The Human Transcription Factors

Conclusion

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

Description

Description:

nuclear respiratory factor 1 [Source:HGNC Symbol;Acc:HGNC:7996]

Entrez Summary

This gene encodes a protein that homodimerizes and functions as a transcription factor which activates the expression of some key metabolic genes regulating cellular growth and nuclear genes required for respiration, heme biosynthesis, and mitochondrial DNA transcription and replication. The protein has also been associated with the regulation of neurite outgrowth. Alternative splicing results in multiple transcript variants. Confusion has occurred in bibliographic databases due to the shared symbol of NRF1 for this gene and for

Ensembl ID:

ENSG00000106459

External Link:

CisBP

Interpro

IPR019525; IPR019526;

Protein Domain:

ENSP00000309826

Protein Domain:

ENSP00000376922

Protein Domain:

ENSP00000376924

Domain:

Protein: ENSP00000309826	DBD: NRF	Other: Nrf1_DNA-bind, Nrf1_activ_bdg
Protein: ENSP00000376922	DBD: NRF	Other: Nrf1_DNA-bind, Nrf1_activ_bdg
Protein: ENSP00000376924	DBD: NRF	Other: Nrf1_DNA-bind, Nrf1_activ_bdg

Previous Annotations

Source	Annotation
TF-CAT classification	Indeterminate - There is no evidence for or against this genes role as a TF__DNA Binding Transactivation_ PMIDS:9580677
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.	other
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:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IDA - PMID:19674972 \| IMP - PMID:19674972
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
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
Misc	HocoMoco		Direct
Misc	HOMER		Direct

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": 283, "endStyle": "straight", "aliStart": 75, "text": "Nrf1_DNA-bind", "colour": "#9999ff", "aliEnd": 283, "start": 75, "href": "http://pfam.xfam.org/family/PF10491.7", "type": "pfama", "display": "true", "metadata": {"end": 283, "description": "In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human [1]. Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila [2]. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Swiss-Prot:Q8C4C0, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [3].", "database": "PfamA", "aliStart": 75, "scoreName": "E-value", "accession": "PF10491.7", "start": 75, "score": 1.3e-116, "identifier": "NLS-binding and DNA-binding and dimerisation domains of Nrf1", "type": "DBD", "aliEnd": 283}}, {"startStyle": "straight", "end": 503, "endStyle": "jagged", "aliStart": 450, "text": "Nrf1_activ_bdg", "colour": "#9999ff", "aliEnd": 490, "start": 449, "href": "http://pfam.xfam.org/family/PF10492.7", "type": "pfama", "display": "true", "metadata": {"end": 503, "description": "In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human [1]. Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila [2]. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Swiss:Q8C4C0, there is an activation domain at 303-469, the most conserved part of which is this domain 446-469.  Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [3]. The family Nrf1_DNA-bind is associated with this domain towards the N-terminal, as is the N terminal of the activation domain.", "database": "PfamA", "aliStart": 450, "scoreName": "E-value", "accession": "PF10492.7", "start": 449, "score": 0.0008699999999999999, "identifier": "Nrf1 activator activation site binding domain", "type": "DBD", "aliEnd": 490}}], "length": 504}

TF Info Page for NRF1 (Unknown)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution