Calr (calreticulin) - Rat Genome Database

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Gene: Calr (calreticulin) Rattus norvegicus
Analyze
Symbol: Calr
Name: calreticulin
RGD ID: 620288
Description: Exhibits several functions, including hormone binding activity; metal ion binding activity; and peptide binding activity. Involved in several processes, including cellular response to lithium ion; response to estradiol; and response to testosterone. Localizes to several cellular components, including acrosomal vesicle; endoplasmic reticulum; and perinuclear region of cytoplasm. Biomarker of vitamin B12 deficiency. Human ortholog(s) of this gene implicated in essential thrombocythemia; myelofibrosis; sideroblastic anemia; and thrombocytosis. Orthologous to human CALR (calreticulin); PARTICIPATES IN calcium/calcium-mediated signaling pathway; antigen processing and presentation pathway; Chagas disease pathway; INTERACTS WITH 1,3-dinitrobenzene; 17alpha-ethynylestradiol; 2,2,2-tetramine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CABP3; CALBP; calcium-binding protein 3; calregulin; CRP55; endoplasmic reticulum resident protein 60; ERp60; HACBP
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21923,308,525 - 23,313,420 (+)NCBI
Rnor_6.0 Ensembl1925,956,771 - 25,961,666 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01925,956,771 - 25,961,666 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01936,932,394 - 36,937,289 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41924,964,775 - 24,969,670 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11924,969,631 - 24,974,494 (+)NCBI
Celera1922,865,445 - 22,870,340 (+)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
(Z)-3-butylidenephthalide  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,4-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-methylcholanthrene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-methylumbelliferyl acetate  (ISO)
7,12-dimethyltetraphene  (ISO)
8-Br-cAMP  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (ISO)
alpha-naphthoflavone  (EXP)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
ampicillin  (ISO)
arsenous acid  (ISO)
avobenzone  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
boric acid  (ISO)
bortezomib  (ISO)
Brodifacoum  (EXP)
bucladesine  (ISO)
buspirone  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
calyculin a  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
chloropicrin  (ISO)
chloroquine  (ISO)
chlorpromazine  (EXP)
chlorpyrifos  (EXP)
choline  (ISO)
chromium atom  (ISO)
chromones  (ISO)
cisplatin  (EXP,ISO)
clobetasol  (ISO)
clofibrate  (EXP)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
CU-O LINKAGE  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (EXP,ISO)
D-glucose  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (EXP)
dinophysistoxin 1  (ISO)
doxorubicin  (EXP,ISO)
dutasteride  (ISO)
elemental selenium  (ISO)
ellagic acid  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
fenbuconazole  (ISO)
flutamide  (EXP)
folic acid  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gentamycin  (EXP,ISO)
glafenine  (EXP)
glucose  (ISO)
halothane  (EXP)
homocysteine  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP,ISO)
ionomycin  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
isoprenaline  (ISO)
kojic acid  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
lithium atom  (EXP)
lithium chloride  (ISO)
lithium hydride  (EXP)
lithocholic acid  (EXP)
lovastatin  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
methotrexate  (ISO)
mitoxantrone  (ISO)
monosodium L-glutamate  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nicotine  (ISO)
Nonidet P-40  (ISO)
okadaic acid  (ISO)
oxidopamine  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (EXP,ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
procymidone  (EXP)
progesterone  (EXP,ISO)
Propiverine  (EXP)
resveratrol  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
salubrinal  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
streptozocin  (EXP)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
Tautomycin  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
trichloroethene  (EXP)
triphenylstannane  (ISO)
tunicamycin  (EXP,ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)
warfarin  (ISO)
zearalenone  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cardiac muscle cell differentiation  (IEP)
cellular response to lithium ion  (IEP)
cellular response to organic substance  (IEP)
cellular senescence  (ISO)
cortical actin cytoskeleton organization  (ISO)
endoplasmic reticulum unfolded protein response  (IBA)
negative regulation of intracellular steroid hormone receptor signaling pathway  (ISO)
negative regulation of neuron differentiation  (ISO)
negative regulation of retinoic acid receptor signaling pathway  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
negative regulation of translation  (ISO)
negative regulation of trophoblast cell migration  (ISO)
peptide antigen assembly with MHC class I protein complex  (ISO)
positive regulation of cell cycle  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of dendritic cell chemotaxis  (ISO)
positive regulation of endothelial cell migration  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of NIK/NF-kappaB signaling  (ISO)
positive regulation of phagocytosis  (ISO)
positive regulation of substrate adhesion-dependent cell spreading  (ISO)
protein export from nucleus  (ISO)
protein folding  (IBA,TAS)
protein localization to nucleus  (ISO)
protein stabilization  (ISO,ISS)
regulation of cell cycle  (ISO)
regulation of meiotic nuclear division  (ISO)
response to drug  (IEP)
response to estradiol  (IEP)
response to organic substance  (IEP)
response to testosterone  (IEP)
spermatogenesis  (IEP)

Molecular Function

References

References - curated
1. Ahmad S, etal., J Proteomics. 2015 Sep 8;127(Pt A):178-84. doi: 10.1016/j.jprot.2015.04.035. Epub 2015 May 14.
2. Blake CA, etal., Exp Biol Med (Maywood). 2005 Dec;230(11):800-7.
3. Chen B, etal., Biol Psychiatry. 2000 Oct 1;48(7):658-64.
4. Conrad ME, etal., Gastroenterology. 1993 Jun;104(6):1700-4.
5. Copray JC, etal., J Chem Neuroanat. 1996 Jul;11(1):57-65.
6. Cunningham TJ, etal., Exp Neurol. 2000 Jun;163(2):457-68.
7. Decca MB, etal., J Biol Chem. 2007 Mar 16;282(11):8237-45. Epub 2006 Dec 29.
8. Di Jeso B, etal., Biochem J. 2003 Mar 1;370(Pt 2):449-58.
9. Ellgaard L, etal., J Mol Biol 2002 Sep 27;322(4):773-84.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. GOA data from the GO Consortium
12. Hong SH, etal., Cancer Res. 2004 Aug 1;64(15):5504-10.
13. Iakova P, etal., EMBO J. 2004 Jan 28;23(2):406-17. Epub 2004 Jan 15.
14. Imanaka-Yoshida K, etal., J Mol Cell Cardiol. 1996 Mar;28(3):553-62.
15. Jansen G, etal., Mol Cell Proteomics. 2012 Sep;11(9):710-23. doi: 10.1074/mcp.M111.016550. Epub 2012 Jun 4.
16. Kageyama K, etal., J Biol Chem 2002 May 31;277(22):19255-64.
17. Kypreou KP, etal., Proteomics. 2008 Jun;8(12):2407-19.
18. Lee D and Michalak M, BMB Rep. 2010 Mar;43(3):151-7.
19. Li B, etal., Haematologica. 2014 Nov;99(11):1697-700. doi: 10.3324/haematol.2014.109249. Epub 2014 Jul 4.
20. Macias M, etal., Eur J Biochem. 2003 Mar;270(5):832-40.
21. Marty C, etal., Blood. 2016 Mar 10;127(10):1317-24. doi: 10.1182/blood-2015-11-679571. Epub 2015 Nov 25.
22. MGD data from the GO Consortium
23. Nakamura M, etal., Exp Cell Res. 1993 Mar;205(1):101-10.
24. Nangalia J, etal., N Engl J Med. 2013 Dec 19;369(25):2391-405. doi: 10.1056/NEJMoa1312542. Epub 2013 Dec 10.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. OMIM Disease Annotation Pipeline
27. Park S, etal., Cancer Genet. 2015 Dec;208(12):630-5. doi: 10.1016/j.cancergen.2015.11.001. Epub 2015 Nov 10.
28. Pipeline to import KEGG annotations from KEGG into RGD
29. Rardin MJ, etal., J Biol Chem. 2008 May 30;283(22):15440-50. doi: 10.1074/jbc.M709547200. Epub 2008 Apr 2.
30. RGD automated data pipeline
31. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. RGD automated import pipeline for gene-chemical interactions
33. Shao L, etal., Life Sci. 2006 Feb 16;78(12):1317-23. Epub 2005 Oct 19.
34. Simovich MJ, etal., Am J Hematol 2002 Mar;69(3):164-70.
35. Somogyi E, etal., Matrix Biol. 2003 Apr;22(2):179-91.
36. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
37. Tefferi A, etal., Leukemia. 2014 Jul;28(7):1494-500. doi: 10.1038/leu.2014.57. Epub 2014 Feb 5.
38. Tharin S, etal., J Cell Physiol. 1996 Mar;166(3):547-60.
39. Theocharides AP, etal., Blood. 2016 Jun 23;127(25):3253-9. doi: 10.1182/blood-2016-02-696310. Epub 2016 Mar 24.
40. Yao QM, etal., Hematology. 2015 Oct;20(9):517-22. doi: 10.1179/1607845415Y.0000000009. Epub 2015 Apr 10.
41. Yoshioka Y, etal., Fukuoka Igaku Zasshi. 2001 May;92(5):201-16.
42. Zhu N, etal., Endocrinology. 1998 Oct;139(10):4337-44.
Additional References at PubMed
PMID:1497655   PMID:1911778   PMID:2241926   PMID:2395661   PMID:3513762   PMID:7876339   PMID:8107809   PMID:8251535   PMID:8666824   PMID:10862152   PMID:11149926   PMID:11408579  
PMID:11825569   PMID:11842220   PMID:11859136   PMID:12648529   PMID:12676993   PMID:14517290   PMID:15131110   PMID:15136153   PMID:15489334   PMID:15977177   PMID:15998798   PMID:16140380  
PMID:16198296   PMID:16260597   PMID:16502470   PMID:16854843   PMID:17187072   PMID:17916189   PMID:17923681   PMID:18303859   PMID:18413143   PMID:19199708   PMID:19346238   PMID:19851281  
PMID:19946888   PMID:20308067   PMID:20551380   PMID:20880849   PMID:21187406   PMID:21263072   PMID:21423176   PMID:21532570   PMID:21590275   PMID:21630459   PMID:21652723   PMID:21892174  
PMID:22147490   PMID:22377355   PMID:22572157   PMID:22658674   PMID:23011799   PMID:23376485   PMID:23395171   PMID:23530063   PMID:23564462   PMID:23575574   PMID:23818963   PMID:23972286  
PMID:24252779   PMID:24589181   PMID:24813996   PMID:24930861   PMID:24998604   PMID:27425249   PMID:27435297   PMID:29453988   PMID:29925877   PMID:30188326   PMID:31505169   PMID:31669485  


Genomics

Comparative Map Data
Calr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21923,308,525 - 23,313,420 (+)NCBI
Rnor_6.0 Ensembl1925,956,771 - 25,961,666 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01925,956,771 - 25,961,666 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01936,932,394 - 36,937,289 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41924,964,775 - 24,969,670 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11924,969,631 - 24,974,494 (+)NCBI
Celera1922,865,445 - 22,870,340 (+)NCBICelera
Cytogenetic Map19q11NCBI
CALR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1912,938,578 - 12,944,489 (+)EnsemblGRCh38hg38GRCh38
GRCh381912,938,609 - 12,944,489 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371913,049,423 - 13,055,303 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361912,910,423 - 12,916,303 (+)NCBINCBI36hg18NCBI36
Build 341912,910,422 - 12,916,303NCBI
Celera1912,939,147 - 12,945,035 (+)NCBI
Cytogenetic Map19p13.13NCBI
HuRef1912,621,315 - 12,627,203 (+)NCBIHuRef
CHM1_11913,049,914 - 13,055,824 (+)NCBICHM1_1
Calr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39885,568,717 - 85,573,560 (-)NCBIGRCm39mm39
GRCm39 Ensembl885,568,479 - 85,573,563 (-)Ensembl
GRCm38884,842,088 - 84,846,931 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,841,850 - 84,846,934 (-)EnsemblGRCm38mm10GRCm38
MGSCv37887,365,987 - 87,370,830 (-)NCBIGRCm37mm9NCBIm37
MGSCv36887,731,955 - 87,736,972 (-)NCBImm8
Celera889,141,243 - 89,146,089 (-)NCBICelera
Cytogenetic Map8C3NCBI
cM Map841.21NCBI
Calr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541531,985,147 - 31,989,372 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541531,985,147 - 31,989,372 (+)NCBIChiLan1.0ChiLan1.0
CALR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11913,242,900 - 13,249,416 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1913,242,900 - 13,249,416 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01912,501,013 - 12,506,909 (+)NCBIMhudiblu_PPA_v0panPan3
CALR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12049,251,390 - 49,255,291 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2049,251,777 - 49,255,245 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2049,123,639 - 49,127,542 (-)NCBI
ROS_Cfam_1.02049,768,253 - 49,772,156 (-)NCBI
UMICH_Zoey_3.12048,979,448 - 48,983,351 (-)NCBI
UNSW_CanFamBas_1.02049,405,934 - 49,409,839 (-)NCBI
UU_Cfam_GSD_1.02049,648,459 - 49,652,362 (-)NCBI
Calr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118208,355,637 - 208,360,018 (-)NCBI
SpeTri2.0NW_0049366591,994,695 - 1,999,070 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl266,098,225 - 66,102,340 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1266,098,263 - 66,102,074 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2266,283,767 - 66,287,604 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CALR
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1611,618,691 - 11,624,299 (+)NCBI
ChlSab1.1 Ensembl611,618,396 - 11,623,792 (+)Ensembl
Calr
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624901511,295 - 515,208 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127635288Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19129558305Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19129558305Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19132379055Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191073992926201726Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191529452433991703Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191593952838798459Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192445572643907843Rat
61328Eae8Experimental allergic encephalomyelitis QTL 84nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)192445762737140233Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:445
Count of miRNA genes:252
Interacting mature miRNAs:292
Transcripts:ENSRNOT00000004091
Prediction methods:Microtar, Miranda, Rnahybrid
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 21 15 15 16 24
Medium 3 43 42 26 19 26 8 11 74 19 17 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004091   ⟹   ENSRNOP00000004091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1925,956,771 - 25,961,666 (-)Ensembl
RefSeq Acc Id: NM_022399   ⟹   NP_071794
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21923,308,525 - 23,313,420 (+)NCBI
Rnor_6.01925,956,771 - 25,961,666 (-)NCBI
Rnor_5.01936,932,394 - 36,937,289 (-)NCBI
RGSC_v3.41924,964,775 - 24,969,670 (+)RGD
Celera1922,865,445 - 22,870,340 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_071794   ⟸   NM_022399
- Peptide Label: precursor
- UniProtKB: P18418 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004091   ⟸   ENSRNOT00000004091

Transcriptome

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

Promoters
RGD ID:13701025
Promoter ID:EPDNEW_R11549
Type:multiple initiation site
Name:Calr_1
Description:calreticulin
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_6.01925,961,674 - 25,961,734EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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)
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
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
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/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
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 (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
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
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
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
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
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 (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
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
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 (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 (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
WKY/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
WKY/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
WKY/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
WKY/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
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 25959739 25959740 C T snv MR/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620288 AgrOrtholog
Ensembl Genes ENSRNOG00000003029 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000004091 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004091 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.10.250.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5623178 IMAGE-MGC_LOAD
InterPro Calret/calnex UniProtKB/Swiss-Prot
  Calret/calnex_CS UniProtKB/Swiss-Prot
  Calreticulin UniProtKB/Swiss-Prot
  Calreticulin/calnexin_P_dom_sf UniProtKB/Swiss-Prot
  ConA-like_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:64202 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72450 IMAGE-MGC_LOAD
NCBI Gene 64202 ENTREZGENE
PANTHER PTHR11073 UniProtKB/Swiss-Prot
Pfam Calreticulin UniProtKB/Swiss-Prot
PhenoGen Calr PhenoGen
PIRSF Calreticulin UniProtKB/Swiss-Prot
PRINTS CALRETICULIN UniProtKB/Swiss-Prot
PROSITE CALRETICULIN_1 UniProtKB/Swiss-Prot
  CALRETICULIN_2 UniProtKB/Swiss-Prot
  CALRETICULIN_REPEAT UniProtKB/Swiss-Prot
  ER_TARGET UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49899 UniProtKB/Swiss-Prot
  SSF63887 UniProtKB/Swiss-Prot
UniProt CALR_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P10452 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Calr  calreticulin      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Calr  calreticulin      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction associates with co-chaperone thiol-disulvide oxidoreductase ERp57 727436
gene_process involved in cardiac and neural development 704416
gene_process promotes differentiation-dependent apoptosis via suppression of Akt signalling 704416