IRF3
interferon regulatory factor 3

This gene encodes a member of the interferon regulatory transcription factor (IRF) family. The encoded protein is found in an inactive cytoplasmic form that upon serine/threonine phosphorylation forms a complex with CREBBP. This complex translocates to the nucleus and activates the transcription of interferons alpha and beta, as well as other interferon-induced genes. The protein plays an important role in the innate immune response against DNA and RNA viruses. Mutations in this gene are associated with Encephalopathy, acute, infection-induced, herpes-specific, 7. [provided by RefSeq, Sep 2020]

Member of: DE-1 Developmental clusters: GC6
Biological processes 82 terms
DNA binding (GO:0003677)DNA damage response (GO:0006974)DNA-binding transcription activator activity (GO:0001216)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)MDA-5 signaling pathway (GO:0039530)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)TRIF-dependent toll-like receptor signaling pathway (GO:0035666)antiviral innate immune response (GO:0140374)apoptotic process (GO:0006915)cGAS/STING signaling pathway (GO:0140896)cell surface receptor signaling pathway (GO:0007166)cellular response to exogenous dsRNA (GO:0071360)cellular response to virus (GO:0098586)cellular response to virus (GO:0098586)chromatin (GO:0000785)chromatin (GO:0000785)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasmic pattern recognition receptor signaling pathway (GO:0002753)cytosol (GO:0005829)cytosol (GO:0005829)defense response to virus (GO:0051607)defense response to virus (GO:0051607)identical protein binding (GO:0042802)identical protein binding (GO:0042802)immune system process (GO:0002376)innate immune response (GO:0045087)mRNA transcription (GO:0009299)macrophage apoptotic process (GO:0071888)mitochondrion (GO:0005739)mitochondrion (GO:0005739)negative regulation of transcription by RNA polymerase II (GO:0000122)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of canonical NF-kappaB signal transduction (GO:0043123)positive regulation of cytokine production (GO:0001819)positive regulation of cytokine production involved in inflammatory response (GO:1900017)positive regulation of innate immune response (GO:0045089)positive regulation of interferon-alpha production (GO:0032727)positive regulation of interferon-alpha production (GO:0032727)positive regulation of interferon-beta production (GO:0032728)positive regulation of interferon-beta production (GO:0032728)positive regulation of interferon-beta production (GO:0032728)positive regulation of interferon-beta production (GO:0032728)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of type I interferon production (GO:0032481)positive regulation of type I interferon production (GO:0032481)programmed cell death (GO:0012501)promoter-specific chromatin binding (GO:1990841)protein binding (GO:0005515)protein binding (GO:0005515)protein domain specific binding (GO:0019904)protein homodimerization activity (GO:0042803)protein homodimerization activity (GO:0042803)regulation of DNA-templated transcription (GO:0006355)regulation of apoptotic process (GO:0042981)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)toll-like receptor 4 signaling pathway (GO:0034142)transcription cis-regulatory region binding (GO:0000976)type I interferon-mediated signaling pathway (GO:0060337)
Expression (TPM)
IRF3 — as a Regulated Gene

TFs regulating IRF3 0 TFs

Transcription factors with Perturb-seq knockdown data for IRF3. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = IRF3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to IRF3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of IRF3, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr19:49,403,611–49,404,247 261.9 kb Distal (>10kb) Multiome 305
chr19:49,432,343–49,432,785 233.3 kb Distal (>10kb) Multiome 103
chr19:49,436,149–49,436,821 229.4 kb Distal (>10kb) Multiome 248
chr19:49,441,067–49,441,861 224.3 kb Distal (>10kb) Multiome 223
chr19:49,442,072–49,444,054 222.9 kb Distal (>10kb) Multiome 914
chr19:49,451,347–49,452,239 214.0 kb Distal (>10kb) Multiome 764
chr19:49,452,723–49,453,850 212.5 kb Distal (>10kb) Multiome 847
chr19:49,476,063–49,476,551 189.5 kb Distal (>10kb) Multiome 244
chr19:49,487,027–49,488,279 178.4 kb Distal (>10kb) Multiome 964
chr19:49,495,613–49,496,661 169.6 kb Distal (>10kb) Multiome 919
chr19:49,500,403–49,501,353 165.1 kb Distal (>10kb) Multiome 405
chr19:49,512,565–49,513,700 152.8 kb Distal (>10kb) Multiome 655
chr19:49,527,651–49,528,221 137.9 kb Distal (>10kb) Multiome 354
chr19:49,533,232–49,534,476 131.8 kb Distal (>10kb) Multiome 534
chr19:49,555,629–49,557,180 109.7 kb Distal (>10kb) Multiome 294
chr19:49,580,125–49,580,813 85.2 kb Distal (>10kb) Multiome 848
chr19:49,589,601–49,594,008 72.3 kb Distal (>10kb) Multiome 994
chr19:49,638,063–49,638,728 27.6 kb Distal (>10kb) Multiome 237
chr19:49,639,671–49,642,787 25.4 kb Distal (>10kb) Multiome 1067
chr19:49,664,165–49,665,096 1.3 kb Proximal (<10kb) Multiome 679
chr19:49,665,345–49,666,430 62 bp At TSS Multiome 721
chr19:49,672,105–49,672,787 6.5 kb Proximal (<10kb) Multiome 625
chr19:49,675,666–49,675,902 9.8 kb Proximal (<10kb) 84
chr19:49,676,058–49,678,754 11.1 kb Distal (>10kb) Multiome 1033
chr19:49,680,433–49,681,147 14.9 kb Distal (>10kb) Multiome 435
chr19:49,690,485–49,691,761 25.3 kb Distal (>10kb) Multiome 327
chr19:49,746,188–49,746,748 80.6 kb Distal (>10kb) Multiome 283
chr19:49,766,231–49,767,440 100.8 kb Distal (>10kb) Multiome 718
chr19:49,802,146–49,802,787 136.6 kb Distal (>10kb) Multiome 200
chr19:49,805,226–49,805,871 139.7 kb Distal (>10kb) Multiome 245
chr19:49,808,201–49,809,746 143.1 kb Distal (>10kb) Multiome 509
chr19:49,812,926–49,813,834 147.6 kb Distal (>10kb) Multiome 650
chr19:49,817,356–49,818,721 152.4 kb Distal (>10kb) Multiome 784
chr19:49,850,394–49,852,067 185.0 kb Distal (>10kb) Multiome 862
chr19:49,866,817–49,868,124 201.5 kb Distal (>10kb) Multiome 874
chr19:49,869,068–49,870,398 203.8 kb Distal (>10kb) Multiome 832
chr19:49,875,842–49,878,576 211.9 kb Distal (>10kb) Multiome 1153
chr19:49,889,853–49,891,381 224.6 kb Distal (>10kb) Multiome 640
chr19:49,928,884–49,930,473 264.1 kb Distal (>10kb) Multiome 1141

Genome Browser

Genomic view of the IRF3 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr19:49,393,611 – 49,940,473
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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