Apaf1 (apoptotic peptidase activating factor 1) - Rat Genome Database

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Gene: Apaf1 (apoptotic peptidase activating factor 1) Rattus norvegicus
Analyze
Symbol: Apaf1
Name: apoptotic peptidase activating factor 1
RGD ID: 620575
Description: Enables heat shock protein binding activity and identical protein binding activity. Involved in several processes, including animal organ development; cardiac muscle cell apoptotic process; and cellular response to transforming growth factor beta stimulus. Located in cytoplasm. Part of apoptosome. Used to study visual epilepsy. Biomarker of brain ischemia; colon cancer; middle cerebral artery infarction; and muscular atrophy. Orthologous to human APAF1 (apoptotic peptidase activating factor 1); PARTICIPATES IN intrinsic apoptotic pathway; Alzheimer's disease pathway; amyotrophic lateral sclerosis pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: apaf-1; apoptotic protease activating factor 1; apoptotic protease-activating factor 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
mRatBN7.2725,494,143 - 25,579,540 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl725,494,609 - 25,579,540 (-)Ensembl
Rnor_6.0731,699,309 - 31,784,192 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl731,699,885 - 31,784,192 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0731,791,073 - 31,872,984 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4727,932,908 - 28,020,533 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1727,953,178 - 28,040,804 (-)NCBI
Celera722,620,761 - 22,706,298 (-)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-naringenin  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-D  (ISO)
2,4-dinitrophenol  (ISO)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-methylcholanthrene  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4-hydroxyphenyl retinamide  (ISO)
4-nonylphenol  (EXP)
4-phenylbutyric acid  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-O-methylguanine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
alloxan  (EXP)
apigenin  (EXP,ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
azadirachtin A  (ISO)
bafilomycin A1  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bifenthrin  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bufalin  (ISO)
butyric acid  (ISO)
cadmium dichloride  (ISO)
cadmium sulfide  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carnosic acid  (ISO)
casticin  (ISO)
ceric oxide  (ISO)
chlorpyrifos  (ISO)
cholesterol  (EXP)
choline  (ISO)
cimetidine  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
coenzyme Q10  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
curcumin  (EXP,ISO)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyfluthrin  (ISO)
cylindrospermopsin  (ISO)
cypermethrin  (ISO)
DDE  (EXP)
diarsenic trioxide  (EXP,ISO)
diazinon  (EXP)
diclofenac  (ISO)
dieldrin  (EXP)
diepoxybutane  (ISO)
diethyl maleate  (ISO)
diethyldithiocarbamic acid  (ISO)
dioscin  (ISO)
dioxygen  (EXP)
doxorubicin  (EXP,ISO)
ellagic acid  (ISO)
endosulfan  (EXP,ISO)
epichlorohydrin  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (EXP)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
eugenol  (ISO)
flavone  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fructose  (ISO)
furan  (EXP)
furosemide  (EXP)
genistein  (ISO)
gentamycin  (EXP)
gingerol  (ISO)
glucaric acid  (ISO)
glyphosate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hydroxyurea  (ISO)
indole-3-methanol  (ISO)
isoflurane  (EXP)
isoprenaline  (ISO)
ivermectin  (ISO)
kainic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lead nitrate  (ISO)
leptomycin B  (ISO)
linuron  (EXP)
lipopolysaccharide  (ISO)
mancozeb  (ISO)
mangiferin  (ISO)
MeIQx  (ISO)
melittin  (EXP,ISO)
metformin  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
morin  (ISO)
N-acetyl-L-cysteine  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
neomycin  (ISO)
nickel atom  (ISO)
nicotinamide  (ISO)
ochratoxin A  (EXP,ISO)
okadaic acid  (ISO)
ouabain  (ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
paeoniflorin  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pentobarbital  (EXP)
perfluorononanoic acid  (ISO)
peroxynitrous acid  (EXP)
phenethyl isothiocyanate  (ISO)
phenobarbital  (EXP,ISO)
PhIP  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
propofol  (EXP)
propylparaben  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
safrole  (ISO)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (ISO)
sodium fluoride  (ISO)
tanespimycin  (ISO)
taurine  (EXP)
tauroursodeoxycholic acid  (EXP)
tert-butyl hydroperoxide  (EXP,ISO)
topotecan  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP,ISO)
troglitazone  (EXP)
urethane  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (ISO)
vemurafenib  (ISO)
vinclozolin  (EXP)
WIN 55212-2  (ISO)
zebularine  (ISO)
zinc oxide  (ISO)
zoledronic acid  (ISO)

References

References - curated
1. Baker DJ and Hepple RT, Exp Gerontol. 2006 Nov;41(11):1149-56. Epub 2006 Oct 6.
2. Bhattacharjee M, etal., Int Immunol. 2008 Dec;20(12):1489-505. Epub 2008 Oct 17.
3. Choi SA, etal., FEBS Lett. 2006 Oct 2;580(22):5275-82. Epub 2006 Sep 11.
4. Chong ZZ, etal., J Cereb Blood Flow Metab 2003 Mar;23(3):320-30.
5. Corvaro M, etal., Cancer Biol Ther. 2007 Feb;6(2):209-17. Epub 2007 Feb 25.
6. Erol B, etal., Andrology. 2017 Jan;5(1):119-124. doi: 10.1111/andr.12268. Epub 2016 Oct 16.
7. Erol B, etal., Kaohsiung J Med Sci. 2015 Sep;31(9):454-62. doi: 10.1016/j.kjms.2015.06.005. Epub 2015 Jul 22.
8. Freathy C, etal., Hepatology. 2000 Oct;32(4 Pt 1):750-60.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Henshall DC, etal., Cell Death Differ. 2001 Dec;8(12):1169-81.
12. Honarpour N, etal., Proc Natl Acad Sci U S A 2001 Aug 14;98(17):9683-7.
13. Kawamoto Y, etal., Brain Res. 2014 Jul 7;1571:39-48. doi: 10.1016/j.brainres.2014.05.007. Epub 2014 May 13.
14. Kotipatruni RR, etal., Neurochem Res. 2011 Nov;36(11):2063-74. doi: 10.1007/s11064-011-0530-2. Epub 2011 Jul 7.
15. Li T, etal., Biomed Pharmacother. 2017 Dec;96:153-164. doi: 10.1016/j.biopha.2017.09.102. Epub 2017 Oct 2.
16. MGD data from the GO Consortium
17. Mochizuki H, etal., Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10918-23. doi: 10.1073/pnas.191107398. Epub 2001 Sep 4.
18. Mondragon L, etal., J Med Chem. 2008 Feb 14;51(3):521-9. Epub 2008 Jan 16.
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. Online Mendelian Inheritance in Man, OMIM (TM).
21. Orzáez M, etal., PLoS One. 2014 Oct 20;9(10):e110979. doi: 10.1371/journal.pone.0110979. eCollection 2014.
22. Ota K, etal., J Biochem (Tokyo) 2002 Jan;131(1):131-5.
23. Pipeline to import KEGG annotations from KEGG into RGD
24. RGD automated data pipeline
25. RGD automated import pipeline for gene-chemical interactions
26. Saini MK, etal., Nutr Cancer. 2012 Apr;64(3):409-18. doi: 10.1080/01635581.2012.655402. Epub 2012 Feb 27.
27. Siniscalco D, etal., Pharmacol Res. 2008 Mar;57(3):223-33. Epub 2008 Feb 2.
28. Song S, etal., Biochem Biophys Res Commun. 2015 Sep 18;465(2):299-304. doi: 10.1016/j.bbrc.2015.08.028. Epub 2015 Aug 8.
29. Song XF, etal., Nephron. 2017;135(1):77-86. doi: 10.1159/000450585. Epub 2016 Sep 24.
30. Thompson HJ, etal., Cancer Res. 2004 Feb 15;64(4):1541-5.
31. Tran TH, etal., J Biol Chem. 2007 Jul 13;282(28):20340-50. Epub 2007 May 4.
32. Wright KM, etal., J Cell Biol. 2004 Oct 25;167(2):303-13.
33. Xu XH, etal., Acta Pharmacol Sin. 2007 Aug;28(8):1097-104.
34. Yagmurdur H, etal., Acta Anaesthesiol Scand. 2008 Mar;52(3):350-7. Epub 2008 Jan 16.
35. Yakovlev AG, etal., J Neurosci. 2001 Oct 1;21(19):7439-46.
36. Yoshida H, etal., Cell 1998 Sep 18;94(6):739-50.
37. Zhang S, etal., Neurochem Int. 2013 Nov;63(5):522-32. doi: 10.1016/j.neuint.2013.08.008. Epub 2013 Sep 4.
38. Zhang Z, etal., Exp Eye Res. 2012 Jan;94(1):98-108. Epub 2011 Nov 28.
Additional References at PubMed
PMID:9216040   PMID:9267021   PMID:9753320   PMID:10830166   PMID:11821383   PMID:15271982   PMID:15703386   PMID:15776018   PMID:15877105   PMID:15907471   PMID:16183742   PMID:16207793  
PMID:16375719   PMID:16407291   PMID:19056867   PMID:21827945   PMID:27443636   PMID:27580417   PMID:31212066  


Genomics

Comparative Map Data
Apaf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2725,494,143 - 25,579,540 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl725,494,609 - 25,579,540 (-)Ensembl
Rnor_6.0731,699,309 - 31,784,192 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl731,699,885 - 31,784,192 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0731,791,073 - 31,872,984 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4727,932,908 - 28,020,533 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1727,953,178 - 28,040,804 (-)NCBI
Celera722,620,761 - 22,706,298 (-)NCBICelera
Cytogenetic Map7q13NCBI
APAF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1298,645,290 - 98,735,433 (+)EnsemblGRCh38hg38GRCh38
GRCh381298,645,141 - 98,735,433 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371299,039,068 - 99,129,211 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361297,563,209 - 97,653,342 (+)NCBINCBI36hg18NCBI36
Build 341297,541,545 - 97,631,678NCBI
Celera1298,703,974 - 98,794,106 (+)NCBI
Cytogenetic Map12q23.1NCBI
HuRef1296,100,029 - 96,190,306 (+)NCBIHuRef
CHM1_11299,004,024 - 99,094,151 (+)NCBICHM1_1
Apaf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391090,825,173 - 90,918,688 (-)NCBIGRCm39mm39
GRCm39 Ensembl1090,825,173 - 90,918,632 (-)Ensembl
GRCm381090,989,311 - 91,082,743 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1090,989,311 - 91,082,770 (-)EnsemblGRCm38mm10GRCm38
MGSCv371090,452,056 - 90,545,488 (-)NCBIGRCm37mm9NCBIm37
MGSCv361090,420,401 - 90,512,501 (-)NCBImm8
Celera1092,983,615 - 93,080,742 (-)NCBICelera
Cytogenetic Map10C2NCBI
cM Map1045.47NCBI
Apaf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540534,623,267 - 34,693,677 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540534,619,780 - 34,693,616 (+)NCBIChiLan1.0ChiLan1.0
APAF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11299,637,622 - 99,726,946 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1299,637,622 - 99,726,939 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01296,224,515 - 96,311,246 (+)NCBIMhudiblu_PPA_v0panPan3
APAF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11538,026,893 - 38,160,842 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1538,028,132 - 38,114,987 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1538,408,276 - 38,554,051 (+)NCBI
ROS_Cfam_1.01538,689,945 - 38,835,971 (+)NCBI
UMICH_Zoey_3.11537,961,882 - 38,107,501 (+)NCBI
UNSW_CanFamBas_1.01538,054,503 - 38,200,556 (+)NCBI
UU_Cfam_GSD_1.01538,328,187 - 38,474,238 (+)NCBI
Apaf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494521,806,281 - 21,891,969 (-)NCBI
SpeTri2.0NW_00493649214,818,561 - 14,902,231 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APAF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl585,166,628 - 85,258,364 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1585,166,616 - 85,258,751 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2589,443,106 - 89,580,992 (-)NCBISscrofa10.2Sscrofa10.2susScr3
APAF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11193,942,137 - 94,024,728 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1193,942,103 - 94,024,457 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037151,034,383 - 151,120,759 (-)NCBIVero_WHO_p1.0
Apaf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247508,835,521 - 8,940,957 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)71816950526029351Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)72055570529891047Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:110
Count of miRNA genes:90
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000010869
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
Medium 2 20 14 6 19 6 56 20 33 11
Low 1 23 43 35 35 8 11 18 15 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010869   ⟹   ENSRNOP00000010869
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl725,494,609 - 25,579,540 (-)Ensembl
Rnor_6.0 Ensembl731,699,885 - 31,784,192 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115920   ⟹   ENSRNOP00000081242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl725,494,609 - 25,579,540 (-)Ensembl
RefSeq Acc Id: NM_023979   ⟹   NP_076469
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2725,494,596 - 25,579,540 (-)NCBI
Rnor_6.0731,699,872 - 31,784,192 (-)NCBI
Rnor_5.0731,791,073 - 31,872,984 (-)NCBI
RGSC_v3.4727,932,908 - 28,020,533 (-)RGD
Celera722,620,761 - 22,706,298 (-)RGD
Sequence:
RefSeq Acc Id: XM_008765263   ⟹   XP_008763485
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2725,494,143 - 25,575,368 (-)NCBI
Rnor_6.0731,699,309 - 31,770,327 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_076469   ⟸   NM_023979
- UniProtKB: Q9EPV5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763485   ⟸   XM_008765263
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000010869   ⟸   ENSRNOT00000010869
RefSeq Acc Id: ENSRNOP00000081242   ⟸   ENSRNOT00000115920
Protein Domains
CARD   NB-ARC

Transcriptome

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

Promoters
RGD ID:13695139
Promoter ID:EPDNEW_R5664
Type:multiple initiation site
Name:Apaf1_1
Description:apoptotic peptidase activating factor 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_6.0731,784,141 - 31,784,201EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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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
Damaging Variants


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 25557498 25557499 C T snv BUF/N (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 31762152 31762153 C T snv BUF/N (2020), Buf/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620575 AgrOrtholog
Ensembl Genes ENSRNOG00000008022 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000010869 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000010869 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot
  2.130.10.10 UniProtKB/Swiss-Prot
InterPro Apaf-1 UniProtKB/Swiss-Prot
  APAF1_C UniProtKB/Swiss-Prot
  APAF1_CARD_dom UniProtKB/Swiss-Prot
  CARD UniProtKB/Swiss-Prot
  DEATH-like_dom_sf UniProtKB/Swiss-Prot
  G-protein_beta_WD-40_rep UniProtKB/Swiss-Prot
  NB-ARC UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot
  WD40_repeat UniProtKB/Swiss-Prot
  WD40_repeat_CS UniProtKB/Swiss-Prot
  WD40_repeat_dom UniProtKB/Swiss-Prot
  WD40_repeat_dom_sf UniProtKB/Swiss-Prot
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot
KEGG Report rno:78963 UniProtKB/Swiss-Prot
NCBI Gene 78963 ENTREZGENE
Pfam APAF1_C UniProtKB/Swiss-Prot
  CARD UniProtKB/Swiss-Prot
  NB-ARC UniProtKB/Swiss-Prot
  WD40 UniProtKB/Swiss-Prot
PhenoGen Apaf1 PhenoGen
PIRSF Apop_pept_activating-1 UniProtKB/Swiss-Prot
PRINTS GPROTEINBRPT UniProtKB/Swiss-Prot
PROSITE CARD UniProtKB/Swiss-Prot
  WD_REPEATS_1 UniProtKB/Swiss-Prot
  WD_REPEATS_2 UniProtKB/Swiss-Prot
  WD_REPEATS_REGION UniProtKB/Swiss-Prot
SMART WD40 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47986 UniProtKB/Swiss-Prot
  SSF50978 UniProtKB/Swiss-Prot
  SSF52540 UniProtKB/Swiss-Prot
UniProt APAF_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Apaf1  apoptotic peptidase activating factor 1    apoptotic protease activating factor 1  Name updated 1299863 APPROVED
2002-08-07 Apaf1  apoptotic protease activating factor 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expression suppressed within 4 weeks after birth in brain tissue 1299279