Aifm1 (apoptosis inducing factor, mitochondria associated 1) - Rat Genome Database

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Gene: Aifm1 (apoptosis inducing factor, mitochondria associated 1) Rattus norvegicus
Analyze
Symbol: Aifm1
Name: apoptosis inducing factor, mitochondria associated 1
RGD ID: 620817
Description: Predicted to enable DNA binding activity; FAD binding activity; and NAD(P)H oxidase H2O2-forming activity. Involved in several processes, including cellular response to lipid; cellular response to nitric oxide; and cellular response to oxygen-glucose deprivation. Located in cytosol; mitochondrion; and nucleus. Biomarker of middle cerebral artery infarction; retinal detachment; retinitis pigmentosa; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease X-linked recessive 4; X-linked deafness 5; and combined oxidative phosphorylation deficiency 6. Orthologous to several human genes including TXNDC12 (thioredoxin domain containing 12); PARTICIPATES IN ceramide signaling pathway; apoptotic cell death pathway; INTERACTS WITH (+)-schisandrin B; (+)-sesamin; (Z)-3-butylidenephthalide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Aif; apoptosis-inducing factor 1, mitochondrial; apoptosis-inducing factor 1, mitochondrial-like; apoptosis-inducing factor, mitochondrion-associated 1; LOC103694586; Pdcd8; programmed cell death 8; programmed cell death 8 (apoptosis-inducing factor); programmed cell death protein 8
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
mRatBN7.2X127,650,223 - 127,689,356 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX127,650,226 - 127,689,256 (-)Ensembl
Rnor_6.0X135,304,063 - 135,343,062 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX135,304,066 - 135,343,087 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X135,375,533 - 135,414,532 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X134,868,878 - 134,908,166 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X134,942,310 - 134,981,599 (-)NCBI
CeleraX126,598,666 - 126,637,656 (-)NCBICelera
Cytogenetic MapXq36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(+)-sesamin  (EXP)
(+)-Tetrandrine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(-)-gambogic acid  (ISO)
(-)-selegiline  (ISO)
(S)-ropivacaine  (ISO)
(Z)-3-butylidenephthalide  (EXP,ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrotoluene  (EXP)
2-(4-iodo-2,5-dimethoxyphenyl)-1-methylethylamine  (EXP)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3-chloropropane-1,2-diol  (ISO)
3-methyladenine  (EXP)
4-hydroperoxycyclophosphamide  (ISO)
4-hydroxynon-2-enal  (ISO)
5-fluorouracil  (ISO)
5-Hydroxycapric acid  (EXP)
6-bromoindirubin-3'-oxime  (ISO)
8-Br-cAMP  (ISO)
9'-cis-neoxanthin  (ISO)
acrolein  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucose  (EXP)
all-trans-neoxanthin  (ISO)
all-trans-retinoic acid  (ISO)
alpha-mangostin  (ISO)
alpha-pinene  (ISO)
alvocidib  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
arsenic acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
artesunate  (ISO)
astaxanthin  (ISO)
atrazine  (ISO)
azide  (EXP)
beauvericin  (ISO)
benzamide  (ISO)
benzo[a]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
Brodifacoum  (EXP)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
canertinib  (ISO)
cantharidin  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
casticin  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (EXP,ISO)
chrysazin  (ISO)
ciguatoxin CTX1B  (ISO)
cilostazol  (ISO)
cisplatin  (ISO)
clonidine  (ISO)
clonidine (amino form)  (ISO)
clonidine (imino form)  (ISO)
cobalt dichloride  (ISO)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumarins  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
D-glucose  (EXP)
Deguelin  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (EXP,ISO)
diazinon  (EXP)
diazoxide  (EXP)
dichlorvos  (EXP)
diclofenac  (ISO)
dimethyl sulfoxide  (ISO)
disodium selenite  (ISO)
dizocilpine maleate  (EXP)
doxorubicin  (ISO)
ellagic acid  (ISO)
enniatin  (EXP)
entinostat  (ISO)
erdosteine  (ISO)
ethanol  (ISO)
excitatory amino acid agonist  (EXP)
fisetin  (ISO)
flutamide  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
glucose  (EXP)
glutathione  (ISO)
glyphosate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hexachlorobenzene  (EXP)
homoeriodictyol  (ISO)
hydrogen peroxide  (EXP,ISO)
iodoacetic acid  (ISO)
isoflurane  (EXP)
isotretinoin  (ISO)
ivermectin  (ISO)
kainic acid  (ISO)
KN-93  (ISO)
lactacystin  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (EXP)
mangiferin  (EXP)
mechlorethamine  (ISO)
metformin  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
minocycline  (EXP,ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monobenzyl phthalate  (ISO)
monocrotophos  (ISO)
monoethyl phthalate  (ISO)
morin  (EXP)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-tosyl-L-phenylalanyl chloromethyl ketone  (ISO)
nelfinavir  (ISO)
nickel dichloride  (EXP)
niclosamide  (ISO)
nitric oxide  (ISO)
nitrofen  (ISO)
nitroprusside  (ISO)
norfloxacin  (ISO)
ochratoxin A  (ISO)
ouabain  (ISO)
oxidopamine  (EXP,ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
perifosine  (ISO)
phenanthridone  (ISO)
phenobarbital  (ISO)
phenylephrine  (ISO)
phosphatidylcholine  (ISO)
phytosphingosine  (ISO)
picoxystrobin  (ISO)
Pranoprofen  (ISO)
quercetin  (EXP,ISO)
reactive oxygen species  (EXP,ISO)
resveratrol  (EXP,ISO)
rosmarinic acid  (ISO)
rotenone  (EXP,ISO)
rubitecan  (ISO)
S-nitroso-N-acetyl-D-penicillamine  (ISO)
sappanchalcone  (ISO)
SB 203580  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (EXP,ISO)
Soman  (EXP)
sorafenib  (ISO)
streptozocin  (EXP,ISO)
sulfasalazine  (ISO)
sulforaphane  (ISO)
sulindac  (ISO)
swainsonine  (EXP)
tephrosin  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thimerosal  (ISO)
thymol  (ISO)
thymol sulfate(1-)  (ISO)
thymoquinone  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
Triptolide  (ISO)
ursolic acid  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
wortmannin  (EXP)
Z-Val-Phe-H  (EXP)
zearalenone  (ISO)
zinc sulfate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Baker DJ and Hepple RT, Exp Gerontol. 2006 Nov;41(11):1149-56. Epub 2006 Oct 6.
2. Braun JS, etal., J Clin Invest. 2002 Jan;109(1):19-27.
3. Cao G, etal., J Cereb Blood Flow Metab. 2003 Oct;23(10):1137-50.
4. Colak D, etal., Genomics. 2009 Jul;94(1):20-31. doi: 10.1016/j.ygeno.2009.03.003. Epub 2009 Mar 28.
5. Fonfria E, etal., Eur J Neurosci 2002 Nov;16(10):2013-6.
6. GOA data from the GO Consortium
7. Hisatomi T, etal., Am J Pathol. 2001 Apr;158(4):1271-8.
8. Kondo K, etal., J Biol Chem. 2010 Apr 23;285(17):13079-91. doi: 10.1074/jbc.M109.044206. Epub 2010 Feb 22.
9. Lee JH, etal., Anat Cell Biol. 2012 Mar;45(1):26-37. doi: 10.5115/acb.2012.45.1.26. Epub 2012 Mar 31.
10. Li WJ and Oh SJ, Neurourol Urodyn. 2010 Sep;29(7):1332-7. doi: 10.1002/nau.20869.
11. MGD data from the GO Consortium
12. NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. OMIM Disease Annotation Pipeline
14. Ozaki T, etal., PLoS One. 2013 Aug 9;8(8):e71650. doi: 10.1371/journal.pone.0071650. eCollection 2013.
15. Pipeline to import KEGG annotations from KEGG into RGD
16. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
17. Plesnila N, etal., J Cereb Blood Flow Metab. 2004 Apr;24(4):458-66.
18. Pytlowany M, etal., Acta Biochim Pol. 2008;55(2):339-47. Epub 2008 Jun 14.
19. RGD automated data pipeline
20. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. RGD automated import pipeline for gene-chemical interactions
22. RGD comprehensive gene curation
23. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
24. Xiao TT, etal., PLoS One. 2014 Feb 13;9(2):e88856. doi: 10.1371/journal.pone.0088856. eCollection 2014.
25. Xu A, etal., Biochem Biophys Res Commun. 2013 Jun 14;435(4):627-33. doi: 10.1016/j.bbrc.2013.05.033. Epub 2013 May 16.
26. Yang X, etal., Neuroscience. 2017 Mar 27;346:74-80. doi: 10.1016/j.neuroscience.2017.01.010. Epub 2017 Jan 17.
27. Yu W, etal., BMC Neurosci. 2014 Jun 10;15:73. doi: 10.1186/1471-2202-15-73.
28. Zhang X, etal., J Neurochem. 2002 Jul;82(1):181-91.
29. Zhang Y and Bhavnani BR, BMC Neurosci. 2006 Jun 15;7:49.
30. Zhao H, etal., J Cereb Blood Flow Metab. 2004 Jun;24(6):681-92.
31. Zhu C, etal., J Neurochem. 2003 Jul;86(2):306-17.
Additional References at PubMed
PMID:12963035   PMID:14651853   PMID:14707049   PMID:15271982   PMID:15379992   PMID:15489334   PMID:15703386   PMID:15775970   PMID:16077187   PMID:16469926   PMID:17050806   PMID:17094969  
PMID:17292393   PMID:17632284   PMID:18056262   PMID:18508388   PMID:18559257   PMID:18614015   PMID:18782186   PMID:18845835   PMID:19039676   PMID:19061880   PMID:19094082   PMID:19139267  
PMID:19433269   PMID:19633014   PMID:19833151   PMID:19944742   PMID:20111043   PMID:20360685   PMID:20833797   PMID:20850531   PMID:21387140   PMID:21467298   PMID:21502359   PMID:21873635  
PMID:23006905   PMID:23217327   PMID:24191052   PMID:25283819   PMID:26004228   PMID:26206088   PMID:26316108   PMID:26963167   PMID:27178839   PMID:27377128   PMID:27735993   PMID:28411026  
PMID:31654209   PMID:32319616   PMID:32338336   PMID:33940381  


Genomics

Comparative Map Data
Aifm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X127,650,223 - 127,689,356 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX127,650,226 - 127,689,256 (-)Ensembl
Rnor_6.0X135,304,063 - 135,343,062 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX135,304,066 - 135,343,087 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X135,375,533 - 135,414,532 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X134,868,878 - 134,908,166 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X134,942,310 - 134,981,599 (-)NCBI
CeleraX126,598,666 - 126,637,656 (-)NCBICelera
Cytogenetic MapXq36NCBI
AIFM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX130,124,666 - 130,165,879 (-)EnsemblGRCh38hg38GRCh38
GRCh38X130,129,362 - 130,165,841 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X129,263,337 - 129,299,815 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X129,091,018 - 129,127,489 (-)NCBINCBI36hg18NCBI36
Build 34X128,988,871 - 129,025,343NCBI
CeleraX129,649,901 - 129,686,423 (-)NCBI
Cytogenetic MapXq26.1NCBI
HuRefX118,659,694 - 118,695,647 (-)NCBIHuRef
CHM1_1X129,174,949 - 129,211,491 (-)NCBICHM1_1
Aifm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X47,563,821 - 47,602,440 (-)NCBIGRCm39mm39
GRCm39 EnsemblX47,563,821 - 47,602,440 (-)Ensembl
GRCm38X48,474,944 - 48,513,563 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX48,474,944 - 48,513,563 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X45,828,121 - 45,866,603 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X44,719,571 - 44,758,053 (-)NCBImm8
CeleraX35,976,732 - 36,015,059 (-)NCBICelera
Cytogenetic MapXA5NCBI
cM MapX25.68NCBI
Aifm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554734,891,955 - 4,926,428 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554734,891,955 - 4,925,705 (+)NCBIChiLan1.0ChiLan1.0
AIFM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X129,550,287 - 129,586,271 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX129,550,287 - 129,586,271 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X119,256,425 - 119,292,612 (-)NCBIMhudiblu_PPA_v0panPan3
AIFM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X101,275,027 - 101,307,551 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX101,275,017 - 101,307,367 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX87,452,794 - 87,485,312 (-)NCBI
ROS_Cfam_1.0X103,131,319 - 103,163,843 (-)NCBI
UMICH_Zoey_3.1X100,548,672 - 100,581,159 (-)NCBI
UNSW_CanFamBas_1.0X102,394,696 - 102,427,200 (-)NCBI
UU_Cfam_GSD_1.0X102,173,062 - 102,205,583 (-)NCBI
Aifm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X99,510,362 - 99,545,953 (-)NCBI
SpeTri2.0NW_0049364791,441,508 - 1,477,133 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AIFM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX106,670,519 - 106,708,317 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X106,676,596 - 106,708,290 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X122,445,239 - 122,476,575 (-)NCBISscrofa10.2Sscrofa10.2susScr3
AIFM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X105,383,408 - 105,419,146 (-)NCBI
ChlSab1.1 EnsemblX105,382,693 - 105,419,095 (-)Ensembl
Vero_WHO_p1.0NW_02366606542,809,379 - 42,845,438 (-)NCBI
Aifm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247979,346,620 - 9,384,531 (-)NCBI

Position Markers
RH133831  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X127,685,256 - 127,685,467 (+)MAPPERmRatBN7.2
Rnor_6.0X135,339,092 - 135,339,302NCBIRnor6.0
Rnor_5.0X135,410,562 - 135,410,772UniSTSRnor5.0
RGSC_v3.4X134,904,196 - 134,904,406UniSTSRGSC3.4
CeleraX126,633,686 - 126,633,896UniSTS
RH 3.4 MapX920.4UniSTS
Cytogenetic MapXq35UniSTS
AA901280  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X127,650,284 - 127,650,463 (+)MAPPERmRatBN7.2
Rnor_6.0X135,304,125 - 135,304,303NCBIRnor6.0
Rnor_5.0X135,375,595 - 135,375,773UniSTSRnor5.0
RGSC_v3.4X134,868,940 - 134,869,118UniSTSRGSC3.4
CeleraX126,598,728 - 126,598,906UniSTS
RH 3.4 MapX922.2UniSTS
Cytogenetic MapXq35UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:127
Count of miRNA genes:98
Interacting mature miRNAs:102
Transcripts:ENSRNOT00000008503
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 36 11 8
Low 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008503   ⟹   ENSRNOP00000008503
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX127,650,226 - 127,689,256 (-)Ensembl
Rnor_6.0 EnsemblX135,304,079 - 135,343,087 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084848   ⟹   ENSRNOP00000074241
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX127,650,226 - 127,689,246 (-)Ensembl
Rnor_6.0 EnsemblX135,304,066 - 135,342,996 (-)Ensembl
RefSeq Acc Id: NM_031356   ⟹   NP_112646
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X127,650,223 - 127,689,356 (-)NCBI
Rnor_6.0X135,304,063 - 135,343,062 (-)NCBI
Rnor_5.0X135,375,533 - 135,414,532 (-)NCBI
RGSC_v3.4X134,868,878 - 134,908,166 (-)RGD
CeleraX126,598,666 - 126,637,656 (-)RGD
Sequence:
RefSeq Acc Id: XM_039100097   ⟹   XP_038956025
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X127,650,223 - 127,689,335 (-)NCBI
RefSeq Acc Id: XM_039100098   ⟹   XP_038956026
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X127,650,223 - 127,689,332 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_112646   ⟸   NM_031356
- Peptide Label: precursor
- UniProtKB: Q9JM53 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008503   ⟸   ENSRNOT00000008503
RefSeq Acc Id: ENSRNOP00000074241   ⟸   ENSRNOT00000084848
RefSeq Acc Id: XP_038956025   ⟸   XM_039100097
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038956026   ⟸   XM_039100098
- Peptide Label: isoform X2
Protein Domains
AIF-MLS   AIF_C   Pyr_redox_2

Transcriptome

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

Promoters
RGD ID:13702018
Promoter ID:EPDNEW_R12536
Type:initiation region
Name:Aifm1_1
Description:apoptosis inducing factor, mitochondria associated 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12537  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X135,343,073 - 135,343,133EPDNEW
RGD ID:13702013
Promoter ID:EPDNEW_R12537
Type:single initiation site
Name:Aifm1_2
Description:apoptosis inducing factor, mitochondria associated 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12536  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X135,343,175 - 135,343,235EPDNEW

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)
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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)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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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
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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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
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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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
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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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
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LEW/Crl (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
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/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
M520/NRrrcMcwi (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
MHS/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
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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)
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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)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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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:620817 AgrOrtholog
Ensembl Genes ENSRNOG00000006067 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008503 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000074241 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008503 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000084848 UniProtKB/TrEMBL
Gene3D-CATH 3.30.390.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.50.50.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7105761 IMAGE-MGC_LOAD
InterPro AIF_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD/NAD-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD/NAD-binding_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FAD/NAD-linked_Rdtase_dimer_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MGARP_N UniProtKB/TrEMBL
KEGG Report rno:83533 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91436 IMAGE-MGC_LOAD
NCBI Gene 83533 ENTREZGENE
Pfam AIF-MLS UniProtKB/TrEMBL
  AIF_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pyr_redox_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Aifm1 PhenoGen
Superfamily-SCOP SSF51905 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55424 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K7K2_RAT UniProtKB/TrEMBL
  AIFM1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q548E3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Aifm1  apoptosis inducing factor, mitochondria associated 1  LOC103694586  apoptosis-inducing factor 1, mitochondrial-like  Data Merged 737654 PROVISIONAL
2015-11-25 Aifm1  apoptosis inducing factor, mitochondria associated 1  Aifm1  apoptosis-inducing factor, mitochondrion-associated 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103694586  apoptosis-inducing factor 1, mitochondrial-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-02-25 Aifm1  apoptosis-inducing factor, mitochondrion-associated 1  Pdcd8  programmed cell death 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Pdcd8  programmed cell death 8    programmed cell death 8 (apoptosis-inducing factor)  Name updated 1299863 APPROVED
2002-08-07 Pdcd8  programmed cell death 8 (apoptosis-inducing factor)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation undergoes translocation from mitochondria to the nucleus in cerebellar granule cells in response to oxidative stress 633556