphogenesis; and spinal cord development. Located in axon and neuronal cell body. Biomarker of lung non-small cell carcinoma. Orthologous to human ROBO1 (roundabout guidance receptor 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC102551586; LOC683548; roundabout homolog 1; roundabout, axon guidance receptor, homolog 1; similar to roundabout homolog 1; uncharacterized LOC102551586
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Robo1Tn(sb-T2/Bart3)2.327Mcwi  
Genetic Models: F344-Robo1Tn(sb-T2/Bart3)2.327Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21110,580,863 - 11,621,672 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1110,580,908 - 11,620,203 (+)Ensembl
Rnor_6.0119,079,291 - 10,146,302 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl119,642,365 - 10,143,317 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01113,314,508 - 13,808,775 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41110,784,947 - 11,720,646 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11110,784,946 - 11,720,646 (+)NCBI
Celera1110,598,877 - 11,659,942 (+)NCBICelera
Cytogenetic Map11p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3-methylcholanthrene  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
androgen antagonist  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP)
Butylparaben  (EXP)
carbon nanotube  (ISO)
chrysene  (ISO)
clobetasol  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
DDE  (EXP)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
entinostat  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
folic acid  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
linuron  (EXP)
manganese(II) chloride  (EXP)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (ISO)
nickel dichloride  (ISO)
nitrofen  (EXP)
paracetamol  (EXP,ISO)
permethrin  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (ISO)
quercetin  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tebufenpyrad  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (IEA,ISO)
aorta development  (ISO)
aortic valve morphogenesis  (ISO)
axon guidance  (IDA,ISO)
axon midline choice point recognition  (IEA,IEP,ISO)
cell migration involved in sprouting angiogenesis  (IEA,ISO)
central nervous system development  (IEP)
chemorepulsion involved in postnatal olfactory bulb interneuron migration  (IEA,ISO)
coronary vasculature development  (ISO)
endocardial cushion formation  (ISO)
heart development  (ISO)
homophilic cell adhesion via plasma membrane adhesion molecules  (IBA,IEA,ISO)
kidney development  (ISO)
mammary duct terminal end bud growth  (ISO)
negative regulation of cell migration  (IEA,ISO,ISS)
negative regulation of cell population proliferation  (ISO)
negative regulation of chemokine-mediated signaling pathway  (IEA,ISO)
negative regulation of gene expression  (ISO)
negative regulation of mammary gland epithelial cell proliferation  (IEA,ISO)
negative regulation of negative chemotaxis  (IEA,ISO)
olfactory bulb interneuron development  (ISO)
outflow tract septum morphogenesis  (ISO)
positive regulation of axonogenesis  (IEA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of MAP kinase activity  (IEA,ISO)
positive regulation of Notch signaling pathway involved in heart induction  (ISO)
positive regulation of Rho protein signal transduction  (IEA,ISO,ISS)
positive regulation of vascular endothelial growth factor signaling pathway  (IEA,ISO)
pulmonary valve morphogenesis  (ISO)
regulation of dendrite morphogenesis  (IMP)
Roundabout signaling pathway  (IEA,ISO,ISS)
spinal cord development  (IEP)
synapse organization  (IBA)
ventricular septum development  (ISO)
ventricular septum morphogenesis  (ISO)

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10433822   PMID:11222645   PMID:11404413   PMID:11672528   PMID:11748139   PMID:12504588   PMID:15084255   PMID:15091338   PMID:16254601   PMID:16439476   PMID:17360927   PMID:17848514  
PMID:18566128   PMID:18829537   PMID:19351956   PMID:19783284   PMID:21385766   PMID:25691540   PMID:25807483   PMID:26529257   PMID:26764532   PMID:27686659   PMID:27893610   PMID:28973045  


Genomics

Comparative Map Data
Robo1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21110,580,863 - 11,621,672 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1110,580,908 - 11,620,203 (+)Ensembl
Rnor_6.0119,079,291 - 10,146,302 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl119,642,365 - 10,143,317 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01113,314,508 - 13,808,775 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41110,784,947 - 11,720,646 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11110,784,946 - 11,720,646 (+)NCBI
Celera1110,598,877 - 11,659,942 (+)NCBICelera
Cytogenetic Map11p11NCBI
ROBO1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl378,597,239 - 79,767,998 (-)EnsemblGRCh38hg38GRCh38
GRCh38378,597,239 - 79,767,998 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37378,646,389 - 79,817,148 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36378,729,080 - 79,721,751 (-)NCBINCBI36hg18NCBI36
Build 34378,729,079 - 79,721,751NCBI
Celera379,390,331 - 80,561,510 (-)NCBI
Cytogenetic Map3p12.3NCBI
HuRef378,666,127 - 79,837,569 (-)NCBIHuRef
CHM1_1378,599,244 - 79,770,223 (-)NCBICHM1_1
Robo1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391671,824,406 - 72,844,379 (+)NCBIGRCm39mm39
GRCm39 Ensembl1672,105,194 - 72,842,983 (+)Ensembl
GRCm381672,027,518 - 73,047,491 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1672,308,306 - 73,046,095 (+)EnsemblGRCm38mm10GRCm38
MGSCv371672,663,394 - 73,046,345 (+)NCBIGRCm37mm9NCBIm37
MGSCv361672,546,574 - 72,928,773 (+)NCBImm8
Celera1672,912,535 - 73,307,241 (+)NCBICelera
Cytogenetic Map16C3.1NCBI
Robo1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540713,107,235 - 13,487,053 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540712,593,911 - 13,485,723 (+)NCBIChiLan1.0ChiLan1.0
ROBO1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1380,579,716 - 81,001,219 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl380,581,388 - 81,569,308 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0378,707,802 - 79,876,519 (-)NCBIMhudiblu_PPA_v0panPan3
ROBO1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1318,082,363 - 8,594,623 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl317,626,126 - 8,593,728 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha317,536,253 - 8,593,279 (+)NCBI
ROS_Cfam_1.0317,481,760 - 8,614,235 (+)NCBI
UMICH_Zoey_3.1317,442,809 - 8,564,392 (+)NCBI
UNSW_CanFamBas_1.0317,499,515 - 8,626,174 (+)NCBI
UU_Cfam_GSD_1.0317,883,361 - 9,008,850 (+)NCBI
Robo1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049718,782,876 - 9,791,545 (+)NCBI
SpeTri2.0NW_0049365054,329,428 - 4,711,310 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ROBO1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13175,505,366 - 176,479,482 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113175,348,223 - 176,479,482 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213186,417,282 - 186,884,529 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ROBO1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12297,178,093 - 98,363,647 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2298,222,891 - 98,363,219 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604168,583,685 - 69,736,220 (-)NCBIVero_WHO_p1.0
Robo1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248744,234,640 - 5,359,333 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D11Rat80  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21110,853,326 - 10,853,485 (+)MAPPERmRatBN7.2
Rnor_6.0119,353,931 - 9,354,089NCBIRnor6.0
Rnor_5.01113,033,392 - 13,033,550UniSTSRnor5.0
RGSC_v3.41110,929,300 - 10,929,459RGDRGSC3.4
RGSC_v3.41110,929,301 - 10,929,459UniSTSRGSC3.4
RGSC_v3.11110,929,301 - 10,929,459RGD
Celera1110,738,560 - 10,738,718UniSTS
RH 3.4 Map1155.6UniSTS
RH 3.4 Map1155.6RGD
RH 2.0 Map11699.1RGD
Cytogenetic Map11p11UniSTS
D11Got12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21110,878,704 - 10,878,889 (+)MAPPERmRatBN7.2
Rnor_6.0119,379,473 - 9,379,657NCBIRnor6.0
Rnor_5.01113,058,934 - 13,059,118UniSTSRnor5.0
RGSC_v3.41110,954,676 - 10,954,861RGDRGSC3.4
RGSC_v3.41110,954,677 - 10,954,861UniSTSRGSC3.4
RGSC_v3.11110,954,677 - 10,954,861RGD
Celera1110,763,938 - 10,764,122UniSTS
RH 3.4 Map1157.1UniSTS
RH 3.4 Map1157.1RGD
RH 2.0 Map11691.9RGD
Cytogenetic Map11p11UniSTS
D11Got11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21110,996,010 - 10,996,213 (+)MAPPERmRatBN7.2
Rnor_6.0119,513,253 - 9,513,455NCBIRnor6.0
Rnor_5.01113,186,038 - 13,186,240UniSTSRnor5.0
RGSC_v3.41111,071,150 - 11,071,353RGDRGSC3.4
RGSC_v3.41111,071,151 - 11,071,353UniSTSRGSC3.4
RGSC_v3.11111,071,150 - 11,071,353RGD
Celera1110,880,219 - 10,880,421UniSTS
RH 2.0 Map11701.2RGD
Cytogenetic Map11p11UniSTS
BF386615  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21111,123,162 - 11,123,338 (+)MAPPERmRatBN7.2
Rnor_6.0119,627,493 - 9,627,668NCBIRnor6.0
Rnor_5.01113,299,572 - 13,299,747UniSTSRnor5.0
RGSC_v3.41111,199,161 - 11,199,336UniSTSRGSC3.4
Celera1111,000,733 - 11,000,908UniSTS
Cytogenetic Map11p11UniSTS
BF386668  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21111,450,901 - 11,451,076 (+)MAPPERmRatBN7.2
Rnor_6.0119,972,564 - 9,972,738NCBIRnor6.0
Rnor_5.01113,639,815 - 13,639,989UniSTSRnor5.0
RGSC_v3.41111,541,525 - 11,541,699UniSTSRGSC3.4
Celera1111,321,282 - 11,321,456UniSTS
Cytogenetic Map11p11UniSTS
BF390471  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21111,353,350 - 11,353,541 (+)MAPPERmRatBN7.2
Rnor_6.0119,873,986 - 9,874,176NCBIRnor6.0
Rnor_5.01113,541,478 - 13,541,668UniSTSRnor5.0
RGSC_v3.41111,442,349 - 11,442,539UniSTSRGSC3.4
Celera1111,229,410 - 11,229,600UniSTS
Cytogenetic Map11p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)11121836709Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat


Genetic Models
This gene Robo1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:18
Count of miRNA genes:17
Interacting mature miRNAs:18
Transcripts:ENSRNOT00000042384
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 16 14 6 6 70 22 30 1
Low 1 26 42 34 19 34 8 9 4 13 11 10 8
Below cutoff 2 1 1 1 1 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_022188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768533 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768534 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF041082 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000042384   ⟹   ENSRNOP00000044134
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1110,580,908 - 11,620,203 (+)Ensembl
Rnor_6.0 Ensembl119,642,413 - 10,143,317 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087080   ⟹   ENSRNOP00000069709
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1111,137,915 - 11,617,375 (+)Ensembl
Rnor_6.0 Ensembl119,642,365 - 10,141,977 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104951   ⟹   ENSRNOP00000096544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1111,227,474 - 11,620,203 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112268   ⟹   ENSRNOP00000082395
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1111,227,489 - 11,620,203 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117698   ⟹   ENSRNOP00000085459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1111,227,258 - 11,620,203 (+)Ensembl
RefSeq Acc Id: NM_022188   ⟹   NP_071524
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21110,711,946 - 11,618,688 (+)NCBI
Rnor_6.0119,209,568 - 10,143,317 (+)NCBI
Rnor_5.01113,314,508 - 13,808,775 (+)NCBI
RGSC_v3.41110,784,947 - 11,720,646 (+)RGD
Celera1110,598,877 - 11,659,942 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768533   ⟹   XP_008766755
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,228,112 - 11,620,420 (+)NCBI
Rnor_6.0119,732,020 - 10,145,049 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768534   ⟹   XP_008766756
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,228,112 - 11,620,420 (+)NCBI
Rnor_6.0119,732,020 - 10,145,049 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008768536   ⟹   XP_008766758
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,228,112 - 11,620,420 (+)NCBI
Rnor_6.0119,732,020 - 10,145,049 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598056   ⟹   XP_017453545
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,137,900 - 11,621,672 (+)NCBI
Rnor_6.0119,642,005 - 10,146,302 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598057   ⟹   XP_017453546
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,137,900 - 11,621,672 (+)NCBI
Rnor_6.0119,642,005 - 10,146,302 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598058   ⟹   XP_017453547
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,137,900 - 11,621,672 (+)NCBI
Rnor_6.0119,642,005 - 10,146,302 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598059   ⟹   XP_017453548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21110,580,863 - 11,621,672 (+)NCBI
Rnor_6.0119,079,291 - 10,146,302 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598060   ⟹   XP_017453549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21110,580,863 - 11,621,672 (+)NCBI
Rnor_6.0119,079,291 - 10,146,302 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598061   ⟹   XP_017453550
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21110,870,672 - 11,621,672 (+)NCBI
Rnor_6.0119,371,435 - 10,146,302 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598062   ⟹   XP_017453551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,137,900 - 11,621,672 (+)NCBI
Rnor_6.0119,642,005 - 10,146,302 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598063   ⟹   XP_017453552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,228,112 - 11,620,420 (+)NCBI
Rnor_6.0119,732,020 - 10,145,049 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017598064   ⟹   XP_017453553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,137,900 - 11,621,672 (+)NCBI
Rnor_6.0119,642,005 - 10,146,302 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088605   ⟹   XP_038944533
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21110,870,671 - 11,621,672 (+)NCBI
RefSeq Acc Id: XM_039088607   ⟹   XP_038944535
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21111,417,344 - 11,621,672 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_071524   ⟸   NM_022188
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_008766755   ⟸   XM_008768533
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_008766756   ⟸   XM_008768534
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_008766758   ⟸   XM_008768536
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017453548   ⟸   XM_017598059
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453549   ⟸   XM_017598060
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017453550   ⟸   XM_017598061
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017453545   ⟸   XM_017598056
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017453551   ⟸   XM_017598062
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017453547   ⟸   XM_017598058
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017453546   ⟸   XM_017598057
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017453553   ⟸   XM_017598064
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017453552   ⟸   XM_017598063
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: ENSRNOP00000069709   ⟸   ENSRNOT00000087080
RefSeq Acc Id: ENSRNOP00000044134   ⟸   ENSRNOT00000042384
RefSeq Acc Id: XP_038944533   ⟸   XM_039088605
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038944535   ⟸   XM_039088607
- Peptide Label: isoform X13
RefSeq Acc Id: ENSRNOP00000082395   ⟸   ENSRNOT00000112268
RefSeq Acc Id: ENSRNOP00000096544   ⟸   ENSRNOT00000104951
RefSeq Acc Id: ENSRNOP00000085459   ⟸   ENSRNOT00000117698
Protein Domains
Fibronectin type-III   Ig-like   Ig-like C2-type

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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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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)
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)
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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)
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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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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:61941 AgrOrtholog
Ensembl Genes ENSRNOG00000029614 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000044134 UniProtKB/TrEMBL
  ENSRNOP00000069709 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042384 UniProtKB/TrEMBL
  ENSRNOT00000087080 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Robo1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:58946 UniProtKB/Swiss-Prot
NCBI Gene 58946 ENTREZGENE
PANTHER PTHR12231:SF243 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Robo1 PhenoGen
PROSITE FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGv UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Transposagen Robo1 Transposagen
UniProt A0A0G2JW21_RAT UniProtKB/TrEMBL
  F1LQI2_RAT UniProtKB/TrEMBL
  O55005 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Robo1  roundabout guidance receptor 1  LOC102551586  uncharacterized LOC102551586  Data Merged 737654 PROVISIONAL
2013-12-17 LOC102551586  uncharacterized LOC102551586      Symbol and Name status set to provisional 70820 PROVISIONAL
2013-04-17 Robo1  roundabout, axon guidance receptor, homolog 1 (Drosophila)  LOC683548  similar to roundabout homolog 1  Data Merged 737654 PROVISIONAL
2006-11-19 LOC683548  similar to roundabout homolog 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Robo1  roundabout homolog 1 (Drosophila)       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_product member of the subfamily of immunoglobulin superfamily proteins 61733