Aif1 (allograft inflammatory factor 1) - Rat Genome Database

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Gene: Aif1 (allograft inflammatory factor 1) Rattus norvegicus
Analyze
Symbol: Aif1
Name: allograft inflammatory factor 1
RGD ID: 61924
Description: Predicted to have actin filament binding activity and calcium ion binding activity. Involved in several processes, including cellular response to morphine; positive regulation of muscle hyperplasia; and positive regulation of nitrogen compound metabolic process. Localizes to cytosol; lamellipodium; and perikaryon. Predicted to colocalize with actin filament and ruffle membrane. Used to study type 1 diabetes mellitus. Biomarker of brain disease (multiple); glomerulonephritis; meningoencephalitis; and motor neuron disease. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus. Orthologous to human AIF1 (allograft inflammatory factor 1); INTERACTS WITH (+)-pilocarpine; (S)-colchicine; 1-naphthyl isothiocyanate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AIF-1; balloon angioplasty responsive transcript; balloon angioplasty-responsive transcript 1; BART-1; Bart1; iba1; ionized calcium binding adapter molecule 1; ionized calcium-binding adapter molecule 1; microglia response factor; mrf-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,646,784 - 3,652,670 (+)NCBI
Rnor_6.0 Ensembl205,161,333 - 5,166,448 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,161,350 - 5,167,176 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,234,609 - 7,240,454 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,714,428 - 3,716,327 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,714,654 - 3,716,552NCBI
Celera204,373,127 - 4,375,026 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(S)-colchicine  (EXP)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,5-hexanedione  (EXP)
2-nitrofluorene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,3'-diindolylmethane  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
8-OH-DPAT  (ISO)
acetamide  (EXP)
aconitine  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
allyl isothiocyanate  (EXP)
alpha-D-galactose  (ISO)
amentoflavone  (ISO)
aminoguanidine  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
apocynin  (ISO)
arsenous acid  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
cadmium dichloride  (EXP)
calcitriol  (EXP)
carbon nanotube  (ISO)
chloroprene  (ISO)
chlorpyrifos  (EXP)
chrysene  (ISO)
cisplatin  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
cyprodinil  (ISO)
dabigatran  (ISO)
decabromodiphenyl ether  (EXP)
diarsenic trioxide  (ISO)
diisopropyl fluorophosphate  (EXP)
diuron  (EXP)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (EXP)
ethylmalonic acid  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
galactose  (ISO)
gentamycin  (EXP)
ginsenoside Re  (ISO)
glyburide  (EXP,ISO)
hexachlorobenzene  (EXP)
Ibudilast  (EXP)
isoprenaline  (ISO)
kainic acid  (EXP)
lead diacetate  (EXP,ISO)
lipopolysaccharide  (EXP,ISO)
lycopene  (ISO)
Magnolol  (ISO)
maneb  (ISO)
manganese(II) chloride  (ISO)
medroxyprogesterone acetate  (ISO)
mepanipyrim  (ISO)
methamphetamine  (ISO)
methylmalonic acid  (EXP)
methylmercury chloride  (ISO)
minocycline  (ISO)
morphine  (EXP)
mycophenolic acid  (EXP)
N-[2-[4-(2-methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl)cyclohexanecarboxamide  (ISO)
N-butylbenzenesulfonamide  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodimethylamine  (EXP)
NADP zwitterion  (EXP)
NADP(+)  (EXP)
nevirapine  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
Nonylphenol  (EXP)
Norbinaltorphimine  (ISO)
oxaliplatin  (EXP)
oxybenzone  (EXP)
p-menthan-3-ol  (ISO)
paraquat  (ISO)
permethrin  (ISO)
pirinixic acid  (EXP)
pravastatin  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (EXP)
Pyridostigmine bromide  (ISO)
pyrimethanil  (ISO)
quercetin  (EXP)
quinoline  (ISO)
resveratrol  (EXP)
rotenone  (EXP)
rottlerin  (ISO)
SCH 23390  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
sodium dodecyl sulfate  (ISO)
sodium fluoride  (ISO)
sulpiride  (ISO)
tacrolimus hydrate  (ISO)
tadalafil  (ISO)
tamibarotene  (ISO)
Tesaglitazar  (EXP)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
thioacetamide  (EXP,ISO)
titanium dioxide  (ISO)
tolcapone  (EXP)
toluene  (EXP,ISO)
topotecan  (EXP)
tributylstannane  (EXP)
trimethyltin  (ISO)
valproic acid  (ISO)
vincaleukoblastine  (EXP)
zaragozic acid A  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin crosslink formation  (ISO)
actin filament bundle assembly  (IBA,ISO,ISS)
actin filament polymerization  (ISO,ISS)
cellular response to extracellular stimulus  (IEP)
cellular response to hormone stimulus  (IEP)
cellular response to hydroperoxide  (IEP)
cellular response to interferon-gamma  (IEP,ISO)
cellular response to morphine  (IEP)
cellular response to oxidative stress  (ISO)
cerebellum development  (IEP)
inflammatory response  (IEP)
macrophage activation  (NAS)
negative regulation of apoptotic process  (IDA,IMP)
negative regulation of gene expression  (IMP)
negative regulation of smooth muscle cell chemotaxis  (ISO)
negative regulation of smooth muscle cell proliferation  (ISO)
parallel actin filament bundle assembly  (ISO)
phagocytosis, engulfment  (ISO,ISS)
positive regulation of cell migration  (IDA,IMP,ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of chemokine production  (ISO)
positive regulation of chemotaxis  (ISO)
positive regulation of fibroblast growth factor production  (ISO)
positive regulation of G1/S transition of mitotic cell cycle  (ISO,ISS)
positive regulation of interleukin-6 production  (ISO)
positive regulation of monocyte chemotaxis  (ISO,ISS)
positive regulation of mononuclear cell migration  (ISO)
positive regulation of muscle hyperplasia  (IMP)
positive regulation of nitric oxide biosynthetic process  (IDA,IMP)
positive regulation of protein phosphorylation  (IMP)
positive regulation of smooth muscle cell chemotaxis  (ISO,ISS)
positive regulation of smooth muscle cell proliferation  (IMP,ISO,ISS)
positive regulation of T cell migration  (ISO,ISS)
positive regulation of T cell proliferation  (ISO,ISS)
Rac protein signal transduction  (ISO,ISS)
response to axon injury  (IEP)
response to cytokine  (IEP)
response to electrical stimulus  (IEP)
response to glucocorticoid  (IEP)
ruffle assembly  (IBA,ISO,ISS)

Cellular Component
actin filament  (IBA,ISO,ISS)
cell projection  (IDA)
cytoplasm  (IDA,ISO)
cytosol  (IDA,ISO,ISS)
lamellipodium  (IDA,ISO,ISS)
nucleus  (ISO,ISS)
perikaryon  (IDA)
perinuclear region of cytoplasm  (ISO)
phagocytic cup  (ISO,ISS)
ruffle  (ISO)
ruffle membrane  (IBA,IEA,ISO,ISS)

Molecular Function

References

References - curated
1. Almolda B, etal., J Neuroimmunol. 2009 Apr 30;209(1-2):65-80. Epub 2009 Feb 26.
2. Autieri MV, etal., DNA Cell Biol 1996 Apr;15(4):297-304.
3. Autieri MV, etal., Lab Invest 1995 Jun;72(6):656-61.
4. Beiter T, etal., J Neuroimmunol. 2005 Mar;160(1-2):25-31. Epub 2004 Dec 15.
5. Chen ZW, etal., Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13879-84.
6. Eike MC, etal., Genes Immun. 2009 Mar;10(2):141-50. Epub 2008 Nov 6.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Girard S, etal., Neuroscience. 2009 Jan 23;158(2):673-82. Epub 2008 Oct 30.
9. GOA data from the GO Consortium
10. Hathway GJ, etal., Pain. 2009 Apr 30.
11. Herden C, etal., Neuropathol Appl Neurobiol. 2005 Oct;31(5):512-21.
12. Hirsch J, etal., Mol Cell Proteomics. 2006 Jun;5(6):979-86. Epub 2006 Feb 24.
13. Horvath RJ and DeLeo JA, J Neurosci. 2009 Jan 28;29(4):998-1005.
14. Horvath RJ, etal., J Neurochem. 2008 Oct;107(2):557-69. Epub 2008 Sep 18.
15. Jakubs K, etal., J Neurosci. 2008 Nov 19;28(47):12477-88.
16. Jakubs K, etal., Neuron. 2006 Dec 21;52(6):1047-59.
17. Kalm M, etal., J Neuroimmunol. 2009 Jan 3;206(1-2):70-5. Epub 2008 Dec 13.
18. Lee JK, etal., Neurosci Lett. 2009 Jan 30;450(2):136-41. Epub 2008 Dec 6.
19. Lepore AC, etal., Nat Neurosci. 2008 Nov;11(11):1294-301. Epub 2008 Oct 19.
20. MGD data from the GO Consortium
21. Mishima T, etal., Int J Mol Med. 2008 Feb;21(2):181-7.
22. Nakano T, etal., Neurosci Lett. 2009 Sep 18;461(2):110-5. Epub 2009 Jun 9.
23. Narita M, etal., Neurosci Lett. 2007 Feb 27;414(1):21-5. Epub 2006 Dec 15.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. Nixon K, etal., Neurobiol Dis. 2008 Aug;31(2):218-29. Epub 2008 May 3.
26. Penas C, etal., J Neurotrauma. 2009 May;26(5):763-79.
27. Postler E, etal., J Neuroimmunol. 2000 Apr 3;104(1):85-91.
28. Rappold PM, etal., Brain Res. 2006 May 17;1089(1):171-8. Epub 2006 Apr 25.
29. RGD automated data pipeline
30. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31. RGD automated import pipeline for gene-chemical interactions
32. Rivera EJ, etal., J Alzheimers Dis. 2005 Dec;8(3):247-68.
33. Romcy-Pereira RN, etal., Physiol Behav. 2009 Aug 4;98(1-2):44-52. Epub 2009 Apr 20.
34. Sakuma M, etal., J Neural Transm. 2008;115(3):413-22. Epub 2008 Feb 26.
35. Saraswathy S, etal., Invest Ophthalmol Vis Sci. 2006 Aug;47(8):3656-63.
36. Shapiro LA, etal., Brain Res. 2009 Apr 17;1266:29-36. Epub 2009 Feb 26.
37. Sommerville LJ, etal., Cardiovasc Res. 2009 Jan 1;81(1):206-15. Epub 2008 Sep 8.
38. Tanaka S, etal., J Neurosci 1998 Aug 15;18(16):6358-69.
39. Thored P, etal., Glia. 2009 Jun;57(8):835-49.
40. Tsubata Y, etal., Kidney Int. 2006 Dec;70(11):1948-54. Epub 2006 Oct 11.
41. Tsuda M, etal., Glia. 2008 Mar;56(4):378-86.
42. Utans U, etal., J Clin Invest 1995 Jun;95(6):2954-62.
43. Vega-Avelaira D, etal., Brain Behav Immun. 2007 Jul;21(5):617-23. Epub 2006 Dec 8.
44. Wang P, etal., Brain Res. 2008 Oct 21;1236:1-7. Epub 2008 Aug 8.
45. Wixey JA, etal., J Neuroimmunol. 2009 Jul 25;212(1-2):35-43. Epub 2009 May 17.
46. Yang ZF, etal., Int Immunol. 2005 Nov;17(11):1391-7. Epub 2005 Sep 12.
47. Yang ZF, etal., Liver Transpl. 2007 Apr;13(4):558-65.
48. Zhang Z, et al., Acta Neuropathol. 2007 Jun;113(6):675-82. Epub 2007 Jan 31.
Additional References at PubMed
PMID:8713135   PMID:9614071   PMID:10934045   PMID:11500035   PMID:11557666   PMID:12477932   PMID:12887599   PMID:14756805   PMID:15060004   PMID:15117732   PMID:15575896   PMID:16049345  
PMID:16987989   PMID:17011575   PMID:17565360   PMID:18699778   PMID:19745784   PMID:19815232   PMID:19861972   PMID:20572385   PMID:22116621   PMID:23701965   PMID:24571083   PMID:24796669  
PMID:26713069   PMID:28601280   PMID:29864618  


Genomics

Comparative Map Data
Aif1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,646,784 - 3,652,670 (+)NCBI
Rnor_6.0 Ensembl205,161,333 - 5,166,448 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0205,161,350 - 5,167,176 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0207,234,609 - 7,240,454 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,714,428 - 3,716,327 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,714,654 - 3,716,552NCBI
Celera204,373,127 - 4,375,026 (-)NCBICelera
Cytogenetic Map20p12NCBI
AIF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl631,615,217 - 31,617,021 (+)EnsemblGRCh38hg38GRCh38
GRCh38631,615,212 - 31,617,015 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37631,583,011 - 31,584,792 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,691,012 - 31,692,777 (+)NCBINCBI36hg18NCBI36
Build 34631,691,767 - 31,692,777NCBI
Celera633,181,222 - 33,183,026 (+)NCBI
Cytogenetic Map6p21.33NCBI
HuRef631,369,335 - 31,370,975 (+)NCBIHuRef
CHM1_1631,585,122 - 31,586,938 (+)NCBICHM1_1
Aif1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,389,962 - 35,395,050 (-)NCBIGRCm39mm39
GRCm39 Ensembl1735,389,967 - 35,395,044 (-)Ensembl
GRCm381735,170,986 - 35,176,083 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,170,991 - 35,176,068 (-)EnsemblGRCm38mm10GRCm38
MGSCv371735,307,937 - 35,312,946 (-)NCBIGRCm37mm9NCBIm37
MGSCv361734,779,048 - 34,784,057 (-)NCBImm8
Celera1738,267,928 - 38,272,936 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.59NCBI
Aif1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955437157,509 - 158,919 (+)NCBIChiLan1.0ChiLan1.0
AIF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1632,166,301 - 32,168,125 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,166,301 - 32,168,125 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0631,276,215 - 31,278,051 (+)NCBIMhudiblu_PPA_v0panPan3
AIF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,104,350 - 1,106,179 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,104,394 - 1,106,177 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,240,799 - 1,242,629 (+)NCBI
ROS_Cfam_1.0121,249,600 - 1,251,430 (+)NCBI
UMICH_Zoey_3.1121,108,905 - 1,110,735 (+)NCBI
UNSW_CanFamBas_1.0121,176,225 - 1,178,056 (+)NCBI
UU_Cfam_GSD_1.0121,243,086 - 1,244,917 (+)NCBI
Aif1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,651,964 - 35,653,851 (+)NCBI
SpeTri2.0NW_0049367271,907,493 - 1,909,350 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AIF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,711,722 - 23,731,671 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1723,711,752 - 23,731,191 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,520,797 - 27,540,237 (-)NCBISscrofa10.2Sscrofa10.2susScr3
AIF1
(Chlorocebus sabaeus - African green monkey)
No map positions available.
Aif1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,590,071 - 24,591,913 (-)NCBI

Position Markers
RH135373  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0205,161,383 - 5,162,109NCBIRnor6.0
Rnor_5.0207,234,642 - 7,235,368UniSTSRnor5.0
RGSC_v3.4203,715,568 - 3,716,294UniSTSRGSC3.4
Celera204,373,160 - 4,373,886UniSTS
RH 3.4 Map2053.6UniSTS
Cytogenetic Map20p12UniSTS
MARC_5857-5858:997299374:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0205,162,192 - 5,162,779NCBIRnor6.0
Rnor_5.0207,235,451 - 7,236,038UniSTSRnor5.0
RGSC_v3.4203,714,898 - 3,715,485UniSTSRGSC3.4
Celera204,373,969 - 4,374,556UniSTS
Cytogenetic Map20p12UniSTS
Aif1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0205,162,202 - 5,162,960NCBIRnor6.0
Rnor_5.0207,235,461 - 7,236,219UniSTSRnor5.0
RGSC_v3.4203,714,717 - 3,715,475UniSTSRGSC3.4
Celera204,373,979 - 4,374,737UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2015192000Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2020187706567419Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2031518156896013Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2031518156896013Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2039105555533640Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2040391135875448Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2048554689899946Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)20485546810800530Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:115
Count of miRNA genes:82
Interacting mature miRNAs:88
Transcripts:ENSRNOT00000001135, ENSRNOT00000001138
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 1 47 36 19 36 19 10 21 11
Low 1 36 10 5 5 8 11 53 25 20 8
Below cutoff 6 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB000818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC094348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF299328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC081822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474121 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D82069 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM053942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231499 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000323 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U10894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U17919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U33471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000001135   ⟹   ENSRNOP00000001135
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,161,356 - 5,163,247 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000001138   ⟹   ENSRNOP00000001138
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,161,333 - 5,166,252 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076331   ⟹   ENSRNOP00000068279
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,161,350 - 5,166,448 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076979
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,161,350 - 5,163,660 (-)Ensembl
RefSeq Acc Id: NM_017196   ⟹   NP_058892
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,650,771 - 3,652,670 (+)NCBI
Rnor_6.0205,161,350 - 5,163,249 (-)NCBI
Rnor_5.0207,234,609 - 7,240,454 (-)NCBI
RGSC_v3.4203,714,428 - 3,716,327 (+)RGD
Celera204,373,127 - 4,375,026 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256061   ⟹   XP_006256123
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,650,718 - 3,652,670 (+)NCBI
Rnor_6.0205,161,350 - 5,163,366 (-)NCBI
Rnor_5.0207,234,609 - 7,240,454 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256062   ⟹   XP_006256124
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,647,747 - 3,652,670 (+)NCBI
Rnor_6.0205,161,350 - 5,166,254 (-)NCBI
Rnor_5.0207,234,609 - 7,240,454 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256063   ⟹   XP_006256125
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,646,784 - 3,652,670 (+)NCBI
Rnor_6.0205,161,350 - 5,167,176 (-)NCBI
Rnor_5.0207,234,609 - 7,240,454 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256065   ⟹   XP_006256127
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,647,577 - 3,652,670 (+)NCBI
Rnor_6.0205,161,350 - 5,166,443 (-)NCBI
Rnor_5.0207,234,609 - 7,240,454 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098495   ⟹   XP_038954423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,647,751 - 3,652,670 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_058892   ⟸   NM_017196
- UniProtKB: P55009 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256125   ⟸   XM_006256063
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006256127   ⟸   XM_006256065
- Peptide Label: isoform X3
- UniProtKB: P55009 (UniProtKB/Swiss-Prot),   F1LRC2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256124   ⟸   XM_006256062
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006256123   ⟸   XM_006256061
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000068279   ⟸   ENSRNOT00000076331
RefSeq Acc Id: ENSRNOP00000001135   ⟸   ENSRNOT00000001135
RefSeq Acc Id: ENSRNOP00000001138   ⟸   ENSRNOT00000001138
RefSeq Acc Id: XP_038954423   ⟸   XM_039098495
- Peptide Label: isoform X3
Protein Domains
EF-hand

Transcriptome

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

Promoters
RGD ID:13701399
Promoter ID:EPDNEW_R11923
Type:initiation region
Name:Aif1_1
Description:allograft inflammatory factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11924  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,163,247 - 5,163,307EPDNEW
RGD ID:13701401
Promoter ID:EPDNEW_R11924
Type:initiation region
Name:Aif1_2
Description:allograft inflammatory factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11923  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,166,223 - 5,166,283EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61924 AgrOrtholog
Ensembl Genes ENSRNOG00000000853 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001135 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000001138 UniProtKB/TrEMBL
  ENSRNOP00000068279 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001135 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000001138 UniProtKB/TrEMBL
  ENSRNOT00000076331 ENTREZGENE, UniProtKB/TrEMBL
InterPro AIF1/AIF1L UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29427 UniProtKB/Swiss-Prot
NCBI Gene 29427 ENTREZGENE
PANTHER PTHR10356 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Aif1 PhenoGen
PROSITE EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt AIF1_RAT UniProtKB/Swiss-Prot
  F1LRC2 ENTREZGENE, UniProtKB/TrEMBL
  P55009 ENTREZGENE
UniProt Secondary P55007 UniProtKB/Swiss-Prot
  P70491 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-04-06 Aif1  allograft inflammatory factor 1   Bart1  balloon angioplasty responsive transcript  Data Merged 737654 APPROVED
2002-08-07 Bart1  balloon angioplasty responsive transcript      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Aif1  allograft inflammatory factor 1       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains two strongly hydrophilic and one hydrophobic region, suggesting a type II integral membrane protein 632014
gene_mapping found within the rat major histocompatibility RT1 complex 1300431
gene_process may play a role in macrophage activation and function 724707
gene_regulation transiently expressed in response to vascular trauma 632014
gene_regulation transiently expressed in response to vascular trauma 632015