The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	High-throughput in vitro

Description

Description:	interferon regulatory factor 8 [Source:HGNC Symbol;Acc:HGNC:5358]
Entrez Summary	TBA
Ensembl ID:	ENSG00000140968
External Link:	T107585_1.02
Interpro	IPR001346; IPR008984; IPR019471; IPR019817;
Protein Domain:
Protein: ENSP00000268638	DBD: Interferon regulatory factor (IRF)	Other: IRF-3, MH2
Protein: ENSP00000458047	DBD: Interferon regulatory factor (IRF)	Other:
Protein: ENSP00000456992	DBD: Interferon regulatory factor (IRF)	Other: IRF-3
Protein: ENSP00000455452	DBD: Interferon regulatory factor (IRF)	Other: IRF-3, MH2
Protein: ENSP00000455816	DBD: Interferon regulatory factor (IRF)	Other:
Protein: ENSP00000455048	DBD: Interferon regulatory factor (IRF)	Other:
Protein: ENSP00000455760	DBD: Interferon regulatory factor (IRF)	Other:
Protein: ENSP00000456395	DBD: Interferon regulatory factor (IRF)	Other: IRF-3, MH2

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:1460054 10734131
Vaquerizas 2009 TF classification "a" Has direct evidence of TF function; "b" Has evidence for an orthologous TF; "c" contains likely DBDs, but has no functional evidence; "x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription; "other" category contains proteins without clear DBDs they curated from external sources.	a
CisBP considers it as a TF?	Yes
TFclass considers it as a TF?	Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"	Yes
GO-Info	GO:0003705 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity TAS - PMID:1460054
Initial Assessment 1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding; 1a2 There is high confidence data for a close ortholog (as defined in CisBP); 2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model; 2a2 There is lower confidence evidence for an close ortholog; 3a There is decent circumstantial evidence for its role as a TF or not; 4a Two or more datasets predict it as a TF; 5a One of the source datasets predicts is as a TF	1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
HT-SELEX	Jolma2013		Direct
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
HT-SELEX	Yin2017		Inferred - IRF4 (80% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - IRF4 (80% AA Identity, Homo sapiens)
PBM	Badis09		Inferred - Irf4 (80% AA Identity, Mus musculus)
ChIP-seq	ENCODE		Inferred - IRF4 (80% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IRF4 (80% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IRF4 (80% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IRF4 (80% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - IRF4 (80% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - IRF4 (80% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - IRF4 (80% AA Identity, Homo sapiens)

Structure

Structure	PDB	Not_Covered

Experimental History

Method	Constructs
Tried in PBM? (Whether the protein was tried in PBM or not)
Tried in HT-SELEX (Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information? (Tried with another method and failed?)

External Contribution

Name
Email
Comment
Reference

{"regions": [{"startStyle": "curved", "end": 113, "endStyle": "curved", "aliStart": 9, "text": "IRF", "colour": "#009900", "aliEnd": 113, "start": 9, "href": "http://pfam.xfam.org/family/PF00605.15", "type": "pfama", "display": "true", "metadata": {"end": 113, "description": "This family of transcription factors are important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. Three of the five conserved tryptophan residues bind to DNA.", "database": "PfamA", "aliStart": 9, "scoreName": "E-value", "accession": "PF00605.15", "start": 9, "score": 4e-42, "identifier": "Interferon regulatory factor transcription factor", "type": "DBD", "aliEnd": 113}}, {"startStyle": "straight", "end": 382, "endStyle": "straight", "aliStart": 204, "text": "IRF-3", "colour": "#9999ff", "aliEnd": 381, "start": 202, "href": "http://pfam.xfam.org/family/PF10401.7", "type": "pfama", "display": "true", "metadata": {"end": 382, "description": "This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein.  These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1).          Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha,beta-stimulated gene). IRF-3 preexists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection.", "database": "PfamA", "aliStart": 204, "scoreName": "E-value", "accession": "PF10401.7", "start": 202, "score": 2.4999999999999995e-65, "identifier": "Interferon-regulatory factor 3", "type": "DBD", "aliEnd": 381}}, {"startStyle": "jagged", "end": 350, "endStyle": "jagged", "aliStart": 262, "text": "MH2", "colour": "#9999ff", "aliEnd": 337, "start": 256, "href": "http://pfam.xfam.org/family/PF03166.12", "type": "pfama", "display": "true", "metadata": {"end": 350, "description": "This is the MH2 (MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C-terminus of MH2 [1-3].", "database": "PfamA", "aliStart": 262, "scoreName": "E-value", "accession": "PF03166.12", "start": 256, "score": 0.00028, "identifier": "MH2 domain", "type": "DBD", "aliEnd": 337}}], "length": 427}

{"regions": [{"startStyle": "straight", "end": 178, "endStyle": "straight", "aliStart": 1, "text": "IRF-3", "colour": "#9999ff", "aliEnd": 177, "start": 1, "href": "http://pfam.xfam.org/family/PF10401.7", "type": "pfama", "display": "true", "metadata": {"end": 178, "description": "This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein.  These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1).          Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha,beta-stimulated gene). IRF-3 preexists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection.", "database": "PfamA", "aliStart": 1, "scoreName": "E-value", "accession": "PF10401.7", "start": 1, "score": 2.4999999999999995e-65, "identifier": "Interferon-regulatory factor 3", "type": "DBD", "aliEnd": 177}}, {"startStyle": "jagged", "end": 150, "endStyle": "jagged", "aliStart": 58, "text": "MH2", "colour": "#9999ff", "aliEnd": 133, "start": 51, "href": "http://pfam.xfam.org/family/PF03166.12", "type": "pfama", "display": "true", "metadata": {"end": 150, "description": "This is the MH2 (MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C-terminus of MH2 [1-3].", "database": "PfamA", "aliStart": 58, "scoreName": "E-value", "accession": "PF03166.12", "start": 51, "score": 0.0001, "identifier": "MH2 domain", "type": "DBD", "aliEnd": 133}}], "length": 223}

{"regions": [{"startStyle": "straight", "end": 178, "endStyle": "straight", "aliStart": 1, "text": "IRF-3", "colour": "#9999ff", "aliEnd": 177, "start": 1, "href": "http://pfam.xfam.org/family/PF10401.7", "type": "pfama", "display": "true", "metadata": {"end": 178, "description": "This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein.  These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1).          Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha,beta-stimulated gene). IRF-3 preexists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection.", "database": "PfamA", "aliStart": 1, "scoreName": "E-value", "accession": "PF10401.7", "start": 1, "score": 2.3999999999999993e-65, "identifier": "Interferon-regulatory factor 3", "type": "DBD", "aliEnd": 177}}, {"startStyle": "jagged", "end": 149, "endStyle": "jagged", "aliStart": 58, "text": "MH2", "colour": "#9999ff", "aliEnd": 133, "start": 51, "href": "http://pfam.xfam.org/family/PF03166.12", "type": "pfama", "display": "true", "metadata": {"end": 149, "description": "This is the MH2 (MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C-terminus of MH2 [1-3].", "database": "PfamA", "aliStart": 58, "scoreName": "E-value", "accession": "PF03166.12", "start": 51, "score": 0.0001, "identifier": "MH2 domain", "type": "DBD", "aliEnd": 133}}], "length": 220}

TF Info Page for IRF8 (IRF)