Gene: Irf6

Basic information

Tag Content
Uniprot ID P97431; Q91VD0;
Entrez ID 54139
Genbank protein ID AAB36714.1; EDL12956.1; BAE25628.1; BAE25338.1; AAH08515.1;
Genbank nucleotide ID XM_006497262.3; XM_006497263.3; NM_016851.2;
Ensembl protein ID ENSMUSP00000075839
Ensembl nucleotide ID ENSMUSG00000026638
Gene name Interferon regulatory factor 6
Gene symbol Irf6
Organism Mus musculus
NCBI taxa ID 10090
Cleft type CPO
Developmental stage E14.0, E13.5, E14.5
Data sources Manually collected
Reference 23406900; 17041603; 20424327; 17041610; 20196077; 19439425;
Functional description Probable DNA-binding transcriptional activator. Key determinant of the keratinocyte proliferation-differentiation switch involved in appropriate epidermal development. Plays a role in regulating mammary epithelial cell proliferation. May regulate WDR65 transcription.
Sequence
MALHPRRVRL KPWLVAQVDS GLYPGLIWLH RDSKRFQIPW KHATRHSPQQ EEENTIFKAW 60
AVETGKYQEG VDDPDPAKWK AQLRCALNKS REFNLMYDGT KEVPMNPVKI YQVCDIPQTQ 120
GSVINPGSTG SAPWDEKDND VDEDEEEDEL EQSQHHVPIQ DTFPFLNING SPMAPASVGN 180
CSVGNCSPES VWPKTEPLEM EVPQAPIQPF YSSPELWISS LPMTDLDIKF QYRGKEYGQT 240
MTVSNPQGCR LFYGDLGPMP DQEELFGPVS LEQVKFPGPE HITNEKQKLF TSKLLDVMDR 300
GLILEVSGHA IYAIRLCQCK VYWSGPCAPS LAAPNLIERQ KKVKLFCLET FLSELIAHQK 360
GQIEKQPPFE IYLCFGEEWP DGKPLERKLI LVQVIPVVAR MIYEMFSGDF TRSFDSGSVR 420
LQISTPDIKD NIVAQLKQLY RILQTQESWQ PMQPAPSMQL PQALPAQ 467

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression during embryonic days (E11.5~E18.5) ~ adult days (Ps) in the lip and palate tissues. (X-axis: days, Y-axis: tissues)

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Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Relation Gene symbol Entrez ID UniProt ID Cleft type Developmental stage Species Evidence Details
1:1 orthologIRF6102190443A0A452EQT2Capra hircusPredictionMore>>
1:1 orthologIRF6100051502A0A3Q2HQB9Equus caballusPredictionMore>>
1:1 orthologIRF63664O14896CPO,CL/PHomo sapiensPublicationMore>>
1:1 orthologIrf654139P97431CPOE14.0, E13.5, E14.5Mus musculusPublicationMore>>
1:1 orthologIRF6457701A0A2I3TSL3Pan troglodytesPredictionMore>>
1:1 orthologIRF6397521E9LK28Sus scrofaPredictionMore>>
1:1 orthologIrf6364081D4AAV0Rattus norvegicusPredictionMore>>
1:1 orthologirf6393570Q6PGZ7Danio rerioPredictionMore>>

Identified variants/mutations related to cleft phenotype

Gene symbol Significant Variants/SNPS Methods PubMed ID
IRF6rs1319435-C/CPCR25853057
IRF6rs642961PCR using Taqman assay method25896037
IRF6rs7545538MiSeq Benchtop Sequencer (Illumina)25592222
IRF6rs642961Genewide tagging25896061
IRF6c.2T>C; PCR23713753
IRF6c.635delG; PCR23713753
IRF6c.627delC; PCR23713753
IRF6c.610C>T; PCR23713753
IRF6c.1234C>TPCR23713753
IRF6c.21_23del(AGTCCGGCTAAAG); PCR23713753
IRF6rs642961Linkage disequilibrium22887868
IRF6rs2235371Genotyping21039277
IRF6rs642961Genotyping20799332
IRF6rs642961Genotyping20121942
IRF6rs2235371PCR19734457
IRF6rs2235375PCR19734457
IRF6rs1856161Genotyping19536891
IRF6rs2235371Genotyping19536891
IRF6rs2235377Genotyping19536891
IRF6rs2073485; TDT19388848
IRF6rs599021TDT19388848
IRF6rs4844880;TDT19388848
IRF6rs4844880Genotyping18278815
IRF6c.1259G>A; PCR-RFLP; sequencing18506368
IRF6c.396C>TPCR-RFLP; sequencing18506368
IRF6c.123C>T; PCR-RFLP; sequencing18506368
IRF6rs861019Sequencing18209213
IRF6rs7552506Sequencing18209213
IRF6c.201C>A; p.Y67*DNA Sequencing17549393
IRF6rs2235371TDT17438386
IRF6rs2013162TDT17438386
IRF6CC5.6GTPCR; direct sequencing16998136
IRF6c.342T>APCR; direct sequencing16998136
IRF6c.566delAPCR; direct sequencing16998136
IRF6c.748C>TPCR; direct sequencing16998136
IRF6c.756C>APCR; direct sequencing16998136
IRF6c.989C>APCR; direct sequencing16998136
IRF6c.1209C>GPCR; direct sequencing16998136
IRF6c.1316delTPCR; direct sequencing16998136
IRF6c.250C>TDirect sequencing16160700
IRF6c.353_354delAGDirect sequencing16160700
IRF6c.358C>TDirect sequencing16160700
IRF6c.749G>ADirect sequencing16160700
IRF6c.1075C>TDirect sequencing16160700
IRF6c.1198C>TDirect sequencing16160700
IRF6c.1219delTDirect sequencing16160700
IRF6c.1234C>TDirect sequencing16160700
IRF6c.1271C>GDirect sequencing16160700
IRF6c.100A>GDirect sequencing16160700
IRF6rs2013162Genotyping16132054
IRF6rs1319435Genotyping16096995
IRF6rs2013162Genotyping16096995
IRF6rs2235375Genotyping16096995
IRF6rs2235543Genotyping16096995
IRF6c.820G>APCR15994871
IRF6rs2235375TDT15558496
IRF6rs2013162TDT15558496
IRF6c.250C>T; p.R84CDirect sequencing15472655
IRF6c.25C>T; p.R9W Direct sequencing15472655
IRF6p.V274ITDT15317890
IRF6c.650G>ALInkage analysis15013698
IRF6c.65T>C; Genotyping14757865
IRF6c.47C>T; Genotyping14757865
IRF6c.298A>G; Genotyping14757865
IRF6c.755T>C; Genotyping14757865
IRF6c.775C>TGenotyping14757865
IRF6c.191T>C; Genotyping14757865
IRF6c.1186C>T; PCR14618417
IRF6c.17162delPCR14618417
IRF6c.134G>A; PCR14618417
IRF6c.1461C>T; r.1461c>t; p.R400WDirect sequencing12920575
IRF6c.1400G>A; r.1400g>a; p.W379X; Direct sequencing12920575
IRF6c.279C>T; r.279c>t; p.R6C; Direct sequencing12920575
IRF6c.268C>T; r.268c>t; p.A2V;Direct sequencing12920575
IRF6c.74G>CGenotyping12964020
IRF6c.399delC; Genotyping12964020
IRF6c.39G>A; p.Trp13*Targeted sequencing26346622
IRF6c.250C>T; p.R84CTargeted sequencing26346622
IRF6c.254G>T; p.Cys85PheTargeted sequencing26346622
IRF6c.1060+1G>TTargeted sequencing26346622
IRF6c.165delC; p.Ile56Phefs*7Targeted sequencing26346622
IRF6c.379delG; p.Gly127Valfs*43Targeted sequencing26346622
IRF6c.1289_1297del; p.Asp430_Ile423delTargeted sequencing26346622
IRF6rs861019; c.73A>G Direct sequencing; PCRNo PMID: Sup Ref #1
IRF6rs2013162; c.459C>A; p.Ser153Ser Direct sequencing; PCRNo PMID: Sup Ref #1
IRF6rs2235372; c.820G>A; p.V274I Direct sequencing; PCRNo PMID: Sup Ref #1
IRF6rs2235371PCR; LRT17702008
IRF6c.87_160delinsC; p.His30IlefsX9PCR18247422
IRF6c.16dupC; p.Arg6ProfsX15PCR18247422
IRF6rs2236908C>G; GenotypingNo PMID: Sup Ref #2
IRF6rs2230907G>T; GenotypingNo PMID: Sup Ref #2
IRF6rs2235373C>T; GenotypingNo PMID: Sup Ref #2
IRF6rs2235375C>GGenotypingNo PMID: Sup Ref #2
IRF6rs2236909T>C; GenotypingNo PMID: Sup Ref #2
IRF6rs642961G>AGenotyping21683068
IRF6rs2235371G>A; p.Val274IleGenotyping23169698
IRF6rs2235371C>TGenotyping31609978
IRF6rs2235377T>CGenotyping31609978
IRF6rs12405750C>TGenotyping31609978
IRF6rs10863790A>CGenotyping31609978
IRF6rs72741048A>TGenotyping31609978
IRF6rs189000G>AGenotyping31609978
IRF6rs1387934C>TGenotyping31609978
IRF6rs11119345A>GGWAS; EMMAX; and TWAS33137956
IRF6rs861020A>GGenotyping20564431
IRF6rs590223A>GGenotyping20572854
IRF6rs2073485G>AGenotyping23921572
IRF6rs2235371C>TGenotyping23921572
IRF6rs2236909G>AGenotyping23921572
IRF6rs861020G>AGenotyping23921572
IRF6rs2235371G>AGenotyping and TDT26714022
IRF6c.820G>APCR19419265
IRF6rs2235371; p.V274I TaqMan23029012
IRF6rs2235371C>T; p.V274IPCR23940636
IRF6rs2013162C>APCR23940636
IRF6rs861020G>AGWAS28232668
IRF6rs642961G>AGWAS28232668
IRF6rs2064163C>AGWAS28232668
IRF6rs9430019G>AGWAS28232668
IRF6rs642961G>APCR-RFLP20544801
IRF6c.1088-1091delTCTA; p.Ile363Argfs*395 (heterozygous)WES and Sanger sequencing32582293
IRF6c.1198C>T; p.R400W (heterozygous)WES and Sanger sequencing32945398
IRF6g.209963979; c.921C>T; p.Ser307SerWES and Sanger sequencing32784565
IRF6rs2235371C>TTaqMan allelic discrimination assay31495697
IRF6c.273A>T; p.Arg91Ser (heterozygous)PCR30195270
IRF6c.362G>T; p.Gly121Val (heterozygous)PCR30195270
IRF6c.443A>G; p.Asp148Gly; c.457T>C; p.Ser153Ala; c.490C>G; p.Pro164Ala (triple compound heterozygous)PCR30195270
IRF6c.514C>T; p.Pro172Ser (Heterozygous)PCR30195270
IRF6c.543C>T; p.Cys181Cys (heterozygous)PCR30195270
IRF6c.595G>A; p.Glu199Lys (heterozygous)PCR30195270
IRF6c.635G>A; p.Ser212Asn (homozygous)PCR30195270
IRF6c.1173G>T; p.Leu391Phe; c.1175T>G; p.Val392Gly (compound heterozygous)PCR30195270
IRF6c;26G>A; p.Arg9Gln (heterozygous) WES and Sanger sequencing30053123
IRF6rs630065T>CGenotyping21462296
IRF6rs17389541A>GGenotyping21462296
IRF6c.535G>A; p.V179IWES and Sanger sequencing26449438
IRF6rs10863790Genotyping and GWAS20436469
IRF6c.961C>T; p.Val321MetWES33136784
IRF6rs11119345Genotyping and GWAS27033726
IRF6rs56057644Genotyping and GWAS27033726
IRF6rs1044516Genotyping and GWAS27033726
IRF6rs20273485GWAS20436469
IRF6rs2013162GWAS20436469
IRF6rs861020GWAS20436469
IRF6rs10863790GWAS20436469
IRF6haplotype combination rs2064163-rs2235371 GWAS3221112
IRF6haplotype combination rs11119388-rs2235371GWAS3221112

Other genetic variants/mutations

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Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID GO Term Evidence
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specificIBA
GO:0003677 DNA bindingIDA
GO:0003700 DNA-binding transcription factor activityIDA
GO:0005515 protein bindingIPI
GO:0043565 sequence-specific DNA bindingISO
GO:0044212 transcription regulatory region DNA bindingIEA

GO:Biological Process

GO ID GO Term Evidence
GO:0002376 immune system processIBA
GO:0007050 cell cycle arrestISO
GO:0008285 negative regulation of cell population proliferationISO
GO:0008285 negative regulation of cell population proliferationIGI
GO:0030216 keratinocyte differentiationIMP
GO:0043588 skin developmentIMP
GO:0043588 skin developmentIGI
GO:0043616 keratinocyte proliferationIMP
GO:0043616 keratinocyte proliferationIGI
GO:0045893 positive regulation of transcription, DNA-templatedIDA
GO:0045944 positive regulation of transcription by RNA polymerase IIISO
GO:0048468 cell developmentIMP
GO:0060021 roof of mouth developmentIMP
GO:0060644 mammary gland epithelial cell differentiationIEP

GO:Cellular Component

GO ID GO Term Evidence
GO:0005634 nucleusIBA
GO:0005654 nucleoplasmISO
GO:0005737 cytoplasmISS
GO:0005737 cytoplasmISO
GO:0005829 cytosolISO
GO:0030054 cell junctionISO

Reactome Pathway

Reactome ID Reactome Term Evidence

Functional annotations

Keywords

Keyword ID Keyword Term
KW-0963 Cytoplasm
KW-0221 Differentiation
KW-0238 DNA-binding
KW-0539 Nucleus
KW-1185 Reference proteome
KW-0804 Transcription
KW-0805 Transcription regulation
KW-0832 Ubl conjugation

Interpro

InterPro ID InterPro Term
IPR019817 Interferon_reg_fac_CS
IPR001346 Interferon_reg_fact_DNA-bd_dom
IPR019471 Interferon_reg_factor-3
IPR017855 SMAD-like_dom_sf
IPR008984 SMAD_FHA_dom_sf
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf

PROSITE

PROSITE ID PROSITE Term
PS00601 IRF_1
PS51507 IRF_2

Pfam

Pfam ID Pfam Term
PF00605 IRF
PF10401 IRF-3

Protein-miRNA interaction