The Human Transcription Factors

Conclusion

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

Description

Description:	LIM homeobox transcription factor 1 beta [Source:HGNC Symbol;Acc:HGNC:6654]
Entrez Summary	TBA
Ensembl ID:	ENSG00000136944
External Link:	T093315_1.02
Interpro	IPR001356; IPR001781; IPR009057; IPR017970;
Protein Domain:
Protein: ENSP00000347684	DBD: Homeodomain	Other: LIM
Protein: ENSP00000362573	DBD: Homeodomain	Other: LIM
Protein: ENSP00000436930	DBD: Homeodomain	Other: LIM
Protein: ENSP00000453580	DBD: Homeodomain	Other: LIM

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_Transactivation_ PMIDS:10767331 11956245 1358758 15785774
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:0003700 sequence-specific DNA binding transcription factor activity IDA - PMID:10767331
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
HT-SELEX	Jolma2013		Direct
HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
HT-SELEX	Yin2017		Inferred - LMX1A (100% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - LMX1A (100% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - LMX1A (100% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Lmx1a (100% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Lmx1b (100% AA Identity, Mus musculus)
B1H	JASPAR		Inferred - CG32105 (84% AA Identity, Drosophila melanogaster)
HT-SELEX	Nitta2015		Inferred - CG32105 (84% AA Identity, Drosophila melanogaster)
B1H	JASPAR		Inferred - CG4328 (82% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - SNAPOd2T00003340001 (74% AA Identity, Oikopleura dioica)

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": 276, "endStyle": "curved", "aliStart": 220, "text": "HD", "colour": "#228B22", "aliEnd": 276, "start": 220, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 276, "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": 220, "scoreName": "E-value", "accession": "PF00046.27", "start": 220, "score": 6.6e-18, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 276}}, {"startStyle": "straight", "end": 111, "endStyle": "straight", "aliStart": 56, "text": "LIM", "colour": "#9999ff", "aliEnd": 110, "start": 56, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 111, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 56, "scoreName": "E-value", "accession": "PF00412.20", "start": 56, "score": 4.2999999999999996e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 110}}, {"startStyle": "straight", "end": 173, "endStyle": "straight", "aliStart": 115, "text": "LIM", "colour": "#9999ff", "aliEnd": 172, "start": 115, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 173, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 115, "scoreName": "E-value", "accession": "PF00412.20", "start": 115, "score": 4.2999999999999996e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 172}}], "length": 407}

{"regions": [{"startStyle": "curved", "end": 276, "endStyle": "curved", "aliStart": 220, "text": "HD", "colour": "#228B22", "aliEnd": 276, "start": 220, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 276, "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": 220, "scoreName": "E-value", "accession": "PF00046.27", "start": 220, "score": 6.4e-18, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 276}}, {"startStyle": "straight", "end": 111, "endStyle": "straight", "aliStart": 56, "text": "LIM", "colour": "#9999ff", "aliEnd": 110, "start": 56, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 111, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 56, "scoreName": "E-value", "accession": "PF00412.20", "start": 56, "score": 4.2e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 110}}, {"startStyle": "straight", "end": 173, "endStyle": "straight", "aliStart": 115, "text": "LIM", "colour": "#9999ff", "aliEnd": 172, "start": 115, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 173, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 115, "scoreName": "E-value", "accession": "PF00412.20", "start": 115, "score": 4.2e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 172}}], "length": 403}

{"regions": [{"startStyle": "curved", "end": 276, "endStyle": "curved", "aliStart": 220, "text": "HD", "colour": "#228B22", "aliEnd": 276, "start": 220, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 276, "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": 220, "scoreName": "E-value", "accession": "PF00046.27", "start": 220, "score": 6.2e-18, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 276}}, {"startStyle": "straight", "end": 111, "endStyle": "straight", "aliStart": 56, "text": "LIM", "colour": "#9999ff", "aliEnd": 110, "start": 56, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 111, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 56, "scoreName": "E-value", "accession": "PF00412.20", "start": 56, "score": 3.9e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 110}}, {"startStyle": "straight", "end": 173, "endStyle": "straight", "aliStart": 115, "text": "LIM", "colour": "#9999ff", "aliEnd": 172, "start": 115, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 173, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 115, "scoreName": "E-value", "accession": "PF00412.20", "start": 115, "score": 3.9e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 172}}], "length": 396}

{"regions": [{"startStyle": "curved", "end": 253, "endStyle": "curved", "aliStart": 197, "text": "HD", "colour": "#228B22", "aliEnd": 253, "start": 197, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 253, "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": 197, "scoreName": "E-value", "accession": "PF00046.27", "start": 197, "score": 6.5e-18, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 253}}, {"startStyle": "straight", "end": 88, "endStyle": "straight", "aliStart": 33, "text": "LIM", "colour": "#9999ff", "aliEnd": 87, "start": 33, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 88, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 33, "scoreName": "E-value", "accession": "PF00412.20", "start": 33, "score": 3.9e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 87}}, {"startStyle": "straight", "end": 150, "endStyle": "straight", "aliStart": 92, "text": "LIM", "colour": "#9999ff", "aliEnd": 149, "start": 92, "href": "http://pfam.xfam.org/family/PF00412.20", "type": "pfama", "display": "true", "metadata": {"end": 150, "description": "This family represents two copies of the LIM structural domain.", "database": "PfamA", "aliStart": 92, "scoreName": "E-value", "accession": "PF00412.20", "start": 92, "score": 3.9e-33, "identifier": "LIM domain", "type": "DBD", "aliEnd": 149}}], "length": 384}

TF Info Page for LMX1B (Homeodomain)