The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	100 perc ID - in vitro

Description

Description:

HMG-box transcription factor 1 [Source:HGNC Symbol;Acc:HGNC:23200]

Entrez Summary

Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of lipid transport; negative regulation of reactive oxygen species biosynthetic process; and negative regulation of transcription by RNA polymerase II. Located in nuclear speck. Biomarker of osteoarthritis. [provided by Alliance of Genome Resources, Apr 2022]

Ensembl ID:

ENSG00000105856

External Link:

CisBP

Interpro

IPR003652; IPR009071; IPR013723; ;

Protein Domain:

ENSP00000222574

Protein Domain:

ENSP00000420500

Protein Domain:

ENSP00000417927

Protein Domain:

ENSP00000418738

Protein Domain:

ENSP00000417631

Protein Domain:

ENSP00000418017

Protein Domain:

ENSP00000475809

Domain:

Protein: ENSP00000222574	DBD: HMG	Other: AXH
Protein: ENSP00000420500	DBD: HMG	Other: AXH
Protein: ENSP00000417927	DBD: HMG	Other:
Protein: ENSP00000418738	DBD: HMG	Other: AXH
Protein: ENSP00000417631	DBD: HMG	Other:
Protein: ENSP00000418017	DBD: HMG	Other: AXH
Protein: ENSP00000475809	DBD: HMG	Other:

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"	No
GO-Info
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
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
PBM	Badis09		Inferred - Hbp1 (100% 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

{"regions": [{"startStyle": "curved", "end": 501, "endStyle": "curved", "aliStart": 435, "text": "HMG", "colour": "#228B22", "aliEnd": 499, "start": 434, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 501, "description": "High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.", "database": "PfamA", "aliStart": 435, "scoreName": "E-value", "accession": "PF00505.17", "start": 434, "score": 5.2e-15, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 499}}, {"startStyle": "jagged", "end": 492, "endStyle": "jagged", "aliStart": 425, "text": "MATa", "colour": "#009900", "aliEnd": 476, "start": 404, "href": "http://pfam.xfam.org/family/PF04769.10", "type": "pfama", "display": "true", "metadata": {"end": 492, "description": "This family includes Saccharomyces cerevisiae mating type protein alpha 1 (Swiss:P01365).  Mat alpha 1 is a transcription activator which activates mating-type alpha-specific genes.  MAT alpha 1 and MCM 1 bind cooperatively to PQ elements upstream of alpha-specific genes [1]. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (Pfam:PF04648) response pathway [1]. In silico modelling of the MAT_Alpha1 domain indicates that its best scoring templates were structures of HMG-box proteins [2], and DOI: 10.4236/ojbiphy.2013.31001. Phylogenetic analysis suggests that the MAT_Alpha1 domain diverged from the MATA_HMG-box subfamily [2]. The name of MATalpha_HMG-box was proposed for the MAT_alpha1 domain [2].", "database": "PfamA", "aliStart": 425, "scoreName": "E-value", "accession": "PF04769.10", "start": 404, "score": 0.002, "identifier": "Mating-type protein MAT alpha 1 HMG-box", "type": "DBD", "aliEnd": 476}}, {"startStyle": "straight", "end": 339, "endStyle": "straight", "aliStart": 215, "text": "AXH", "colour": "#9999ff", "aliEnd": 339, "start": 215, "href": "http://pfam.xfam.org/family/PF08517.10", "type": "pfama", "display": "true", "metadata": {"end": 339, "description": "AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1).  ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans.  The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression [1].", "database": "PfamA", "aliStart": 215, "scoreName": "E-value", "accession": "PF08517.10", "start": 215, "score": 1.1999999999999998e-33, "identifier": "Ataxin-1 and HBP1 module (AXH)", "type": "DBD", "aliEnd": 339}}], "length": 515}

{"regions": [{"startStyle": "curved", "end": 454, "endStyle": "jagged", "aliStart": 427, "text": "HMG", "colour": "#228B22", "aliEnd": 453, "start": 426, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 454, "description": "High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.", "database": "PfamA", "aliStart": 427, "scoreName": "E-value", "accession": "PF00505.17", "start": 426, "score": 0.0011, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 453}}, {"startStyle": "straight", "end": 331, "endStyle": "straight", "aliStart": 207, "text": "AXH", "colour": "#9999ff", "aliEnd": 331, "start": 207, "href": "http://pfam.xfam.org/family/PF08517.10", "type": "pfama", "display": "true", "metadata": {"end": 331, "description": "AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1).  ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans.  The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression [1].", "database": "PfamA", "aliStart": 207, "scoreName": "E-value", "accession": "PF08517.10", "start": 207, "score": 1e-33, "identifier": "Ataxin-1 and HBP1 module (AXH)", "type": "DBD", "aliEnd": 331}}], "length": 455}

{"regions": [{"startStyle": "curved", "end": 141, "endStyle": "curved", "aliStart": 75, "text": "HMG", "colour": "#228B22", "aliEnd": 139, "start": 74, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 141, "description": "High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.", "database": "PfamA", "aliStart": 75, "scoreName": "E-value", "accession": "PF00505.17", "start": 74, "score": 8.6e-16, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 139}}, {"startStyle": "jagged", "end": 133, "endStyle": "jagged", "aliStart": 55, "text": "MATa", "colour": "#009900", "aliEnd": 121, "start": 43, "href": "http://pfam.xfam.org/family/PF04769.10", "type": "pfama", "display": "true", "metadata": {"end": 133, "description": "This family includes Saccharomyces cerevisiae mating type protein alpha 1 (Swiss:P01365).  Mat alpha 1 is a transcription activator which activates mating-type alpha-specific genes.  MAT alpha 1 and MCM 1 bind cooperatively to PQ elements upstream of alpha-specific genes [1]. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (Pfam:PF04648) response pathway [1]. In silico modelling of the MAT_Alpha1 domain indicates that its best scoring templates were structures of HMG-box proteins [2], and DOI: 10.4236/ojbiphy.2013.31001. Phylogenetic analysis suggests that the MAT_Alpha1 domain diverged from the MATA_HMG-box subfamily [2]. The name of MATalpha_HMG-box was proposed for the MAT_alpha1 domain [2].", "database": "PfamA", "aliStart": 55, "scoreName": "E-value", "accession": "PF04769.10", "start": 43, "score": 0.00029, "identifier": "Mating-type protein MAT alpha 1 HMG-box", "type": "DBD", "aliEnd": 121}}], "length": 155}

TF Info Page for HBP1 (HMG/Sox)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution