The Human Transcription Factors

Conclusion

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

Description

Description:	high mobility group 20B [Source:HGNC Symbol;Acc:HGNC:5002]
Entrez Summary	TBA
Ensembl ID:	ENSG00000064961
External Link:
Interpro	IPR009071; ;
Protein Domain:
Protein: ENSP00000328269	DBD: HMG	Other:
Protein: ENSP00000402877	DBD: HMG	Other:
Protein: ENSP00000410924	DBD: HMG	Other:
Protein: ENSP00000465293	DBD: HMG	Other: IncA

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.	x
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
PBM	Zoo_01		Inferred - Hmg20b (94% 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": 138, "endStyle": "curved", "aliStart": 70, "text": "HMG", "colour": "#228B22", "aliEnd": 137, "start": 70, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 138, "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": 70, "scoreName": "E-value", "accession": "PF00505.17", "start": 70, "score": 1.6000000000000002e-19, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 137}}], "length": 318}

{"regions": [{"startStyle": "curved", "end": 138, "endStyle": "curved", "aliStart": 70, "text": "HMG", "colour": "#228B22", "aliEnd": 137, "start": 70, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 138, "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": 70, "scoreName": "E-value", "accession": "PF00505.17", "start": 70, "score": 2.0000000000000002e-20, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 137}}], "length": 142}

{"regions": [{"startStyle": "curved", "end": 138, "endStyle": "curved", "aliStart": 70, "text": "HMG", "colour": "#228B22", "aliEnd": 137, "start": 70, "href": "http://pfam.xfam.org/family/PF00505.17", "type": "pfama", "display": "true", "metadata": {"end": 138, "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": 70, "scoreName": "E-value", "accession": "PF00505.17", "start": 70, "score": 7.8e-20, "identifier": "HMG (high mobility group) box", "type": "DBD", "aliEnd": 137}}], "length": 215}

{"regions": [{"startStyle": "jagged", "end": 119, "endStyle": "jagged", "aliStart": 5, "text": "IncA", "colour": "#9999ff", "aliEnd": 66, "start": 2, "href": "http://pfam.xfam.org/family/PF04156.12", "type": "pfama", "display": "true", "metadata": {"end": 119, "description": "Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C.  trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions [1]. This family probably includes members of the wider Inc family rather than just IncA. Members are usually either 2 or 4TM proteins.", "database": "PfamA", "aliStart": 5, "scoreName": "E-value", "accession": "PF04156.12", "start": 2, "score": 0.0047, "identifier": "IncA protein", "type": "DBD", "aliEnd": 66}}], "length": 185}

TF Info Page for HMG20B (HMG/Sox)