Irf1 (interferon regulatory factor 1) - Rat Genome Database

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Gene: Irf1 (interferon regulatory factor 1) Rattus norvegicus
Analyze
Symbol: Irf1
Name: interferon regulatory factor 1
RGD ID: 2920
Description: Enables sequence-specific DNA binding activity. Involved in several processes, including cellular response to cytokine stimulus; cellular response to exogenous dsRNA; and response to peptide hormone. Located in nucleus. Used to study endometrial adenocarcinoma. Biomarker of allergic conjunctivitis; lung disease; respiratory syncytial virus infectious disease; and ureteral obstruction. Human ortholog(s) of this gene implicated in asthma; gastric adenocarcinoma; lung non-small cell carcinoma; and smallpox. Orthologous to human IRF1 (interferon regulatory factor 1); PARTICIPATES IN Jak-Stat signaling pathway; nuclear factor kappa B signaling pathway; p38 MAPK signaling pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 2,3,7,8-tetrachlorodibenzodioxine; 2-nitrofluorene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: IRF-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
mRatBN7.21037,917,155 - 37,924,166 (+)NCBI
Rnor_6.0 Ensembl1039,109,522 - 39,116,531 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01039,109,530 - 39,116,532 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01038,891,468 - 38,898,470 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41039,220,600 - 39,227,602 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11039,229,846 - 39,236,848 (+)NCBI
Celera1037,260,559 - 37,267,561 (+)NCBICelera
RH 3.4 Map10405.3RGD
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-alpha-viniferin  (ISO)
(-)-demecolcine  (ISO)
(R)-lipoic acid  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-nitropyrene  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-bromohexadecanoic acid  (ISO)
2-nitrofluorene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (EXP)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
9-cis-retinoic acid  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
actinomycin D  (ISO)
aldehydo-D-glucosamine  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (ISO)
beta-naphthoflavone  (EXP,ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (EXP)
cadmium selenide  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
ciglitazone  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dacarbazine  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
diethylstilbestrol  (EXP)
dimethylarsinic acid  (EXP)
divanadium pentaoxide  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fluoranthene  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
gentamycin  (EXP)
geraniol  (ISO)
GW 1929  (ISO)
hexachlorobenzene  (EXP)
indole-3-methanol  (EXP)
isotretinoin  (ISO)
leflunomide  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
mangiferin  (ISO)
mercury atom  (ISO)
mercury dichloride  (ISO)
mercury(0)  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylseleninic acid  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-methyl-N-nitrosourea  (EXP,ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nimesulide  (EXP)
oxaliplatin  (EXP)
p-menthan-3-ol  (ISO)
p-tert-Amylphenol  (EXP)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP,ISO)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
puromycin  (ISO)
pyrrolidine dithiocarbamate  (ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
Ro 41-5253  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
SR 144528  (ISO)
streptozocin  (EXP)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
Tributyltin oxide  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (EXP)
triphenyl phosphate  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
trovafloxacin  (EXP,ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vincristine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
apoptotic process  (IEA,ISO,ISS)
CD8-positive, alpha-beta T cell differentiation  (IEA,ISO)
cellular response to exogenous dsRNA  (IEP)
cellular response to interferon-beta  (IEA,ISO)
cellular response to interleukin-1  (IDA)
cellular response to mechanical stimulus  (IEA,ISO)
cellular response to peptide hormone stimulus  (IDA)
cellular response to retinoic acid  (IEP)
cellular response to tumor necrosis factor  (IDA)
defense response to virus  (IEA,ISO,ISS)
female pregnancy  (IEP)
I-kappaB kinase/NF-kappaB signaling  (IMP)
immune system process  (IBA)
interferon-gamma-mediated signaling pathway  (IEA,ISO,ISS)
negative regulation of cell population proliferation  (IEA)
negative regulation of regulatory T cell differentiation  (IEA,ISO,ISS)
negative regulation of transcription, DNA-templated  (IEA,ISO,ISS)
negative regulation of tyrosine phosphorylation of STAT protein  (IMP)
positive regulation of cell death  (IMP)
positive regulation of interferon-beta production  (IEA,ISO,ISS)
positive regulation of interleukin-12 production  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IEA,IMP,ISO,ISS)
positive regulation of transcription, DNA-templated  (ISO,ISS)
positive regulation of type I interferon production  (ISO,ISS)
regulation of CD8-positive, alpha-beta T cell proliferation  (IEA,ISO,ISS)
regulation of cell cycle  (IEA,ISO,ISS)
regulation of cell population proliferation  (NAS)
regulation of gene expression  (ISO)
regulation of MyD88-dependent toll-like receptor signaling pathway  (IEA,ISO,ISS)
regulation of transcription by RNA polymerase II  (IBA)
regulation of transcription, DNA-templated  (TAS)
response to growth hormone  (IDA)
response to heat  (IEP)

Cellular Component
chromatin  (IEA,ISO)
cytoplasm  (IEA,ISO,ISS)
nucleus  (IBA,IDA,IEA,ISO)

References

References - curated
1. Book McAlexander M and Yu-Lee L, FEBS Lett. 2001 Jan 12;488(1-2):91-4.
2. Choi WH, etal., Biochem Biophys Res Commun. 2005 Apr 1;329(1):125-31.
3. Cooper AM, etal., Infect Immun. 2000 Dec;68(12):6879-82.
4. Cvetkovic I, etal., Cell Mol Life Sci. 2004 May;61(10):1167-75.
5. Dogusan Z, etal., Eur Cytokine Netw. 2000 Sep;11(3):435-42.
6. Dutia BM, etal., Virology. 1999 Sep 1;261(2):173-9.
7. Eason DD, etal., Biochim Biophys Acta. 1999 Jul 7;1446(1-2):140-4.
8. Fukushima A, etal., Microbiol Immunol. 2003;47(10):785-96.
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. Guidotti LG, etal., J Virol. 2002 Mar;76(6):2617-21. doi: 10.1128/jvi.76.6.2617-2621.2002.
12. Horiuchi M, etal., J Neuroinflammation. 2011 Jan 24;8(1):8.
13. Kelley TJ and Elmer HL, J Clin Invest. 2000 Aug;106(3):403-10.
14. Kim JI, etal., Clin Exp Pharmacol Physiol. 2007 Jul;34(7):636-40.
15. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
16. Le Stunff C and Rotwein P, Endocrinology. 1998 Mar;139(3):859-66.
17. Liu MY and Khachigian LM, J Biol Chem. 2009 Dec 11;284(50):35101-12. Epub 2009 Oct 20.
18. MGD data from the GO Consortium
19. Moore F, etal., J Biol Chem. 2011 Jan 14;286(2):929-41. Epub 2010 Oct 27.
20. Mori K, etal., Mol Cell Endocrinol. 2001 Nov 26;184(1-2):77-86.
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Noguchi E, etal., Clin Exp Allergy. 2000 Nov;30(11):1562-7.
23. Nozawa H, etal., Int J Cancer. 1998 Aug 12;77(4):522-7.
24. OMIM Disease Annotation Pipeline
25. Pipeline to import KEGG annotations from KEGG into RGD
26. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
27. Raghavendra Rao VL, etal., J Neurochem 2002 Dec;83(5):1072-86.
28. Raghavendra Rao VL, etal., J Neurosci Res. 2003 Jan 15;71(2):208-19.
29. Reif DM, etal., J Infect Dis. 2008 Jul 1;198(1):16-22. doi: 10.1086/588670.
30. RGD automated data pipeline
31. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
32. RGD automated import pipeline for gene-chemical interactions
33. RGD comprehensive gene curation
34. Rizvi IA, etal., J Surg Res. 2006 Nov;136(1):25-30. Epub 2006 Sep 15.
35. Sampath D, etal., J Clin Invest. 1999 May;103(9):1353-61.
36. Samuelson E, etal., Endocr Relat Cancer. 2009 Mar;16(1):99-111. Epub 2008 Dec 15.
37. Silverstein DM, etal., Kidney Int. 2003 Jul;64(1):25-35.
38. Song G, etal., J Neurochem. 2001 Nov;79(4):804-15.
39. Sun QH, etal., J Interferon Cytokine Res. 2007 Jul;27(7):567-78.
40. Sunil VR, etal., Am J Physiol Lung Cell Mol Physiol. 2002 Apr;282(4):L872-80.
41. Tan H, etal., Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2009 Dec;34(12):1189-95.
42. Teng X, etal., Am J Physiol Cell Physiol 2002 Jan;282(1):C144-52.
43. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
44. Wang TN, etal., Clin Exp Allergy. 2006 Sep;36(9):1147-52.
45. Wieland CW, etal., Infect Immun. 2002 Mar;70(3):1352-8.
46. Yu-Lee LY, etal., Mol Cell Biol 1990 Jun;10(6):3087-94.
Additional References at PubMed
PMID:11359801   PMID:12477932   PMID:14568984   PMID:15509808   PMID:17018642   PMID:17159910   PMID:17516545   PMID:17723228   PMID:18035482   PMID:18084608   PMID:18641303   PMID:19593445  
PMID:19606498   PMID:19851330   PMID:20308629   PMID:20451243   PMID:21389130   PMID:21478870   PMID:21909274   PMID:21937806   PMID:22200613   PMID:22292067   PMID:22367195   PMID:22427665  
PMID:22434733   PMID:23042740   PMID:24119616   PMID:24743731   PMID:26342280  


Genomics

Candidate Gene Status
Irf1 is a candidate Gene for QTL Bmd4
Irf1 is a candidate Gene for QTL Eau7
Comparative Map Data
Irf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21037,917,155 - 37,924,166 (+)NCBI
Rnor_6.0 Ensembl1039,109,522 - 39,116,531 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01039,109,530 - 39,116,532 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01038,891,468 - 38,898,470 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41039,220,600 - 39,227,602 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11039,229,846 - 39,236,848 (+)NCBI
Celera1037,260,559 - 37,267,561 (+)NCBICelera
RH 3.4 Map10405.3RGD
Cytogenetic Map10q22NCBI
IRF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5132,440,440 - 132,508,719 (-)EnsemblGRCh38hg38GRCh38
GRCh385132,481,609 - 132,490,789 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375131,817,301 - 131,826,465 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365131,846,679 - 131,854,326 (-)NCBINCBI36hg18NCBI36
Build 345131,846,683 - 131,854,326NCBI
Celera5127,947,368 - 127,956,530 (-)NCBI
Cytogenetic Map5q31.1NCBI
HuRef5127,009,541 - 127,018,697 (-)NCBIHuRef
CHM1_15131,250,016 - 131,259,179 (-)NCBICHM1_1
Irf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391153,660,841 - 53,669,200 (+)NCBIGRCm39mm39
GRCm39 Ensembl1153,660,841 - 53,669,200 (+)Ensembl
GRCm381153,770,014 - 53,778,374 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1153,770,014 - 53,778,374 (+)EnsemblGRCm38mm10GRCm38
MGSCv371153,583,516 - 53,591,876 (+)NCBIGRCm37mm9NCBIm37
MGSCv361153,613,501 - 53,620,746 (+)NCBImm8
Celera1158,349,840 - 58,358,199 (+)NCBICelera
Cytogenetic Map11B1.3NCBI
cM Map1132.0NCBI
Irf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554083,880,155 - 3,887,973 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554083,882,282 - 3,887,965 (-)NCBIChiLan1.0ChiLan1.0
IRF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15134,066,250 - 134,075,035 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5134,067,441 - 134,075,035 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05127,903,887 - 127,913,843 (-)NCBIMhudiblu_PPA_v0panPan3
IRF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11120,773,801 - 20,781,106 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1120,760,120 - 20,781,608 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1119,575,525 - 19,582,746 (-)NCBI
ROS_Cfam_1.01121,559,527 - 21,566,744 (-)NCBI
UMICH_Zoey_3.11120,278,269 - 20,285,484 (-)NCBI
UNSW_CanFamBas_1.01120,126,105 - 20,133,315 (-)NCBI
UU_Cfam_GSD_1.01120,768,242 - 20,775,474 (-)NCBI
Irf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213115,683,543 - 115,690,876 (+)NCBI
SpeTri2.0NW_0049366472,686,247 - 2,693,633 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IRF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2134,776,134 - 134,783,646 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12134,776,122 - 134,783,646 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22140,229,799 - 140,252,658 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap2q24-q29NCBI
IRF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12335,309,058 - 35,317,765 (-)NCBI
ChlSab1.1 Ensembl2335,307,772 - 35,316,763 (-)Ensembl
Vero_WHO_p1.0NW_02366603442,627,248 - 42,635,033 (+)NCBI
Irf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473339,596,565 - 39,603,428 (+)NCBI

Position Markers
RH94542  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21037,923,609 - 37,923,770 (+)MAPPER
Rnor_6.01039,115,976 - 39,116,136NCBIRnor6.0
Rnor_5.01038,897,914 - 38,898,074UniSTSRnor5.0
RGSC_v3.41039,227,046 - 39,227,206UniSTSRGSC3.4
Celera1037,267,005 - 37,267,165UniSTS
RH 3.4 Map10405.3UniSTS
Cytogenetic Map10q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142669970Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)10144902893Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1076442166221621Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10587753664401490Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10622909575983805Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10752145052521450Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101263951357639513Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101537547462469074Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101646873661468736Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101824639453637634Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101940281464402814Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102152390683549467Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102170776664648311Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102386101566539843Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)102488408447487910Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102723753064648311Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102878928073789280Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)103002135454057745Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103009990975099909Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103009990975099909Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103098380575983805Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103191939778343192Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103317903078179030Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103334319278343192Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103513942480139424Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103566946546851407Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103618592982675365Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103658437353645194Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103658437366539843Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103658456066015527Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:713
Count of miRNA genes:281
Interacting mature miRNAs:359
Transcripts:ENSRNOT00000010968
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 3 18 38 22 19 22 4 27 30 11
Low 25 19 19 19 8 11 70 8 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010968   ⟹   ENSRNOP00000010968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1039,109,522 - 39,116,531 (+)Ensembl
RefSeq Acc Id: NM_012591   ⟹   NP_036723
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21037,917,155 - 37,924,166 (+)NCBI
Rnor_6.01039,109,530 - 39,116,532 (+)NCBI
Rnor_5.01038,891,468 - 38,898,470 (+)NCBI
RGSC_v3.41039,220,600 - 39,227,602 (+)RGD
Celera1037,260,559 - 37,267,561 (+)RGD
Sequence:
RefSeq Acc Id: XM_039085188   ⟹   XP_038941116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21037,917,464 - 37,923,607 (+)NCBI
RefSeq Acc Id: XM_039085189   ⟹   XP_038941117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21037,917,326 - 37,923,607 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036723   ⟸   NM_012591
- Sequence:
RefSeq Acc Id: ENSRNOP00000010968   ⟸   ENSRNOT00000010968
RefSeq Acc Id: XP_038941117   ⟸   XM_039085189
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038941116   ⟸   XM_039085188
- Peptide Label: isoform X1
Transcriptome

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

Promoters
RGD ID:13697183
Promoter ID:EPDNEW_R7707
Type:multiple initiation site
Name:Irf1_1
Description:interferon regulatory 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_6.01039,109,506 - 39,109,566EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2920 AgrOrtholog
Ensembl Genes ENSRNOG00000008144 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010968 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010968 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7099391 IMAGE-MGC_LOAD
InterPro Interferon_reg_fac_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Interferon_reg_fact_DNA-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IRF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IRF1/IRF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24508 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93592 IMAGE-MGC_LOAD
NCBI Gene 24508 ENTREZGENE
PANTHER PTHR11949 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11949:SF3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam IRF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Irf1 PhenoGen
PIRSF IFN_RF1/2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS INTFRNREGFCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE IRF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IRF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IRF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC206594
UniProt IRF1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q6DGG4_RAT UniProtKB/TrEMBL
  Q812C6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Irf1  Interferon regulatory factor 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression isolated from Prl-stimulated T cells 633034
gene_homology protein is 97% and 92% identical to the mouse IRF-1 and human IRF-1 respectively 633034
gene_process regulates growth-inhibitory interferon genes during cell proliferation 633034