The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	In vivo/Misc source

Description

Description:

RE1 silencing transcription factor [Source:HGNC Symbol;Acc:HGNC:9966]

Entrez Summary

This gene was initially identified as a transcriptional repressor that represses neuronal genes in non-neuronal tissues. However, depending on the cellular context, this gene can act as either an oncogene or a tumor suppressor. The encoded protein is a member of the Kruppel-type zinc finger transcription factor family. It represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element. The protein is also found in undifferentiated neuronal progenitor cells and it is thought that this repressor may act as a master negative regulator of neurogenesis. Alternatively spliced transcript variants have been described. [provided by RefSeq, May 2018]

Ensembl ID:

ENSG00000084093

External Link:

CisBP

Interpro

IPR007087; IPR015880;

Protein Domain:

ENSP00000311816

Protein Domain:

ENSP00000479151

Protein Domain:

ENSP00000484836

Protein Domain:

ENSP00000481650

Domain:

Protein: ENSP00000311816	DBD: C2H2 ZF Containing Proteins	Other: zf-C2H2_4, zf-H2C2_5
Protein: ENSP00000479151	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000484836	DBD: C2H2 ZF Containing Proteins	Other: zf-C2H2_4, zf-H2C2_5
Protein: ENSP00000481650	DBD: C2H2 ZF Containing Proteins	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:15240883
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:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IDA - PMID:10449787, PMID:10734093, PMID:21284946 GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor IEA - GO_REF:0000019 GO:0003700 sequence-specific DNA binding transcription factor activity IDA - PMID:19342457
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	2a1, Lower confidence direct evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	ENCODE		Direct
ChIP-seq	JASPAR		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
Misc	HOMER		Direct
Transfac	Transfac	License required	Inferred - Rest (98% AA Identity, Rattus norvegicus)

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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The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 248, "scoreName": "E-value", "accession": "PF00096.24", "start": 248, "score": 3.2e-13, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 270}}, {"startStyle": "curved", "end": 298, "endStyle": "curved", "aliStart": 276, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 298, "start": 276, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 298, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. 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The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. 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The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. 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The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 1060, "scoreName": "E-value", "accession": "PF00096.24", "start": 1060, "score": 3.2e-13, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 1082}}, {"startStyle": "straight", "end": 183, "endStyle": "straight", "aliStart": 159, "text": "zf-H2C2_5", "colour": "#9999ff", "aliEnd": 182, "start": 159, "href": "http://pfam.xfam.org/family/PF13909.4", "type": "pfama", "display": "true", "metadata": {"end": 183, "description": NaN, "database": "PfamA", "aliStart": 159, "scoreName": "E-value", "accession": "PF13909.4", "start": 159, "score": 9.2e-22, "identifier": "C2H2-type zinc-finger domain", "type": "DBD", "aliEnd": 182}}, {"startStyle": "straight", "end": 182, "endStyle": "straight", "aliStart": 159, "text": "zf-C2H2_4", "colour": "#9999ff", "aliEnd": 181, "start": 159, "href": "http://pfam.xfam.org/family/PF13894.4", "type": "pfama", "display": "true", "metadata": {"end": 182, "description": "This family contains a number of divergent C2H2 type zinc fingers.", "database": "PfamA", "aliStart": 159, "scoreName": "E-value", "accession": "PF13894.4", "start": 159, "score": 1e-09, "identifier": "C2H2-type zinc finger", "type": "DBD", "aliEnd": 181}}], "length": 1098}

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The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 304, "scoreName": "E-value", "accession": "PF00096.24", "start": 304, "score": 6.8e-11, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 326}}], "length": 341}

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The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 144, "scoreName": "E-value", "accession": "PF00096.24", "start": 144, "score": 2.0999999999999998e-09, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 166}}, {"startStyle": "curved", "end": 194, "endStyle": "curved", "aliStart": 172, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 194, "start": 172, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 194, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 172, "scoreName": "E-value", "accession": "PF00096.24", "start": 172, "score": 2.0999999999999998e-09, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 194}}, {"startStyle": "curved", "end": 299, "endStyle": "curved", "aliStart": 277, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 299, "start": 277, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 299, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 277, "scoreName": "E-value", "accession": "PF00096.24", "start": 277, "score": 2.0999999999999998e-09, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 299}}], "length": 315}

TF Info Page for REST (C2H2 ZF(non-KRAB))

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution