The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Inferred motif	3 Low specificity DNA-binding protein	In vivo/Misc source		SATBs were analyzed by Gwenael Badis and Mike Berger a decade ago; by PBMs. It did not yield a motif; instead; the signal was very closely proportional to nucleotide content, as the name suggests (Special AT Binding).

Description

Description:

SATB homeobox 2 [Source:HGNC Symbol;Acc:HGNC:21637]

Entrez Summary

This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Feb 2010]

Ensembl ID:

ENSG00000119042

External Link:

CisBP

Interpro

IPR001356; IPR003350; IPR009057; IPR010982;

Protein Domain:

ENSP00000260926

Protein Domain:

ENSP00000388581

Protein Domain:

ENSP00000401112

Protein Domain:

ENSP00000405420

Domain:

Protein: ENSP00000260926	DBD: CUT, Homeodomain	Other: CUTL, ULD
Protein: ENSP00000388581	DBD: CUT, Homeodomain	Other: ULD
Protein: ENSP00000401112	DBD: CUT, Homeodomain	Other: CUTL, ULD
Protein: ENSP00000405420	DBD: CUT, Homeodomain	Other: CUTL, ULD

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene Candidate_DNA-Binding sequence-specific_DNA Binding_ PMIDS:14701874
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	2a2, orthologous lower confidence evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
Transfac	Transfac	License required	Inferred - SATB1 (84% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - SATB1 (84% AA Identity, Homo sapiens)

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": 434, "endStyle": "curved", "aliStart": 356, "text": "CUT", "colour": "#2cb42c", "aliEnd": 434, "start": 355, "href": "http://pfam.xfam.org/family/PF02376.13", "type": "pfama", "display": "true", "metadata": {"end": 434, "description": "The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. ", "database": "PfamA", "aliStart": 356, "scoreName": "E-value", "accession": "PF02376.13", "start": 355, "score": 3.1e-48, "identifier": "CUT domain", "type": "DBD", "aliEnd": 434}}, {"startStyle": "curved", "end": 557, "endStyle": "curved", "aliStart": 482, "text": "CUT", "colour": "#2cb42c", "aliEnd": 556, "start": 479, "href": "http://pfam.xfam.org/family/PF02376.13", "type": "pfama", "display": "true", "metadata": {"end": 557, "description": "The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. ", "database": "PfamA", "aliStart": 482, "scoreName": "E-value", "accession": "PF02376.13", "start": 479, "score": 3.1e-48, "identifier": "CUT domain", "type": "DBD", "aliEnd": 556}}, {"startStyle": "curved", "end": 672, "endStyle": "curved", "aliStart": 616, "text": "HD", "colour": "#228B22", "aliEnd": 671, "start": 615, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 672, "description": "The homeobox domain or homeodomain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [PUBMED:2568852, PUBMED:1357790]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [PUBMED:12445403]. The domain binds DNA through a helix-turn-helix (HTH) structure. ", "database": "PfamA", "aliStart": 616, "scoreName": "E-value", "accession": "PF00046.27", "start": 615, "score": 2.5e-07, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 671}}, {"startStyle": "straight", "end": 233, "endStyle": "straight", "aliStart": 163, "text": "CUTL", "colour": "#9999ff", "aliEnd": 233, "start": 162, "href": "http://pfam.xfam.org/family/PF16557.3", "type": "pfama", "display": "true", "metadata": {"end": 233, "description": "CUTL is part of the N-terminal region of SATB proteins, special AT-rich sequence-binding proteins that are global chromatin organisers and gene expression regulators essential for T-cell development and breast cancer tumour growth and metastasis. CUTL carries a DNA-binding region just as CUT domains do [1].", "database": "PfamA", "aliStart": 163, "scoreName": "E-value", "accession": "PF16557.3", "start": 162, "score": 1.4999999999999998e-42, "identifier": "CUT1-like DNA-binding domain of SATB", "type": "DBD", "aliEnd": 233}}, {"startStyle": "straight", "end": 156, "endStyle": "straight", "aliStart": 59, "text": "ULD", "colour": "#9999ff", "aliEnd": 156, "start": 58, "href": "http://pfam.xfam.org/family/PF16534.3", "type": "pfama", "display": "true", "metadata": {"end": 156, "description": "ULD is an N-terminal oligomerisation domain of SATB or special AT-rich sequence-binding proteins.  SATBs are global chromatin organisers and regulators of gene expression that are essential for T-cell development, breast cancer tumour growth and metastasis. SATBs assemble into a tetramer via the ULD domain, and the tetramerisation of SATBs are essential for recognising specific DNA sequences (such as multiple AT-rich DNA fragments). Thus, SATBs may regulate gene expression directly by binding to various promoters and upstream regions and thereby influencing promoter activity [1].", "database": "PfamA", "aliStart": 59, "scoreName": "E-value", "accession": "PF16534.3", "start": 58, "score": 1.1e-36, "identifier": "Ubiquitin-like oligomerisation domain of SATB", "type": "DBD", "aliEnd": 156}}], "length": 734}

{"regions": [{"startStyle": "curved", "end": 316, "endStyle": "curved", "aliStart": 238, "text": "CUT", "colour": "#2cb42c", "aliEnd": 316, "start": 237, "href": "http://pfam.xfam.org/family/PF02376.13", "type": "pfama", "display": "true", "metadata": {"end": 316, "description": "The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. ", "database": "PfamA", "aliStart": 238, "scoreName": "E-value", "accession": "PF02376.13", "start": 237, "score": 1.5e-48, "identifier": "CUT domain", "type": "DBD", "aliEnd": 316}}, {"startStyle": "curved", "end": 439, "endStyle": "curved", "aliStart": 364, "text": "CUT", "colour": "#2cb42c", "aliEnd": 438, "start": 361, "href": "http://pfam.xfam.org/family/PF02376.13", "type": "pfama", "display": "true", "metadata": {"end": 439, "description": "The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. ", "database": "PfamA", "aliStart": 364, "scoreName": "E-value", "accession": "PF02376.13", "start": 361, "score": 1.5e-48, "identifier": "CUT domain", "type": "DBD", "aliEnd": 438}}, {"startStyle": "curved", "end": 554, "endStyle": "curved", "aliStart": 498, "text": "HD", "colour": "#228B22", "aliEnd": 553, "start": 497, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 554, "description": "The homeobox domain or homeodomain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [PUBMED:2568852, PUBMED:1357790]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [PUBMED:12445403]. The domain binds DNA through a helix-turn-helix (HTH) structure. ", "database": "PfamA", "aliStart": 498, "scoreName": "E-value", "accession": "PF00046.27", "start": 497, "score": 2.4e-07, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 553}}, {"startStyle": "straight", "end": 118, "endStyle": "jagged", "aliStart": 59, "text": "ULD", "colour": "#9999ff", "aliEnd": 115, "start": 58, "href": "http://pfam.xfam.org/family/PF16534.3", "type": "pfama", "display": "true", "metadata": {"end": 118, "description": "ULD is an N-terminal oligomerisation domain of SATB or special AT-rich sequence-binding proteins.  SATBs are global chromatin organisers and regulators of gene expression that are essential for T-cell development, breast cancer tumour growth and metastasis. SATBs assemble into a tetramer via the ULD domain, and the tetramerisation of SATBs are essential for recognising specific DNA sequences (such as multiple AT-rich DNA fragments). Thus, SATBs may regulate gene expression directly by binding to various promoters and upstream regions and thereby influencing promoter activity [1].", "database": "PfamA", "aliStart": 59, "scoreName": "E-value", "accession": "PF16534.3", "start": 58, "score": 7.6e-15, "identifier": "Ubiquitin-like oligomerisation domain of SATB", "type": "DBD", "aliEnd": 115}}], "length": 616}

TF Info Page for SATB2 (CUT; Homeodomain)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution