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 enable 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 mammary gland epithelial cell differentiation; negative regulation of cell population proliferation; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including keratinocyte differentiation; negative regulation of cell population proliferation; and roof of mouth development. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in several diseases, including Van der Woude syndrome; cleft lip; cleft palate; orofacial cleft 6; and popliteal pterygium syndrome. 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
Previously known as: LOC364081
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813107,200,876 - 107,220,083 (+)NCBIGRCr8
mRatBN7.213104,672,179 - 104,691,386 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13104,672,179 - 104,691,386 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13107,189,790 - 107,208,999 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013108,573,644 - 108,592,851 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013105,791,610 - 105,810,817 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.013111,870,121 - 111,889,328 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13111,870,121 - 111,889,328 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013116,425,025 - 116,444,232 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413108,986,973 - 109,006,180 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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->4)-beta-D-glucan  (ISO)
(S)-nicotine  (ISO)
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)
3-chloropropane-1,2-diol  (EXP)
3-Nitrobenzanthrone  (ISO)
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)
alpha-Zearalanol  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (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)
copper(II) chloride  (ISO)
coumestrol  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cyproconazole  (EXP)
DDE  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dichloromethane  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
flusilazole  (EXP)
folic acid  (ISO)
furfural  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
glafenine  (EXP)
lead diacetate  (ISO)
methotrexate  (ISO)
nefazodone  (EXP)
nickel dichloride  (ISO)
nicotine  (ISO)
nimesulide  (EXP)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
PCB138  (EXP)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,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)
sodium arsenite  (ISO)
sodium chloride  (ISO)
tamoxifen  (ISO)
tebuconazole  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
triadimefon  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO)
nucleus  (IBA)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Mutations in IRF6 cause Van der Woude and popliteal pterygium syndromes. Kondo S, etal., Nat Genet. 2002 Oct;32(2):285-9. Epub 2002 Sep 3.
3. Genetic variants in COL2A1, COL11A2, and IRF6 contribute risk to nonsyndromic cleft palate. Nikopensius T, etal., Birth Defects Res A Clin Mol Teratol. 2010 Sep;88(9):748-56. doi: 10.1002/bdra.20700.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
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
GRCr813107,200,876 - 107,220,083 (+)NCBIGRCr8
mRatBN7.213104,672,179 - 104,691,386 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13104,672,179 - 104,691,386 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13107,189,790 - 107,208,999 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013108,573,644 - 108,592,851 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013105,791,610 - 105,810,817 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.013111,870,121 - 111,889,328 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13111,870,121 - 111,889,328 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013116,425,025 - 116,444,232 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413108,986,973 - 109,006,180 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh381209,785,617 - 209,806,142 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1209,785,617 - 209,806,175 (-)EnsemblGRCh38hg38GRCh38
GRCh371209,958,962 - 209,979,487 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361208,027,885 - 208,046,102 (-)NCBINCBI36Build 36hg18NCBI36
Build 341206,349,656 - 206,367,874NCBI
Celera1183,192,156 - 183,210,363 (-)NCBICelera
Cytogenetic Map1q32.2NCBI
HuRef1180,634,114 - 180,654,661 (-)NCBIHuRef
CHM1_11211,231,296 - 211,251,831 (-)NCBICHM1_1
T2T-CHM13v2.01209,032,385 - 209,052,912 (-)NCBIT2T-CHM13v2.0
Irf6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391192,835,420 - 192,854,344 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1192,835,419 - 192,854,331 (+)EnsemblGRCm39 Ensembl
GRCm381193,153,112 - 193,172,036 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1193,153,111 - 193,172,023 (+)EnsemblGRCm38mm10GRCm38
MGSCv371194,979,306 - 194,998,230 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361194,853,878 - 194,872,730 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v2139,591,466 - 39,612,943 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1139,557,629 - 39,581,840 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01185,361,612 - 185,382,516 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11190,226,722 - 190,247,145 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1190,226,727 - 190,247,145 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.078,148,397 - 8,167,818 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl78,148,402 - 8,167,733 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.178,078,084 - 8,097,501 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.078,175,119 - 8,194,534 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.078,313,202 - 8,332,619 (-)NCBIUU_Cfam_GSD_1.0
Irf6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934466,052,551 - 66,071,017 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365573,292,873 - 3,311,369 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12519,648,131 - 19,665,722 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605520,247,186 - 20,267,525 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Irf6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248072,193,798 - 2,206,768 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248072,190,721 - 2,207,183 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Irf6
141 total Variants
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1366451204106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

Markers in Region
RH129787  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.213104,691,181 - 104,691,331 (+)MAPPERmRatBN7.2
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 9 49 113 91 90 59 25 59 6 216 95 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000007333   ⟹   ENSRNOP00000007333
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl13104,672,179 - 104,691,386 (+)Ensembl
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
GRCr813107,200,876 - 107,220,083 (+)NCBI
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  
Ensembl Protein ENSRNOP00000007333.3
RefSeq Acc Id: NP_001102329   ⟸   NM_001108859
- UniProtKB: D4AAV0 (UniProtKB/TrEMBL),   A6JH20 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000007333   ⟸   ENSRNOT00000007333
Protein Domains
IRF tryptophan pentad repeat

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AAV0-F1-model_v2 AlphaFold D4AAV0 1-467 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309645 AgrOrtholog
BioCyc Gene G2FUF-16796 BioCyc
Ensembl Genes ENSRNOG00000005082 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007333.5 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 INTERFERON REGULATORY FACTOR UniProtKB/TrEMBL
  INTERFERON REGULATORY FACTOR 6 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
RatGTEx ENSRNOG00000005082 RatGTEx
SMART IRF UniProtKB/TrEMBL
  IRF-3 UniProtKB/TrEMBL
Superfamily-SCOP SMAD_FHA UniProtKB/TrEMBL
  SSF46785 UniProtKB/TrEMBL
UniProt A6JH20 ENTREZGENE, UniProtKB/TrEMBL
  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