Casp6 (caspase 6) - Rat Genome Database

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Gene: Casp6 (caspase 6) Rattus norvegicus
Analyze
Symbol: Casp6
Name: caspase 6
RGD ID: 70967
Description: Enables endopeptidase activity. Involved in several processes, including acute inflammatory response to non-antigenic stimulus; axonal fasciculation; and positive regulation of programmed cell death. Located in several cellular components, including axon; cytosol; and neuronal cell body. Used to study status epilepticus. Biomarker of brain ischemia; endometritis; middle cerebral artery infarction; and prostate carcinoma. Human ortholog(s) of this gene implicated in ovarian carcinoma. Orthologous to human CASP6 (caspase 6); PARTICIPATES IN apoptotic cell death pathway; INTERACTS WITH (+)-pilocarpine; (R)-noradrenaline; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: apoptotic protease Mch-2; CASP-6; caspase-6; LOC103689977; Mch2; MGC93335
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
mRatBN7.22218,466,063 - 218,478,503 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2218,466,076 - 218,478,502 (+)Ensembl
Rnor_6.02235,341,326 - 235,353,715 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2230,186,198 - 230,198,555 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl2235,341,365 - 235,353,967 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02249,539,649 - 249,552,032 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42227,361,538 - 227,373,844 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12227,348,217 - 227,360,523 (+)NCBI
Celera2210,748,422 - 210,760,763 (+)NCBICelera
Cytogenetic Map2q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-anisomycin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(R)-noradrenaline  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3-chloropropane-1,2-diol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-nonylphenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
azadirachtin A  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bexarotene  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
buspirone  (EXP)
butyric acid  (EXP)
cadmium atom  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
celecoxib  (ISO)
chalcones  (ISO)
chelerythrine  (ISO)
cisplatin  (ISO)
cladribine  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
cypermethrin  (EXP)
Deguelin  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
Di-n-octyl phthalate  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
dimethylarsinic acid  (ISO)
doxorubicin  (EXP,ISO)
entinostat  (ISO)
equol  (ISO)
ethyl methanesulfonate  (ISO)
flavonoids  (EXP)
flavonols  (ISO)
fluoranthene  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
furosemide  (EXP)
gemcitabine  (ISO)
glutathione  (EXP)
glycyrrhizinic acid  (EXP)
glyphosate  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
indometacin  (ISO)
isoprenaline  (ISO)
ivermectin  (ISO)
ketamine  (ISO)
ketoconazole  (EXP)
L-ascorbic acid  (EXP)
leupeptin  (ISO)
lipopolysaccharide  (ISO)
lovastatin  (ISO)
LY294002  (EXP,ISO)
menadione  (EXP)
methamphetamine  (EXP)
methotrexate  (ISO)
methyl beta-cyclodextrin  (ISO)
miconazole  (EXP)
mitoxantrone  (ISO)
monosodium L-glutamate  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-acylsphinganine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosomorpholine  (EXP)
nickel dichloride  (EXP)
nitrates  (EXP)
p-menthan-3-ol  (ISO)
Panduratin A  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenanthrolines  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
propiconazole  (ISO)
propylparaben  (ISO)
quercetin  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
rottlerin  (ISO)
SB 203580  (ISO)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
staurosporine  (ISO)
streptozocin  (EXP)
sunitinib  (ISO)
surfactin  (ISO)
surfactin C  (ISO)
tamoxifen  (ISO)
tauroursodeoxycholic acid  (ISO)
Terfenadine  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (ISO)
topotecan  (ISO)
tributylstannane  (ISO)
trovafloxacin  (EXP)
tunicamycin  (ISO)
ursodeoxycholic acid  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axon  (IDA)
cytoplasm  (IBA,IDA)
cytosol  (IDA,ISO)
neuronal cell body  (IDA)
nucleoplasm  (ISO)
nucleus  (IDA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Allen JW, etal., J Neurosci Res. 2001 Jul 1;65(1):45-53.
2. Asamoto M, etal., Cancer Res. 2001 Jun 15;61(12):4693-700.
3. Bojunga J, etal., Diabetologia. 2004 Dec;47(12):2072-80. Epub 2004 Dec 10.
4. Bozec A, etal., J Clin Endocrinol Metab. 2005 Jan;90(1):17-25. Epub 2004 Oct 26.
5. Capano M, etal., Biochem J 2002 Apr 1;363(Pt 1):29-36.
6. Carlsten M, etal., Cancer Res. 2007 Feb 1;67(3):1317-25.
7. Chang CZ and Wu SC, World Neurosurg. 2016 May;89:474-88. doi: 10.1016/j.wneu.2016.01.061. Epub 2016 Feb 8.
8. D'Agostini F, etal., Carcinogenesis. 2002 Apr;23(4):587-93.
9. Damodaran TV, etal., Neurochem Res. 2006 Mar;31(3):367-81. Epub 2006 May 13.
10. Ferrer I J Neurobiol. 1999 Dec;41(4):549-58.
11. Foley JD, etal., J Biol Chem. 2004 Jul 30;279(31):32142-50. Epub 2004 May 25.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Guimaraes CA, etal., J Biol Chem. 2003 Oct 24;278(43):41938-46. Epub 2003 Aug 12.
14. Guo RF, etal., J Clin Invest. 2000 Nov;106(10):1271-80.
15. Harrison DC, etal., Brain Res Mol Brain Res. 2001 Apr 18;89(1-2):133-46.
16. Henshall DC, etal., Neurobiol Dis 2002 Jul;10(2):71-87.
17. Hikim AP, etal., Endocrinology. 2003 Jul;144(7):3167-75.
18. Hinck L, etal., Biol Reprod 2003 May;68(5):1808-12. Epub 2002 Dec 11.
19. Kaushal GP, etal., Am J Physiol 1998 Mar;274(3 Pt 2):F587-95.
20. KEGG
21. Krepela E, etal., J Cancer Res Clin Oncol. 2006 Jan;132(1):57-68. Epub 2005 Oct 18.
22. Kumar AP, etal., Cell Death Differ. 2007 Oct;14(10):1733-46. Epub 2007 Jun 15.
23. Leblanc V, etal., Reprod Biol Endocrinol. 2003 Aug 27;1:59.
24. Liu Y, etal., Biol Trace Elem Res. 2016 Oct;173(2):345-53. doi: 10.1007/s12011-016-0659-6. Epub 2016 Feb 26.
25. MGD Curation, June 12, 2002
26. MGD data from the GO Consortium
27. Narkilahti S and Pitkanen A, Neuroscience. 2005;131(4):887-97.
28. NCBI rat LocusLink and RefSeq merged data July 26, 2002
29. Omezzine A, etal., Biol Reprod. 2003 Sep;69(3):752-60. Epub 2003 Apr 30.
30. Omezzine A, etal., Endocrinology. 2003 Feb;144(2):648-61.
31. Peng X, etal., Fa Yi Xue Za Zhi. 2007 Oct;23(5):325-7, 331.
32. Pipeline to import KEGG annotations from KEGG into RGD
33. Pompl PN, etal., Arch Neurol. 2003 Mar;60(3):369-76.
34. RGD automated data pipeline
35. RGD automated import pipeline for gene-chemical interactions
36. Singh AB, etal., Kidney Int. 2002 Jul;62(1):106-15.
37. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
38. Vakkala M, etal., Br J Cancer. 1999 Oct;81(4):592-9.
39. Veluthakal R, etal., Am J Physiol Cell Physiol. 2004 Oct;287(4):C1152-62. Epub 2004 Jun 16.
40. Wang Y, etal., J Mol Neurosci. 2015 Aug;56(4):966-976. doi: 10.1007/s12031-015-0562-1. Epub 2015 Apr 22.
41. Wei Y, etal., Cell Physiol Biochem. 2018;46(2):687-698. doi: 10.1159/000488725. Epub 2018 Mar 29.
42. Wu B, etal., Am J Physiol Gastrointest Liver Physiol. 2004 Apr;286(4):G580-7.
43. Xu YM, etal., J Immunol. 2004 Jul 1;173(1):61-7.
Additional References at PubMed
PMID:12888622   PMID:17167422   PMID:20890311   PMID:21492153   PMID:21988832   PMID:22253444   PMID:25416956   PMID:29229552   PMID:31515488   PMID:32014515  


Genomics

Candidate Gene Status
Casp6 is a candidate Gene for QTL Eau5
Comparative Map Data
Casp6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22218,466,063 - 218,478,503 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2218,466,076 - 218,478,502 (+)Ensembl
Rnor_6.02235,341,326 - 235,353,715 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2230,186,198 - 230,198,555 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl2235,341,365 - 235,353,967 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02249,539,649 - 249,552,032 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42227,361,538 - 227,373,844 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12227,348,217 - 227,360,523 (+)NCBI
Celera2210,748,422 - 210,760,763 (+)NCBICelera
Cytogenetic Map2q43NCBI
CASP6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4109,688,622 - 109,703,583 (-)EnsemblGRCh38hg38GRCh38
GRCh384109,688,628 - 109,703,445 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh374110,609,784 - 110,624,601 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364110,829,234 - 110,844,078 (-)NCBINCBI36hg18NCBI36
Build 344110,967,388 - 110,982,233NCBI
Celera4107,903,448 - 107,918,292 (-)NCBI
Cytogenetic Map4q25NCBI
HuRef4106,342,777 - 106,357,627 (-)NCBIHuRef
CHM1_14110,586,394 - 110,601,238 (-)NCBICHM1_1
Casp6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393129,695,064 - 129,707,761 (+)NCBIGRCm39mm39
GRCm39 Ensembl3129,695,074 - 129,707,752 (+)Ensembl
GRCm383129,901,415 - 129,914,112 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3129,901,425 - 129,914,103 (+)EnsemblGRCm38mm10GRCm38
MGSCv373129,604,343 - 129,617,020 (+)NCBIGRCm37mm9NCBIm37
MGSCv363129,893,486 - 129,905,973 (+)NCBImm8
Celera3136,415,853 - 136,428,433 (+)NCBICelera
Cytogenetic Map3G3NCBI
Casp6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955496577,832 - 584,287 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955496575,839 - 584,287 (+)NCBIChiLan1.0ChiLan1.0
CASP6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14112,753,988 - 112,768,836 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4112,753,988 - 112,768,836 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04102,186,215 - 102,201,992 (-)NCBIMhudiblu_PPA_v0panPan3
CASP6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13229,897,706 - 29,910,522 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3229,897,823 - 29,911,469 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3212,119,155 - 12,132,295 (+)NCBI
ROS_Cfam_1.03230,117,004 - 30,130,146 (-)NCBI
UMICH_Zoey_3.13230,111,494 - 30,124,567 (-)NCBI
UNSW_CanFamBas_1.03229,855,989 - 29,869,067 (-)NCBI
UU_Cfam_GSD_1.0329,980,365 - 9,993,491 (+)NCBI
Casp6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530111,030,886 - 11,038,493 (+)NCBI
SpeTri2.0NW_004936563912,502 - 920,025 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CASP6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8112,483,392 - 112,540,550 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18112,519,450 - 112,534,315 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28120,664,346 - 120,678,399 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CASP6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1757,592,632 - 57,616,094 (-)NCBI
ChlSab1.1 Ensembl757,593,342 - 57,607,489 (-)Ensembl
Vero_WHO_p1.0NW_02366603736,243,873 - 36,268,826 (-)NCBI
Casp6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624830170,392 - 179,883 (+)NCBI

Position Markers
BE120979  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22218,476,389 - 218,476,554 (+)MAPPERmRatBN7.2
Rnor_6.02235,351,602 - 235,351,766NCBIRnor6.0
Rnor_6.02230,196,442 - 230,196,606NCBIRnor6.0
Rnor_5.02249,549,919 - 249,550,083UniSTSRnor5.0
RGSC_v3.42227,371,731 - 227,371,895UniSTSRGSC3.4
Celera2210,758,650 - 210,758,814UniSTS
RH 3.4 Map21555.3UniSTS
Cytogenetic Map2q43UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631203Gluco14Glucose level QTL 140.0001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)2206665645219003804Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2218414747240841241Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2189599258226936289Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2184165752229165752Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2199341726234244620Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2190613715226808892Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2202446871237938339Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
2299161Iddm33Insulin dependent diabetes mellitus QTL 332.98blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2206312063220876787Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2215377404237938339Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2185876309219753474Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2185876309219753474Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2189599258234599258Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189599258234599258Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:36
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000013049
Prediction methods: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
Medium
Low 3 8 1 11 1 4 16 8
Below cutoff 2 29 46 33 16 33 3 4 39 37 23 8 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013049   ⟹   ENSRNOP00000013049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2218,466,076 - 218,478,502 (+)Ensembl
Rnor_6.0 Ensembl2230,186,198 - 230,198,555 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078017   ⟹   ENSRNOP00000072472
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2235,341,365 - 235,353,967 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090658   ⟹   ENSRNOP00000071803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2235,341,374 - 235,353,714 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092954   ⟹   ENSRNOP00000075977
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2230,186,214 - 230,197,845 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093110
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2230,190,327 - 230,195,557 (+)Ensembl
RefSeq Acc Id: NM_001271984   ⟹   NP_001258913
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,466,162 - 218,478,503 (+)NCBI
Rnor_6.02235,341,374 - 235,353,715 (+)NCBI
Rnor_5.02249,539,649 - 249,552,032 (+)NCBI
Celera2210,748,422 - 210,760,763 (+)NCBI
Sequence:
RefSeq Acc Id: NM_031775   ⟹   NP_113963
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,466,162 - 218,478,503 (+)NCBI
Rnor_6.02235,341,374 - 235,353,715 (+)NCBI
Rnor_5.02249,539,649 - 249,552,032 (+)NCBI
RGSC_v3.42227,361,538 - 227,373,844 (+)RGD
Celera2210,748,422 - 210,760,763 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761528   ⟹   XP_008759750
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,466,174 - 218,478,503 (+)NCBI
Rnor_6.02235,341,326 - 235,353,565 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591135   ⟹   XP_017446624
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,466,063 - 218,478,503 (+)NCBI
Rnor_6.02235,341,330 - 235,353,565 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113963   ⟸   NM_031775
- UniProtKB: Q6AZ23 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001258913   ⟸   NM_001271984
- UniProtKB: Q6AZ23 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759750   ⟸   XM_008761528
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446624   ⟸   XM_017591135
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071803   ⟸   ENSRNOT00000090658
RefSeq Acc Id: ENSRNOP00000072472   ⟸   ENSRNOT00000078017
RefSeq Acc Id: ENSRNOP00000075977   ⟸   ENSRNOT00000092954
RefSeq Acc Id: ENSRNOP00000013049   ⟸   ENSRNOT00000013049
Protein Domains
CASPASE_P10   CASPASE_P20

Transcriptome

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

Promoters
RGD ID:13691753
Promoter ID:EPDNEW_R2278
Type:multiple initiation site
Name:Casp6_1
Description:caspase 6
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_6.02235,341,366 - 235,341,426EPDNEW

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70967 AgrOrtholog
  RGD:9205219 AgrOrtholog
Ensembl Genes ENSRNOG00000009508 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000052613 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013049 UniProtKB/TrEMBL
  ENSRNOP00000071803 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072472 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075977 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013049 UniProtKB/TrEMBL
  ENSRNOT00000078017 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000090658 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000092954 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123179 IMAGE-MGC_LOAD
InterPro Caspase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Caspase_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Caspase_cys_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Caspase_his_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_C14 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_C14_p10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_C14_p20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_C14A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83584 UniProtKB/TrEMBL
MGC_CLONE MGC:93335 IMAGE-MGC_LOAD
NCBI Gene 83584 ENTREZGENE
PANTHER PTHR10454 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10454:SF206 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB CASP6 RGD
PhenoGen Casp6 PhenoGen
PRINTS IL1BCENZYME UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CASPASE_CYS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CASPASE_HIS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CASPASE_P10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CASPASE_P20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CASc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52129 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1B0GWP9_RAT UniProtKB/TrEMBL
  CASP6_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6AZ23 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Casp6  caspase 6  LOC103689977  caspase-6  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103689977  caspase-6      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-07-09 Casp6  caspase 6      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_product member of the caspase family of cell death proteases 632425