Cd80 (Cd80 molecule) - Rat Genome Database

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Gene: Cd80 (Cd80 molecule) Rattus norvegicus
Analyze
Symbol: Cd80
Name: Cd80 molecule
RGD ID: 2314
Description: Predicted to enable coreceptor activity. Involved in positive regulation of T cell proliferation. Located in cell surface. Used to study adult T-cell leukemia; anti-basement membrane glomerulonephritis; high grade glioma; and periodontal disease. Biomarker of kidney failure. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus. Orthologous to human CD80 (CD80 molecule); PARTICIPATES IN allograft rejection pathway; autoimmune thyroiditis pathway; graft-versus-host disease pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; aldosterone; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: B7-1; Cd80 a rat homolog of the human CD28/CTLA - 4 ligand (B7-1); CD80 antigen; CD80-like; LOC100360171; T-lymphocyte activation antigen CD80
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
mRatBN7.21162,254,543 - 62,293,414 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1162,254,624 - 62,292,030 (-)Ensembl
Rnor_6.01164,815,201 - 64,855,293 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1164,827,635 - 64,855,353 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01167,255,123 - 67,291,544 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41164,045,358 - 64,070,072 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11164,102,946 - 64,127,661 (-)NCBI
Celera1161,768,874 - 61,793,351 (-)NCBICelera
RH 3.4 Map11500.9RGD
Cytogenetic Map11q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,2-dichloroethane  (ISO)
1,4-benzoquinone  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-phenylprop-2-enal  (ISO)
4-methylhistamine  (ISO)
5-aza-2'-deoxycytidine  (ISO)
7,12-dimethyltetraphene  (ISO)
9-cis-retinoic acid  (ISO)
adenosine 5'-[gamma-thio]triphosphate  (ISO)
aldosterone  (EXP)
all-trans-retinoic acid  (ISO)
alpha-hexylcinnamaldehyde  (ISO)
aluminium hydroxide  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
Bandrowski's base  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucan  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
bucladesine  (ISO)
calcitriol  (ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
carmustine  (ISO)
chromium(6+)  (ISO)
clobetasol  (ISO)
clodronic acid  (ISO)
cortisol  (ISO)
daidzein  (ISO)
decabromodiphenyl ether  (EXP)
deoxynivalenol  (ISO)
diethyl maleate  (ISO)
diisononyl phthalate  (ISO)
Dimaprit  (ISO)
dioxygen  (ISO)
endosulfan  (EXP)
eplerenone  (EXP)
estriol  (ISO)
ethyl methanesulfonate  (ISO)
famotidine  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
glucuronoxylomannan  (ISO)
helenalin  (ISO)
histamine  (ISO)
hydroquinone  (ISO)
hydroxycitronellal  (ISO)
imidurea  (ISO)
imiquimod  (ISO)
indirubin-3'-monoxime  (ISO)
indole-3-methanol  (ISO)
ionomycin  (ISO)
irinotecan  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
lupane  (ISO)
methyl methanesulfonate  (ISO)
molybdenum trichloride  (ISO)
monosodium L-glutamate  (ISO)
muramyl dipeptide  (ISO)
N-nitrosodiethylamine  (EXP)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (ISO)
naproxen  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel sulfate  (ISO)
niclosamide  (ISO)
nystatin  (ISO)
paraquat  (EXP)
PCB138  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
poly(I:C)  (ISO)
polymyxin B2  (ISO)
procyanidin B3  (ISO)
progesterone  (ISO)
protein kinase inhibitor  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
ranitidine  (ISO)
resveratrol  (ISO)
Senkirkine  (EXP)
silicon dioxide  (ISO)
simvastatin  (EXP)
sirolimus  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
succimer  (ISO)
sumatriptan  (EXP)
tacrolimus hydrate  (ISO)
thioacetamide  (EXP)
Triptolide  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
zinc protoporphyrin  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Cao J, etal., Int Immunopharmacol. 2012 Aug 20.
2. Collins CB, etal., Gut. 2012 Aug;61(8):1154-62. Epub 2011 Nov 7.
3. Dolff S, etal., Arthritis Res Ther. 2010;12(4):R150. Epub 2010 Jul 23.
4. Duncan DS and Miller SD, PLoS One. 2011 Apr 8;6(4):e18548.
5. Freeman CM, etal., Am J Respir Crit Care Med. 2009 Dec 15;180(12):1179-88. Epub 2009 Sep 3.
6. Gallon L, etal., J Immunol. 1997 Nov 1;159(9):4212-6.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Hanabuchi S, etal., J Virol. 2000 Jan;74(1):428-35.
10. Haspot F, etal., Blood 2002 Mar 15;99(6):2228-34.
11. Huang Y, etal., Inflammation. 2018 Feb;41(1):232-239. doi: 10.1007/s10753-017-0681-7.
12. Jeong YI, etal., Biochem Biophys Res Commun. 2011 Apr 22;407(4):793-800. Epub 2011 Apr 1.
13. Judge TA, etal., Int Immunol 1995 Feb;7(2):171-8.
14. Kawai T, etal., J Immunol. 2000 Feb 15;164(4):2102-9.
15. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
16. Lee-Chang C, etal., Clin Immunol. 2011 Apr;139(1):12-20.
17. Li Q, etal., Cell Immunol. 2011;272(1):53-60. Epub 2011 Sep 29.
18. Lumsden JM, etal., J Immunol. 2000 Jan 1;164(1):79-85.
19. Maeda K, etal., Int Immunol 1997 Jul;9(7):993-1000.
20. MGD data from the GO Consortium
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Page K, etal., J Innate Immun. 2011;3(2):167-79. Epub 2010 Nov 5.
23. Pang S, etal., Eur J Immunol. 2009 Oct;39(10):2716-24.
24. Pechhold K, etal., J Immunol. 2001 Feb 15;166(4):2531-9.
25. Phares TW, etal., J Immunol. 2010 Nov 1;185(9):5607-18. Epub 2010 Sep 27.
26. Pipeline to import KEGG annotations from KEGG into RGD
27. Reynolds J, etal., J Clin Invest. 2000 Mar;105(5):643-51.
28. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
29. RGD automated import pipeline for gene-chemical interactions
30. RGD comprehensive gene curation
31. Roquilly A, etal., PLoS One. 2010 Oct 7;5(10):e13228.
32. Shao H, etal., Curr Eye Res 2002 Nov;25(5):271-7.
33. Sharma S, etal., Pediatr Allergy Immunol. 2012 Jun;23(4):315-23. doi: 10.1111/j.1399-3038.2011.01243.x. Epub 2011 Dec 23.
34. Smith M, etal., Transplant Proc. 2008 Jun;40(5):1598-603.
35. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
36. Toapanta FR and Ross TM, Respir Res. 2009 Nov 18;10:112.
37. Tobita K, etal., Anim Sci J. 2010 Dec;81(6):699-705. doi: 10.1111/j.1740-0929.2010.00795.x. Epub 2010 Oct 7.
38. Visse E, etal., Cancer Gene Ther 1999 Jan-Feb;6(1):37-44.
39. Wu K, etal., Cell Mol Immunol. 2006 Jun;3(3):213-20.
40. Zhang F, etal., Clin Exp Immunol. 2011 May;164(2):256-64. doi: 10.1111/j.1365-2249.2011.04328.x. Epub 2011 Feb 24.
Additional References at PubMed
PMID:1385153   PMID:7544393   PMID:8566034   PMID:9915850   PMID:14560001   PMID:15240714   PMID:15314074   PMID:15568026   PMID:16475216   PMID:17068184   PMID:17376836   PMID:17429054  
PMID:17457373   PMID:18089391   PMID:18684012   PMID:19047410   PMID:23793062   PMID:23981064   PMID:29360807   PMID:32733939  


Genomics

Comparative Map Data
Cd80
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21162,254,543 - 62,293,414 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1162,254,624 - 62,292,030 (-)Ensembl
Rnor_6.01164,815,201 - 64,855,293 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1164,827,635 - 64,855,353 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01167,255,123 - 67,291,544 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41164,045,358 - 64,070,072 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11164,102,946 - 64,127,661 (-)NCBI
Celera1161,768,874 - 61,793,351 (-)NCBICelera
RH 3.4 Map11500.9RGD
Cytogenetic Map11q21NCBI
CD80
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3119,524,293 - 119,559,614 (-)EnsemblGRCh38hg38GRCh38
GRCh383119,524,293 - 119,559,614 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373119,243,140 - 119,278,461 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363120,725,830 - 120,761,171 (-)NCBINCBI36hg18NCBI36
Build 343120,725,831 - 120,761,139NCBI
Celera3117,651,693 - 117,687,039 (-)NCBI
Cytogenetic Map3q13.33NCBI
HuRef3116,618,830 - 116,654,199 (-)NCBIHuRef
CHM1_13119,206,623 - 119,241,981 (-)NCBICHM1_1
Cd80
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391638,277,793 - 38,316,682 (+)NCBIGRCm39mm39
GRCm39 Ensembl1638,275,923 - 38,316,697 (+)Ensembl
GRCm381638,457,430 - 38,495,958 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1638,455,561 - 38,496,335 (+)EnsemblGRCm38mm10GRCm38
MGSCv371638,459,013 - 38,487,015 (+)NCBIGRCm37mm9NCBIm37
MGSCv361638,378,414 - 38,418,102 (+)NCBImm8
Celera1638,869,381 - 38,897,547 (+)NCBICelera
Cytogenetic Map16B4NCBI
cM Map1626.86NCBI
Cd80
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542719,236,445 - 19,261,517 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542719,237,251 - 19,274,001 (-)NCBIChiLan1.0ChiLan1.0
CD80
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13123,559,559 - 123,594,870 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3123,559,559 - 123,594,870 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03116,646,590 - 116,683,725 (-)NCBIMhudiblu_PPA_v0panPan3
CD80
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13323,177,136 - 23,208,421 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3323,177,138 - 23,201,380 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3323,207,369 - 23,231,610 (-)NCBI
ROS_Cfam_1.03323,415,441 - 23,446,725 (-)NCBI
UMICH_Zoey_3.13323,217,902 - 23,242,129 (-)NCBI
UNSW_CanFamBas_1.03323,253,474 - 23,277,692 (-)NCBI
UU_Cfam_GSD_1.03323,822,928 - 23,847,156 (-)NCBI
Cd80
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602131,033,618 - 131,058,267 (+)NCBI
SpeTri2.0NW_0049365366,462,080 - 6,483,450 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD80
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13140,693,382 - 140,728,980 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113140,693,312 - 140,730,541 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213150,031,804 - 150,044,259 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CD80
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12261,258,281 - 61,294,772 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041105,020,341 - 105,055,630 (-)NCBIVero_WHO_p1.0
Cd80
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473128,630,540 - 28,655,297 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH94722  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21162,291,798 - 62,291,983 (+)MAPPERmRatBN7.2
Rnor_6.01164,853,738 - 64,853,922NCBIRnor6.0
Rnor_5.01167,256,456 - 67,256,640UniSTSRnor5.0
RGSC_v3.41164,070,129 - 64,070,313UniSTSRGSC3.4
Celera1161,793,408 - 61,793,592UniSTS
RH 3.4 Map11500.9UniSTS
Cytogenetic Map11q21UniSTS
BF402875  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21162,274,405 - 62,274,498 (+)MAPPERmRatBN7.2
Rnor_6.01164,836,350 - 64,836,442NCBIRnor6.0
Rnor_5.01167,273,465 - 67,273,557UniSTSRnor5.0
RGSC_v3.41164,053,020 - 64,053,112UniSTSRGSC3.4
Celera1161,776,536 - 61,776,628UniSTS
RH 3.4 Map11508.3UniSTS
Cytogenetic Map11q21UniSTS


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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:151
Count of miRNA genes:114
Interacting mature miRNAs:121
Transcripts:ENSRNOT00000002089
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1
Low 3 10 26 10 18 10 8 10 11 10 19 11 8
Below cutoff 33 25 25 25 1 59 25 20

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002089   ⟹   ENSRNOP00000002089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1162,254,624 - 62,292,030 (-)Ensembl
Rnor_6.0 Ensembl1164,828,671 - 64,853,692 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089625   ⟹   ENSRNOP00000071419
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1164,827,635 - 64,855,353 (-)Ensembl
RefSeq Acc Id: NM_012926   ⟹   NP_037058
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,266,744 - 62,291,742 (-)NCBI
Rnor_6.01164,828,688 - 64,853,681 (-)NCBI
Rnor_5.01167,255,123 - 67,291,544 (+)NCBI
RGSC_v3.41164,045,358 - 64,070,072 (-)RGD
Celera1161,768,874 - 61,793,351 (-)RGD
Sequence:
RefSeq Acc Id: XM_006248365   ⟹   XP_006248427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,254,543 - 62,292,593 (-)NCBI
Rnor_6.01164,815,201 - 64,854,521 (-)NCBI
Rnor_5.01167,255,123 - 67,291,544 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088035   ⟹   XP_038943963
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,254,543 - 62,293,414 (-)NCBI
RefSeq Acc Id: XM_039088036   ⟹   XP_038943964
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21162,254,543 - 62,293,393 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_037058   ⟸   NM_012926
- Sequence:
RefSeq Acc Id: XP_006248427   ⟸   XM_006248365
- Peptide Label: isoform X2
- UniProtKB: G3V671 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002089   ⟸   ENSRNOT00000002089
RefSeq Acc Id: ENSRNOP00000071419   ⟸   ENSRNOT00000089625
RefSeq Acc Id: XP_038943963   ⟸   XM_039088035
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038943964   ⟸   XM_039088036
- Peptide Label: isoform X1
Protein Domains
Ig-like

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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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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:2314 AgrOrtholog
Ensembl Genes ENSRNOG00000001527 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002089 UniProtKB/TrEMBL
  ENSRNOP00000071419 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002089 UniProtKB/TrEMBL
  ENSRNOT00000089625 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro CD80_C2-set UniProtKB/TrEMBL
  CD80_IgC UniProtKB/TrEMBL
  Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
KEGG Report rno:25408 UniProtKB/TrEMBL
NCBI Gene 25408 ENTREZGENE
Pfam C2-set_2 UniProtKB/TrEMBL
PhenoGen Cd80 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
SMART SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
TIGR TC221438
UniProt A0A0G2K0F2_RAT UniProtKB/TrEMBL
  G3V671 ENTREZGENE, UniProtKB/TrEMBL
  O35187_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-29 Cd80  Cd80 molecule  LOC100360171  CD80-like  Data Merged 737654 PROVISIONAL
2010-05-06 LOC100360171  CD80-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-09-29 Cd80  Cd80 molecule  Cd80  CD80 antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Cd80  CD80 antigen    Cd80 a rat homolog of the human CD28/CTLA - 4 ligand (B7-1)  Name updated 625702 APPROVED
2002-06-10 Cd80  Cd80 a rat homolog of the human CD28/CTLA - 4 ligand (B7-1)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease may be involved in induction of acute phase of experimental autoimmune anterior uveitis (EAAU) 1298745