The Human Transcription Factors

Conclusion

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

Description

Description:	regulatory factor X3 [Source:HGNC Symbol;Acc:HGNC:9984]
Entrez Summary	TBA
Ensembl ID:	ENSG00000080298
External Link:
Interpro	IPR003150; IPR007668;
Protein Domain:
Protein: ENSP00000303847	DBD: RFX	Other: RFX1_trans_act
Protein: ENSP00000351574	DBD: RFX	Other: RFX1_trans_act
Protein: ENSP00000371434	DBD: RFX	Other: RFX1_trans_act
Protein: ENSP00000482598	DBD: RFX	Other: RFX1_trans_act
Protein: ENSP00000371414	DBD: RFX	Other: RFX1_trans_act
Protein: ENSP00000416189	DBD: RFX	Other: RFX1_trans_act
Protein: ENSP00000410988	DBD: RFX	Other: RFX1_trans_act
Protein: ENSP00000399352	DBD: RFX	Other: RFX1_trans_act
Protein: ENSP00000415594	DBD: RFX	Other:
Protein: ENSP00000411756	DBD: RFX	Other: RFX1_trans_act
Protein: ENSP00000400026	DBD: RFX	Other: HisKA

Previous Annotations

Source	Annotation
TF-CAT classification	No PMIDS:
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:0003700 sequence-specific DNA binding transcription factor activity NAS - PMID:8600444 GO:0003705 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity TAS - PMID:8289803
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	Jolma2010		Direct
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
Misc	HocoMoco		Direct
Misc	HOMER		Direct
PBM	Badis09		Inferred - Rfx3 (94% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - RFX2 (91% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - RFX2 (91% AA Identity, Ornithorhynchus anatinus)
PBM	Zoo_01		Inferred - RFX1 (80% AA Identity, Anolis carolinensis)
HT-SELEX	Yin2017		Inferred - RFX1 (80% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RFX1 (80% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - rfx1a (80% AA Identity, Tetraodon nigroviridis)
Transfac	Transfac	License required	Inferred - RFX1 (80% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RFX1 (80% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RFX1 (80% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - RFX1 (80% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - Rfx1 (80% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - RFX1 (80% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - PHUM046580 (78% AA Identity, Pediculus humanus)
PBM	Zoo_01		Inferred - G4VLF2_SCHMA (77% AA Identity, Schistosoma mansoni)
PBM	Zoo_01		Inferred - Sjc_0102030 (76% AA Identity, Schistosoma japonicum)
HT-SELEX	Yin2017		Inferred - RFX2 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RFX2 (70% AA Identity, Homo sapiens)
SELEX	JASPAR		Inferred - RFX2 (70% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - RFX2 (70% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - RFX2 (70% AA Identity, Homo sapiens)
SMiLE-seq	Isakova2017		Inferred - RFX2 (69% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - GB41876 (67% AA Identity, Apis mellifera)
PBM	CEPD		Inferred - daf-19 (65% AA Identity, Caenorhabditis elegans)
HT-SELEX	Nitta2015		Inferred - Rfx (62% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rfx (62% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rfx (62% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rfx (62% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - Rfx (62% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - XP_002157607.1 (62% AA Identity, Hydra magnipapillata)
PBM	Zoo_01		Inferred - RFX4 (61% AA Identity, Cavia porcellus)
HT-SELEX	Yin2017		Inferred - RFX4 (61% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - RFX4 (61% AA Identity, Homo sapiens)
PBM	Badis09		Inferred - Rfx4 (61% AA Identity, Mus musculus)

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

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{"regions": [{"startStyle": "straight", "end": 47, "endStyle": "jagged", "aliStart": 7, "text": "RFX1_trans_act", "colour": "#9999ff", "aliEnd": 45, "start": 4, "href": "http://pfam.xfam.org/family/PF04589.11", "type": "pfama", "display": "true", "metadata": {"end": 47, "description": "The RFX family is a family of winged-helix DNA binding proteins.  RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region  (Pfam:PF02257) in some mammalian RFX proteins, and is thought to activate  transcription when associated with DNA.  Deletion analysis has identified  the region 233-351 in human RFX1 (Swiss:P22670) as being required for  maximal activation [1].", "database": "PfamA", "aliStart": 7, "scoreName": "E-value", "accession": "PF04589.11", "start": 4, "score": 5.5e-11, "identifier": "RFX1 transcription activation region      ", "type": "DBD", "aliEnd": 45}}, {"startStyle": "jagged", "end": 84, "endStyle": "jagged", "aliStart": 26, "text": "RFX1_trans_act", "colour": "#9999ff", "aliEnd": 78, "start": 23, "href": "http://pfam.xfam.org/family/PF04589.11", "type": "pfama", "display": "true", "metadata": {"end": 84, "description": "The RFX family is a family of winged-helix DNA binding proteins.  RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region  (Pfam:PF02257) in some mammalian RFX proteins, and is thought to activate  transcription when associated with DNA.  Deletion analysis has identified  the region 233-351 in human RFX1 (Swiss:P22670) as being required for  maximal activation [1].", "database": "PfamA", "aliStart": 26, "scoreName": "E-value", "accession": "PF04589.11", "start": 23, "score": 5.5e-11, "identifier": "RFX1 transcription activation region      ", "type": "DBD", "aliEnd": 78}}], "length": 86}

{"regions": [{"startStyle": "straight", "end": 49, "endStyle": "jagged", "aliStart": 7, "text": "RFX1_trans_act", "colour": "#9999ff", "aliEnd": 48, "start": 4, "href": "http://pfam.xfam.org/family/PF04589.11", "type": "pfama", "display": "true", "metadata": {"end": 49, "description": "The RFX family is a family of winged-helix DNA binding proteins.  RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region  (Pfam:PF02257) in some mammalian RFX proteins, and is thought to activate  transcription when associated with DNA.  Deletion analysis has identified  the region 233-351 in human RFX1 (Swiss:P22670) as being required for  maximal activation [1].", "database": "PfamA", "aliStart": 7, "scoreName": "E-value", "accession": "PF04589.11", "start": 4, "score": 1.3999999999999999e-36, "identifier": "RFX1 transcription activation region      ", "type": "DBD", "aliEnd": 48}}, {"startStyle": "jagged", "end": 138, "endStyle": "straight", "aliStart": 24, "text": "RFX1_trans_act", "colour": "#9999ff", "aliEnd": 134, "start": 18, "href": "http://pfam.xfam.org/family/PF04589.11", "type": "pfama", "display": "true", "metadata": {"end": 138, "description": "The RFX family is a family of winged-helix DNA binding proteins.  RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region  (Pfam:PF02257) in some mammalian RFX proteins, and is thought to activate  transcription when associated with DNA.  Deletion analysis has identified  the region 233-351 in human RFX1 (Swiss:P22670) as being required for  maximal activation [1].", "database": "PfamA", "aliStart": 24, "scoreName": "E-value", "accession": "PF04589.11", "start": 18, "score": 1.3999999999999999e-36, "identifier": "RFX1 transcription activation region      ", "type": "DBD", "aliEnd": 134}}], "length": 138}

{"regions": [{"startStyle": "straight", "end": 48, "endStyle": "jagged", "aliStart": 8, "text": "RFX1_trans_act", "colour": "#9999ff", "aliEnd": 48, "start": 4, "href": "http://pfam.xfam.org/family/PF04589.11", "type": "pfama", "display": "true", "metadata": {"end": 48, "description": "The RFX family is a family of winged-helix DNA binding proteins.  RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region  (Pfam:PF02257) in some mammalian RFX proteins, and is thought to activate  transcription when associated with DNA.  Deletion analysis has identified  the region 233-351 in human RFX1 (Swiss:P22670) as being required for  maximal activation [1].", "database": "PfamA", "aliStart": 8, "scoreName": "E-value", "accession": "PF04589.11", "start": 4, "score": 2.6999999999999997e-36, "identifier": "RFX1 transcription activation region      ", "type": "DBD", "aliEnd": 48}}, {"startStyle": "jagged", "end": 138, "endStyle": "straight", "aliStart": 23, "text": "RFX1_trans_act", "colour": "#9999ff", "aliEnd": 134, "start": 17, "href": "http://pfam.xfam.org/family/PF04589.11", "type": "pfama", "display": "true", "metadata": {"end": 138, "description": "The RFX family is a family of winged-helix DNA binding proteins.  RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region  (Pfam:PF02257) in some mammalian RFX proteins, and is thought to activate  transcription when associated with DNA.  Deletion analysis has identified  the region 233-351 in human RFX1 (Swiss:P22670) as being required for  maximal activation [1].", "database": "PfamA", "aliStart": 23, "scoreName": "E-value", "accession": "PF04589.11", "start": 17, "score": 2.6999999999999997e-36, "identifier": "RFX1 transcription activation region      ", "type": "DBD", "aliEnd": 134}}], "length": 184}

TF Info Page for RFX3 (RFX)