Havcr1 (hepatitis A virus cellular receptor 1) - Rat Genome Database

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Gene: Havcr1 (hepatitis A virus cellular receptor 1) Rattus norvegicus
Analyze
Symbol: Havcr1
Name: hepatitis A virus cellular receptor 1
RGD ID: 708425
Description: Predicted to enable phosphatidylserine binding activity and virus receptor activity. Involved in several processes, including phagocytosis, engulfment; response to mycotoxin; and response to testosterone. Located in several cellular components, including apical plasma membrane; cell surface; and phagocytic vesicle. Biomarker of colitis; hypertension; kidney failure (multiple); and proteinuria (multiple). Human ortholog(s) of this gene implicated in atopic dermatitis. Orthologous to human HAVCR1 (hepatitis A virus cellular receptor 1); INTERACTS WITH 1-naphthyl isothiocyanate; 11-deoxycorticosterone; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: HAVcr-1; hepatitis A virus cellular receptor 1 homolog; kidney injury molecule 1; KIM-1; Kim1; t cell immunoglobulin and mucin domain-containing protein 1; TIMD-1
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
mRatBN7.21031,118,667 - 31,151,730 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1031,119,088 - 31,151,698 (+)Ensembl
Rnor_6.01031,813,819 - 31,860,934 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1031,813,814 - 31,848,379 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01031,632,718 - 31,682,172 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41031,834,519 - 31,858,019 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11031,835,567 - 31,859,066 (+)NCBI
Celera1030,573,361 - 30,596,533 (+)NCBICelera
Cytogenetic Map10q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-lipoic acid  (ISO)
(S)-naringenin  (ISO)
(S)-nicotine  (ISO)
1-naphthyl isothiocyanate  (EXP)
11-deoxycorticosterone  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
3-chloropropane-1,2-diol  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
acrylamide  (EXP)
adefovir  (EXP)
aflatoxin B1  (ISO)
allyl alcohol  (ISO)
ammonium chloride  (EXP)
amphotericin B methyl ester  (ISO)
anthocyanin  (EXP)
anthracen-2-amine  (EXP)
aristolochic acid  (ISO)
bacitracin  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
bleomycin A2  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP)
canagliflozin  (EXP)
cefaloridine  (EXP)
chlordecone  (ISO)
chloroform  (ISO)
cholesterol  (EXP)
chromium atom  (EXP)
chromium(6+)  (EXP,ISO)
cidofovir anhydrous  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (EXP)
curcumin  (EXP)
cyanuric acid  (EXP)
cyclosporin A  (EXP,ISO)
dapagliflozin  (EXP)
deferasirox  (EXP,ISO)
desferrioxamine B  (EXP)
diclofenac  (ISO)
doxorubicin  (EXP)
ethanol  (ISO)
ethylene glycol  (EXP,ISO)
fenamic acid  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
formononetin  (EXP)
fructose  (EXP)
gefitinib  (ISO)
gentamycin  (EXP,ISO)
geraniol  (EXP)
glycidol  (ISO)
glyphosate  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
hesperidin  (EXP)
Hexachloro-1,3-butadiene  (EXP)
hydrogen chloride  (ISO)
hydrogen peroxide  (ISO)
icosanoid  (EXP)
iodixanol  (EXP)
iron(III) nitrilotriacetate  (EXP)
isocyanuric acid  (EXP)
isoniazide  (EXP)
ketoconazole  (EXP)
linoleic acid  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
lisinopril dihydrate  (EXP)
losartan  (EXP)
maleic acid  (EXP)
meglumine amidotrizoate  (EXP)
melamine  (EXP)
melatonin  (ISO)
menadione  (ISO)
mercury atom  (EXP)
mercury dichloride  (EXP,ISO)
mercury(0)  (EXP)
metformin  (EXP)
methylmercury chloride  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
Natamycin  (ISO)
nicorandil  (EXP)
nicotine  (ISO)
nitric oxide  (EXP)
nitrofen  (EXP)
nystatin  (ISO)
ochratoxin A  (EXP,ISO)
oleic acid  (ISO)
Ondansetron  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
Pentoxifylline  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
phenol  (ISO)
phenylbutazone  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
polymyxin B2  (ISO)
potassium bromate  (EXP)
potassium dichromate  (EXP)
probenecid  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
salubrinal  (ISO)
sirolimus  (EXP)
sodium arsenite  (EXP,ISO)
sodium cholate  (EXP)
sodium fluoride  (EXP)
streptozocin  (EXP,ISO)
tacrolimus hydrate  (EXP)
tenofovir disoproxil fumarate  (ISO)
testosterone  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetramethylpyrazine  (EXP)
thioacetamide  (EXP)
trichloroethene  (EXP)
umbelliferone  (EXP)
urethane  (ISO)
vancomycin  (EXP,ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Abassi Z, etal., J Urol. 2013 Apr;189(4):1559-66. doi: 10.1016/j.juro.2012.10.029. Epub 2012 Oct 22.
2. Abraham AP, etal., Nephrology (Carlton). 2012 May;17(4):322-9. doi: 10.1111/j.1440-1797.2012.01567.x.
3. Alter ML, etal., Clin Lab. 2012;58(7-8):659-71.
4. Aoyama M, etal., Biochem Biophys Res Commun. 2012 Mar 9;419(2):244-9. doi: 10.1016/j.bbrc.2012.02.001. Epub 2012 Feb 8.
5. Carlsson AC, etal., Eur J Heart Fail. 2013 Apr;15(4):441-6. doi: 10.1093/eurjhf/hfs187. Epub 2012 Dec 7.
6. Cuadros T, etal., Eur J Cancer. 2013 May;49(8):2034-47. doi: 10.1016/j.ejca.2012.12.020. Epub 2013 Jan 23.
7. Eirin A, etal., Nephrol Dial Transplant. 2012 Nov;27(11):4153-61. doi: 10.1093/ndt/gfs370. Epub 2012 Aug 23.
8. Fu WJ, etal., Diabetes Res Clin Pract. 2012 Jan;95(1):105-9. doi: 10.1016/j.diabres.2011.09.031. Epub 2011 Oct 20.
9. Gao LL, etal., Zhongguo Wei Zhong Bing Ji Jiu Yi Xue. 2012 Nov;24(11):647-50.
10. Gardiner L, etal., Am J Nephrol. 2012;35(2):152-63. doi: 10.1159/000335579. Epub 2012 Jan 20.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. Graves PE, etal., J Allergy Clin Immunol. 2005 Sep;116(3):650-6.
13. Han WK, etal., Kidney Int. 2002 Jul;62(1):237-44.
14. Hong MY, etal., Mediators Inflamm. 2012;2012:381358. doi: 10.1155/2012/381358. Epub 2012 Dec 23.
15. Hosohata K, etal., J Appl Toxicol. 2013 Jan 11. doi: 10.1002/jat.2849.
16. Ichimura T, etal., J Biol Chem 1998 Feb 13;273(7):4135-42.
17. Ichimura T, etal., J Clin Invest. 2008 May;118(5):1657-68.
18. Jin ZK, etal., Mol Immunol. 2013 Jul;54(3-4):457-64. doi: 10.1016/j.molimm.2013.01.013. Epub 2013 Feb 27.
19. Khademi M, etal., J Immunol. 2004 Jun 1;172(11):7169-76.
20. Khandrika L, etal., PLoS One. 2012;7(9):e44174. doi: 10.1371/journal.pone.0044174. Epub 2012 Sep 12.
21. Kramer AB, etal., Kidney Int. 2007 Mar;71(5):417-24. Epub 2007 Jan 10.
22. Kuehn EW, etal., Am J Physiol Renal Physiol. 2002 Dec;283(6):F1326-36. Epub 2002 Jul 24.
23. Kwon SH, etal., Clin Exp Nephrol. 2012 Nov 8.
24. Lekawanvijit S, etal., Am J Physiol Heart Circ Physiol. 2012 May 1;302(9):H1884-93. doi: 10.¿1152/¿ajpheart.¿00967.¿2011. Epub 2012 Feb 24.
25. Lieberthal JG, etal., J Rheumatol. 2013 May;40(5):674-683. Epub 2013 Apr 1.
26. MGD data from the GO Consortium
27. Nijboer WN, etal., Am J Transplant. 2009 Aug;9(8):1752-9. Epub 2009 Jun 12.
28. Oh SW, etal., BMC Nephrol. 2013 May 17;14(1):105.
29. OMIM Disease Annotation Pipeline
30. Peters HP, etal., Nephrol Dial Transplant. 2011 Nov;26(11):3581-8. doi: 10.1093/ndt/gfr135. Epub 2011 Apr 5.
31. Prozialeck WC, etal., Toxicol Appl Pharmacol. 2009 Aug 1;238(3):306-14. Epub 2009 Jan 31.
32. Quiros Y, etal., Toxicol Sci. 2013 Apr;132(2):493-501. doi: 10.1093/toxsci/kft007. Epub 2013 Jan 18.
33. Rached E, etal., Toxicol Sci. 2008 Jun;103(2):371-81. Epub 2008 Feb 27.
34. RGD automated data pipeline
35. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
36. RGD automated import pipeline for gene-chemical interactions
37. RGD comprehensive gene curation
38. Rouse RL, etal., Toxicol Pathol. 2013;41(4):662-80. doi: 10.1177/0192623312464122. Epub 2012 Oct 19.
39. Sabbisetti VS, etal., Toxicol Sci. 2013 Jan;131(1):13-25. doi: 10.1093/toxsci/kfs268. Epub 2012 Sep 27.
40. Shanu A, etal., Antioxid Redox Signal. 2013 Mar 1;18(7):756-69. doi: 10.1089/ars.2012.4591. Epub 2012 Oct 16.
41. Soljancic A, etal., Am J Physiol Regul Integr Comp Physiol. 2013 Apr 3.
42. Sonar SS, etal., J Clin Invest. 2010 Aug 2;120(8):2767-81. doi: 10.1172/JCI39543. Epub 2010 Jul 12.
43. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
44. Sundaram N, etal., Am J Hematol. 2011 Jul;86(7):559-66. doi: 10.1002/ajh.22045. Epub 2011 May 31.
45. Toker A, etal., Urology. 2013 Jan;81(1):168-72. doi: 10.1016/j.urology.2012.09.004. Epub 2012 Nov 30.
46. Tomczak J, etal., Pediatr Nephrol. 2013 May 15.
47. Trujillo J, etal., Am J Physiol Renal Physiol. 2008 Nov;295(5):F1574-82. Epub 2008 Sep 24.
48. Vaidya VS, etal., Kidney Int. 2011 Feb;79(4):464-70. doi: 10.1038/ki.2010.404. Epub 2010 Oct 27.
49. van Timmeren MM, etal., Am J Physiol Renal Physiol. 2006 Aug;291(2):F456-64. Epub 2006 Feb 7.
50. Wasilewska A, etal., Pediatr Nephrol. 2011 Apr;26(4):579-86. doi: 10.1007/s00467-011-1773-5. Epub 2011 Jan 31.
51. Zhang J, etal., Toxicol Pathol. 2009;37(5):629-43. Epub 2009 Jun 17.
Additional References at PubMed
PMID:15489334   PMID:16174863   PMID:16387092   PMID:16896183   PMID:17670906   PMID:17934191   PMID:18083575   PMID:19225054   PMID:19371616   PMID:19387469   PMID:20305092   PMID:20458318  
PMID:20566714   PMID:20660082   PMID:21536871   PMID:21905055   PMID:22898836   PMID:23360846   PMID:24158981   PMID:24816434   PMID:24904085   PMID:25087119   PMID:27050864   PMID:27231899  
PMID:27756197   PMID:28075469   PMID:29045706   PMID:29402223   PMID:30431687   PMID:30500779   PMID:31050655   PMID:31373312  


Genomics

Comparative Map Data
Havcr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21031,118,667 - 31,151,730 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1031,119,088 - 31,151,698 (+)Ensembl
Rnor_6.01031,813,819 - 31,860,934 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1031,813,814 - 31,848,379 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01031,632,718 - 31,682,172 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41031,834,519 - 31,858,019 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11031,835,567 - 31,859,066 (+)NCBI
Celera1030,573,361 - 30,596,533 (+)NCBICelera
Cytogenetic Map10q21NCBI
HAVCR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5157,029,413 - 157,059,119 (-)EnsemblGRCh38hg38GRCh38
GRCh385157,028,383 - 157,069,633 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375156,456,424 - 156,486,127 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365156,389,109 - 156,418,065 (-)NCBINCBI36hg18NCBI36
Build 345156,389,014 - 156,418,548NCBI
Celera5152,482,103 - 152,511,651 (-)NCBI
Cytogenetic Map5q33.3NCBI
HuRef5151,544,985 - 151,574,299 (-)NCBIHuRef
CHM1_15155,888,935 - 155,918,725 (-)NCBICHM1_1
Havcr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391146,630,644 - 46,670,405 (+)NCBIGRCm39mm39
GRCm39 Ensembl1146,625,907 - 46,670,405 (+)Ensembl
GRCm381146,739,822 - 46,779,578 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1146,735,080 - 46,779,578 (+)EnsemblGRCm38mm10GRCm38
MGSCv371146,553,725 - 46,593,080 (+)NCBIGRCm37mm9NCBIm37
MGSCv361146,594,600 - 46,622,036 (+)NCBImm8
Celera1151,321,716 - 51,355,068 (+)NCBICelera
Cytogenetic Map11B1.1NCBI
Havcr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540811,047,679 - 11,070,492 (-)NCBIChiLan1.0ChiLan1.0
HAVCR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15158,413,054 - 158,442,481 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5158,413,073 - 158,442,481 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05152,429,337 - 152,459,800 (-)NCBIMhudiblu_PPA_v0panPan3
HAVCR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1453,012,223 - 53,066,611 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl453,046,970 - 53,128,952 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl453,012,234 - 53,033,393 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha452,939,224 - 52,956,256 (+)NCBI
ROS_Cfam_1.0453,479,175 - 53,503,280 (+)NCBI
UMICH_Zoey_3.1453,309,862 - 53,326,891 (+)NCBI
UNSW_CanFamBas_1.0453,416,885 - 53,433,922 (+)NCBI
UU_Cfam_GSD_1.0453,933,785 - 53,950,850 (+)NCBI
Havcr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213107,580,999 - 107,601,858 (+)NCBI
SpeTri2.0NW_0049365156,030,402 - 6,051,161 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HAVCR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11666,162,318 - 66,208,868 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21671,949,487 - 71,963,277 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HAVCR1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12359,422,769 - 59,454,183 (-)NCBI
ChlSab1.1 Ensembl2359,423,334 - 59,453,531 (-)Ensembl
Vero_WHO_p1.0NW_02366603418,176,581 - 18,208,543 (+)NCBI
Havcr1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473332,284,793 - 32,310,980 (+)NCBI

Position Markers
BQ203079  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21031,132,529 - 31,132,683 (+)MAPPERmRatBN7.2
Rnor_6.01031,827,689 - 31,827,842NCBIRnor6.0
Rnor_5.01031,648,824 - 31,648,977UniSTSRnor5.0
RGSC_v3.41031,838,850 - 31,839,003UniSTSRGSC3.4
Celera1030,577,354 - 30,577,507UniSTS
RH 3.4 Map10302.11UniSTS
Cytogenetic Map10q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
631531Iresp2Immunoglobin response QTL26.3blood immunoglobulin E amount (VT:0002492)serum total immunoglobulin E level (CMO:0001542)102291826836400810Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2298480Eau7Experimental allergic uveoretinitis QTL 70.0049uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)102795762634490668Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:510
Count of miRNA genes:262
Interacting mature miRNAs:316
Transcripts:ENSRNOT00000009573
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 1 1
Low 2 9 26 10 18 10 7 7 9 22 12 11 7
Below cutoff 4 18 18 18 1 3 4 6 9 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009573   ⟹   ENSRNOP00000009573
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1031,119,088 - 31,151,698 (+)Ensembl
Rnor_6.0 Ensembl1031,813,814 - 31,848,379 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104970   ⟹   ENSRNOP00000076717
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1031,119,088 - 31,151,698 (+)Ensembl
RefSeq Acc Id: NM_173149   ⟹   NP_775172
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21031,128,531 - 31,151,700 (+)NCBI
Rnor_6.01031,823,688 - 31,846,859 (+)NCBI
Rnor_5.01031,632,718 - 31,682,172 (+)NCBI
RGSC_v3.41031,834,519 - 31,858,019 (+)RGD
Celera1030,573,361 - 30,596,533 (+)RGD
Sequence:
RefSeq Acc Id: XM_006246163   ⟹   XP_006246225
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21031,118,667 - 31,151,730 (+)NCBI
Rnor_6.01031,813,819 - 31,846,859 (+)NCBI
Rnor_5.01031,632,718 - 31,682,172 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_775172   ⟸   NM_173149
- Peptide Label: precursor
- UniProtKB: O54947 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006246225   ⟸   XM_006246163
- Peptide Label: isoform X1
- UniProtKB: G3V6W3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009573   ⟸   ENSRNOT00000009573
RefSeq Acc Id: ENSRNOP00000076717   ⟸   ENSRNOT00000104970
Protein Domains
Ig-like   Ig-like V-type

Transcriptome

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

Promoters
RGD ID:13697130
Promoter ID:EPDNEW_R7655
Type:multiple initiation site
Name:Havcr1_1
Description:hepatitis A virus cellular receptor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01031,814,221 - 31,814,281EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (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
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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)
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)
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)
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)
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
FXLE18/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
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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)
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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)
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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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708425 AgrOrtholog
Ensembl Genes ENSRNOG00000007243 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009573 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009573 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:5599247 IMAGE-MGC_LOAD
InterPro 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_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:286934 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72269 IMAGE-MGC_LOAD
NCBI Gene 286934 ENTREZGENE
Pfam V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB HAVCR1 RGD
PhenoGen Havcr1 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V6W3 ENTREZGENE, UniProtKB/TrEMBL
  HAVR1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Havcr1  hepatitis A virus cellular receptor 1  Havcr1  kidney injury molecule 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Havcr1  kidney injury molecule 1  Kim1    Symbol and Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed at a low level in normal kidney but increases dramatically in postischemic kidney 1299432