The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	3 Low specificity DNA-binding protein	In vivo/Misc source	Only known motifs are from Transfac or HocoMoco - origin is uncertain	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 1 [Source:HGNC Symbol;Acc:HGNC:10541]

Entrez Summary

This gene encodes a matrix protein which binds nuclear matrix and scaffold-associating DNAs through a unique nuclear architecture. The protein recruits chromatin-remodeling factors in order to regulate chromatin structure and gene expression. [provided by RefSeq, Apr 2016]

Ensembl ID:

ENSG00000182568

External Link:

CisBP

Interpro

IPR001356; IPR003350; IPR009057; IPR010982;

Protein Domain:

ENSP00000341024

Protein Domain:

ENSP00000399518

Protein Domain:

ENSP00000399708

Protein Domain:

ENSP00000479866

Protein Domain:

ENSP00000408871

Protein Domain:

ENSP00000390529

Protein Domain:

ENSP00000453908

Domain:

Protein: ENSP00000341024	DBD: CUT, Homeodomain	Other: CUTL, ULD
Protein: ENSP00000399518	DBD: CUT, Homeodomain	Other: CUTL, SUIM_assoc, ULD
Protein: ENSP00000399708	DBD: CUT, Homeodomain	Other: CUTL, ULD
Protein: ENSP00000479866	DBD: CUT, Homeodomain	Other: CUTL, RuvA_C, ULD
Protein: ENSP00000408871	DBD: CUT, Homeodomain	Other: ULD
Protein: ENSP00000390529	DBD: CUT, Homeodomain	Other: ULD
Protein: ENSP00000453908	DBD: CUT, Homeodomain	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding_ PMIDS:1505028 8114718 9340009
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:0001227 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor IDA - PMID:15851481
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
Transfac	Transfac	License required	Direct

Structure

Structure	PDB	2O49

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": "curved", "end": 445, "endStyle": "curved", "aliStart": 368, "text": "CUT", "colour": "#2cb42c", "aliEnd": 445, "start": 366, "href": "http://pfam.xfam.org/family/PF02376.13", "type": "pfama", "display": "true", "metadata": {"end": 445, "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": 368, "scoreName": "E-value", "accession": "PF02376.13", "start": 366, "score": 9.5e-46, "identifier": "CUT domain", "type": "DBD", "aliEnd": 445}}, {"startStyle": "curved", "end": 568, "endStyle": "curved", "aliStart": 493, "text": "CUT", "colour": "#2cb42c", "aliEnd": 567, "start": 489, "href": "http://pfam.xfam.org/family/PF02376.13", "type": "pfama", "display": "true", "metadata": {"end": 568, "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": 493, "scoreName": "E-value", "accession": "PF02376.13", "start": 489, "score": 9.5e-46, "identifier": "CUT domain", "type": "DBD", "aliEnd": 567}}, {"startStyle": "curved", "end": 734, "endStyle": "curved", "aliStart": 678, "text": "HD", "colour": "#228B22", "aliEnd": 733, "start": 677, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 734, "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": 678, "scoreName": "E-value", "accession": "PF00046.27", "start": 677, "score": 6.5e-08, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 733}}, {"startStyle": "straight", "end": 247, "endStyle": "straight", "aliStart": 177, "text": "CUTL", "colour": "#9999ff", "aliEnd": 247, "start": 176, "href": "http://pfam.xfam.org/family/PF16557.3", "type": "pfama", "display": "true", "metadata": {"end": 247, "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": 177, "scoreName": "E-value", "accession": "PF16557.3", "start": 176, "score": 1.4999999999999998e-43, "identifier": "CUT1-like DNA-binding domain of SATB", "type": "DBD", "aliEnd": 247}}, {"startStyle": "straight", "end": 170, "endStyle": "straight", "aliStart": 73, "text": "ULD", "colour": "#9999ff", "aliEnd": 170, "start": 72, "href": "http://pfam.xfam.org/family/PF16534.3", "type": "pfama", "display": "true", "metadata": {"end": 170, "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": 73, "scoreName": "E-value", "accession": "PF16534.3", "start": 72, "score": 2.0999999999999997e-37, "identifier": "Ubiquitin-like oligomerisation domain of SATB", "type": "DBD", "aliEnd": 170}}, {"startStyle": "jagged", "end": 659, "endStyle": "jagged", "aliStart": 591, "text": "SUIM_assoc", "colour": "#9999ff", "aliEnd": 652, "start": 530, "href": "http://pfam.xfam.org/family/PF16619.3", "type": "pfama", "display": "true", "metadata": {"end": 659, "description": "SUIM_assoc is a natively unstructured region on Ataxin 3 proteins that lies immediately C-terminal to the second UIM domain linking it to a third when present.  The function is not known. It is rich in glutamine residues.", "database": "PfamA", "aliStart": 591, "scoreName": "E-value", "accession": "PF16619.3", "start": 530, "score": 0.0057, "identifier": "Unstructured region C-term to UIM in Ataxin3", "type": "DBD", "aliEnd": 652}}], "length": 796}

{"regions": [{"startStyle": "jagged", "end": 66, "endStyle": "straight", "aliStart": 1, "text": "ULD", "colour": "#9999ff", "aliEnd": 66, "start": 1, "href": "http://pfam.xfam.org/family/PF16534.3", "type": "pfama", "display": "true", "metadata": {"end": 66, "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": 1, "scoreName": "E-value", "accession": "PF16534.3", "start": 1, "score": 2.8e-28, "identifier": "Ubiquitin-like oligomerisation domain of SATB", "type": "DBD", "aliEnd": 66}}, {"startStyle": "straight", "end": 124, "endStyle": "jagged", "aliStart": 73, "text": "CUTL", "colour": "#9999ff", "aliEnd": 116, "start": 72, "href": "http://pfam.xfam.org/family/PF16557.3", "type": "pfama", "display": "true", "metadata": {"end": 124, "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": 73, "scoreName": "E-value", "accession": "PF16557.3", "start": 72, "score": 8.199999999999999e-16, "identifier": "CUT1-like DNA-binding domain of SATB", "type": "DBD", "aliEnd": 116}}, {"startStyle": "jagged", "end": 29, "endStyle": "jagged", "aliStart": 8, "text": "RuvA_C", "colour": "#9999ff", "aliEnd": 24, "start": 7, "href": "http://pfam.xfam.org/family/PF07499.11", "type": "pfama", "display": "true", "metadata": {"end": 29, "description": "Homologous recombination is a crucial process  in all living organisms.  In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex  through direct contact with RuvB [1]. Within the Holliday junction, the C-terminal domain  makes no interaction with DNA [1].", "database": "PfamA", "aliStart": 8, "scoreName": "E-value", "accession": "PF07499.11", "start": 7, "score": 0.0044, "identifier": "RuvA, C-terminal domain", "type": "DBD", "aliEnd": 24}}], "length": 139}

{"regions": [{"startStyle": "straight", "end": 116, "endStyle": "jagged", "aliStart": 73, "text": "ULD", "colour": "#9999ff", "aliEnd": 116, "start": 72, "href": "http://pfam.xfam.org/family/PF16534.3", "type": "pfama", "display": "true", "metadata": {"end": 116, "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": 73, "scoreName": "E-value", "accession": "PF16534.3", "start": 72, "score": 1.3e-08, "identifier": "Ubiquitin-like oligomerisation domain of SATB", "type": "DBD", "aliEnd": 116}}], "length": 116}

{"regions": [{"startStyle": "straight", "end": 166, "endStyle": "straight", "aliStart": 73, "text": "ULD", "colour": "#9999ff", "aliEnd": 166, "start": 72, "href": "http://pfam.xfam.org/family/PF16534.3", "type": "pfama", "display": "true", "metadata": {"end": 166, "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": 73, "scoreName": "E-value", "accession": "PF16534.3", "start": 72, "score": 1.5e-35, "identifier": "Ubiquitin-like oligomerisation domain of SATB", "type": "DBD", "aliEnd": 166}}], "length": 166}

TF Info Page for SATB1 (CUT; Homeodomain)

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution