Irf6 (interferon regulatory factor 6) - Rat Genome Database

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Gene: Irf6 (interferon regulatory factor 6) Rattus norvegicus
Analyze
Symbol: Irf6
Name: interferon regulatory factor 6
RGD ID: 1309645
Description: Predicted to have DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including cell cycle arrest; epithelial cell differentiation; and keratinocyte proliferation. Predicted to localize to cell junction; cytosol; and nucleoplasm. Human ortholog(s) of this gene implicated in several diseases, including Van der Woude syndrome; cleft lip; orofacial cleft 6; popliteal pterygium syndrome; and syndactyly. Orthologous to human IRF6 (interferon regulatory factor 6); INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC364081
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
mRatBN7.213104,672,179 - 104,691,386 (+)NCBI
Rnor_6.0 Ensembl13111,870,121 - 111,889,328 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013111,870,121 - 111,889,328 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013116,425,025 - 116,444,232 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413108,986,973 - 109,006,180 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113109,176,076 - 109,195,282 (+)NCBI
Celera13104,102,428 - 104,121,635 (+)NCBICelera
Cytogenetic Map13q27NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3',5'-cyclic AMP  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP,ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butan-1-ol  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
clofibrate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
cyproconazole  (EXP)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dichloromethane  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
flusilazole  (EXP)
folic acid  (ISO)
geraniol  (ISO)
glafenine  (EXP)
methotrexate  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
PCB138  (EXP)
perfluorononanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
tamoxifen  (ISO)
tebuconazole  (ISO)
tetrachloromethane  (ISO)
triadimefon  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (ISO)

References

Additional References at PubMed
PMID:16049006   PMID:17041601   PMID:17041603   PMID:18212048   PMID:19036739   PMID:19056867   PMID:21515572   PMID:21807998   PMID:26077898   PMID:28473536  


Genomics

Comparative Map Data
Irf6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.213104,672,179 - 104,691,386 (+)NCBI
Rnor_6.0 Ensembl13111,870,121 - 111,889,328 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.013111,870,121 - 111,889,328 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013116,425,025 - 116,444,232 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413108,986,973 - 109,006,180 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113109,176,076 - 109,195,282 (+)NCBI
Celera13104,102,428 - 104,121,635 (+)NCBICelera
Cytogenetic Map13q27NCBI
IRF6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1209,785,617 - 209,806,175 (-)EnsemblGRCh38hg38GRCh38
GRCh381209,785,617 - 209,806,142 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371209,958,962 - 209,979,487 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361208,027,885 - 208,046,102 (-)NCBINCBI36hg18NCBI36
Build 341206,349,656 - 206,367,874NCBI
Celera1183,192,156 - 183,210,363 (-)NCBI
Cytogenetic Map1q32.2NCBI
HuRef1180,634,114 - 180,654,661 (-)NCBIHuRef
CHM1_11211,231,296 - 211,251,831 (-)NCBICHM1_1
Irf6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391192,835,420 - 192,854,344 (+)NCBIGRCm39mm39
GRCm39 Ensembl1192,835,419 - 192,854,331 (+)Ensembl
GRCm381193,153,112 - 193,172,036 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1193,153,111 - 193,172,023 (+)EnsemblGRCm38mm10GRCm38
MGSCv371194,979,306 - 194,998,230 (+)NCBIGRCm37mm9NCBIm37
MGSCv361194,853,878 - 194,872,730 (+)NCBImm8
Celera1200,028,192 - 200,047,120 (+)NCBICelera
Cytogenetic Map1H6NCBI
cM Map197.6NCBI
Irf6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554892,415,925 - 2,437,837 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554892,404,773 - 2,434,729 (+)NCBIChiLan1.0ChiLan1.0
IRF6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11190,226,722 - 190,247,145 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1190,226,727 - 190,247,145 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01185,361,612 - 185,382,516 (-)NCBIMhudiblu_PPA_v0panPan3
IRF6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.178,447,826 - 8,467,265 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl78,448,538 - 8,462,661 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha78,024,947 - 8,044,365 (-)NCBI
ROS_Cfam_1.078,148,397 - 8,167,818 (-)NCBI
UMICH_Zoey_3.178,078,084 - 8,097,501 (-)NCBI
UNSW_CanFamBas_1.078,175,119 - 8,194,534 (-)NCBI
UU_Cfam_GSD_1.078,313,202 - 8,332,619 (-)NCBI
Irf6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934466,052,551 - 66,071,017 (+)NCBI
SpeTri2.0NW_0049365573,292,927 - 3,309,002 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IRF6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9133,164,440 - 133,185,628 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19133,164,360 - 133,184,045 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29146,240,235 - 146,259,915 (+)NCBISscrofa10.2Sscrofa10.2susScr3
IRF6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12519,648,131 - 19,665,722 (+)NCBI
Irf6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248072,190,721 - 2,207,183 (+)NCBI

Position Markers
RH129787  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.013111,889,124 - 111,889,273NCBIRnor6.0
Rnor_5.013116,444,028 - 116,444,177UniSTSRnor5.0
RGSC_v3.413109,005,976 - 109,006,125UniSTSRGSC3.4
Celera13104,121,431 - 104,121,580UniSTS
RH 3.4 Map13759.5UniSTS
Cytogenetic Map13q27UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:331
Count of miRNA genes:193
Interacting mature miRNAs:244
Transcripts:ENSRNOT00000007333
Prediction methods: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 12 35 27 17 27 31 12 11
Low 31 22 14 2 14 2 2 74 4 29 2
Below cutoff 6 7 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007333   ⟹   ENSRNOP00000007333
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl13111,870,121 - 111,889,328 (+)Ensembl
RefSeq Acc Id: NM_001108859   ⟹   NP_001102329
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.213104,672,179 - 104,691,386 (+)NCBI
Rnor_6.013111,870,121 - 111,889,328 (+)NCBI
Rnor_5.013116,425,025 - 116,444,232 (+)NCBI
RGSC_v3.413108,986,973 - 109,006,180 (+)RGD
Celera13104,102,428 - 104,121,635 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102329 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL95026 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102329   ⟸   NM_001108859
- UniProtKB: D4AAV0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007333   ⟸   ENSRNOT00000007333
Transcriptome

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

Promoters
RGD ID:13699125
Promoter ID:EPDNEW_R9650
Type:multiple initiation site
Name:Irf6_1
Description:interferon regulatory factor 6
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013111,870,116 - 111,870,176EPDNEW

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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (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
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 (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 (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 (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:1309645 AgrOrtholog
Ensembl Genes ENSRNOG00000005082 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007333 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007333 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
  2.60.200.10 UniProtKB/TrEMBL
InterPro Interferon_reg_fac_CS UniProtKB/TrEMBL
  Interferon_reg_factor UniProtKB/TrEMBL
  Interferon_reg_factor-3 UniProtKB/TrEMBL
  SMAD_dom-like UniProtKB/TrEMBL
  SMAD_FHA_domain UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:364081 UniProtKB/TrEMBL
NCBI Gene 364081 ENTREZGENE
PANTHER PTHR11949 UniProtKB/TrEMBL
Pfam IRF UniProtKB/TrEMBL
  IRF-3 UniProtKB/TrEMBL
PhenoGen Irf6 PhenoGen
PRINTS INTFRNREGFCT UniProtKB/TrEMBL
PROSITE IRF UniProtKB/TrEMBL
  IRF_2 UniProtKB/TrEMBL
SMART IRF UniProtKB/TrEMBL
  IRF-3 UniProtKB/TrEMBL
Superfamily-SCOP SMAD_FHA UniProtKB/TrEMBL
  SSF46785 UniProtKB/TrEMBL
UniProt D4AAV0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Irf6  interferon regulatory factor 6   Irf6_predicted  interferon regulatory factor 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Irf6_predicted  interferon regulatory factor 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED