The Human Transcription Factors

Conclusion

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

Description

Description:	Meis homeobox 3 [Source:HGNC Symbol;Acc:HGNC:29537]
Entrez Summary	TBA
Ensembl ID:	ENSG00000105419
External Link:	T093244_1.02
Interpro	IPR001356; IPR008422; IPR009057; ;
Protein Domain:
Protein: ENSP00000388667	DBD: Homeodomain	Other: Meis_PKNOX_N
Protein: ENSP00000453757	DBD: Homeodomain	Other: Meis_PKNOX_N
Protein: ENSP00000453307	DBD: Homeodomain	Other: Meis_PKNOX_N
Protein: ENSP00000476248	DBD: Homeodomain	Other: Meis_PKNOX_N
Protein: ENSP00000452854	DBD: Homeodomain	Other: Meis_PKNOX_N
Protein: ENSP00000453934	DBD: Homeodomain	Other: Meis_PKNOX_N
Protein: ENSP00000475941	DBD: Homeodomain	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	GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IEA - GO_REF:0000019
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
Methyl-HT-SELEX	Yin2017		Direct
PBM	Berger08		Inferred - Meis3 (100% AA Identity, Mus musculus)
PBM	Berger08		Inferred - Meis1 (96% AA Identity, Mus musculus)
HT-SELEX	Jolma2010		Inferred - MEIS2 (96% AA Identity, Homo sapiens)
HT-SELEX	Jolma2010		Inferred - MEIS2 (96% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - MEIS2 (96% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - MEIS2 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - MEIS2 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - MEIS2 (96% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Meis2 (96% AA Identity, Mus musculus)
SELEX	JASPAR		Inferred - MEIS1 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - MEIS1 (96% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - MEIS1 (96% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - MEIS1 (96% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Meis1 (96% AA Identity, Mus musculus)
Misc	HocoMoco		Inferred - MEIS2 (96% AA Identity, Homo sapiens)
B1H	JASPAR		Inferred - hth (93% AA Identity, Drosophila melanogaster)
PBM	Zoo_01		Inferred - unc-62 (81% AA Identity, Caenorhabditis elegans)
PBM	Zoo_01		Inferred - Cbr-unc-62 (74% AA Identity, Caenorhabditis briggsae)
HT-SELEX	Yin2017		Inferred - PKNOX2 (72% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PKNOX2 (72% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Pknox2 (72% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - PKNOX1 (70% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - PKNOX1 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PKNOX1 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - PKNOX1 (70% AA Identity, Homo sapiens)
PBM	Berger08		Inferred - Pknox1 (70% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - PKNOX1 (70% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - PKNOX1 (70% AA Identity, Homo sapiens)
PBM	Zoo_01		Inferred - Q5EVH4_OIKDI (65% 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": 303, "endStyle": "curved", "aliStart": 248, "text": "HD", "colour": "#228B22", "aliEnd": 302, "start": 246, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 303, "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": 248, "scoreName": "E-value", "accession": "PF00046.27", "start": 246, "score": 1.5e-08, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 302}}, {"startStyle": "straight", "end": 163, "endStyle": "jagged", "aliStart": 96, "text": "Meis_PKNOX_N", "colour": "#9999ff", "aliEnd": 149, "start": 96, "href": "http://pfam.xfam.org/family/PF16493.3", "type": "pfama", "display": "true", "metadata": {"end": 163, "description": "Meis_PKNOX_N is a family found at the N-terminus of Meis, Myeloid ecotropic viral integration site, transcription regulators and PKNOX1 regulators, PBX/knotted 1 homeobox 1, homeobox proteins.", "database": "PfamA", "aliStart": 96, "scoreName": "E-value", "accession": "PF16493.3", "start": 96, "score": 2.3999999999999997e-23, "identifier": "N-terminal of Homeobox Meis and PKNOX1", "type": "DBD", "aliEnd": 149}}], "length": 359}

{"regions": [{"startStyle": "curved", "end": 195, "endStyle": "curved", "aliStart": 140, "text": "HD", "colour": "#228B22", "aliEnd": 194, "start": 138, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 195, "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": 140, "scoreName": "E-value", "accession": "PF00046.27", "start": 138, "score": 1.2e-08, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 194}}, {"startStyle": "jagged", "end": 55, "endStyle": "straight", "aliStart": 24, "text": "Meis_PKNOX_N", "colour": "#9999ff", "aliEnd": 54, "start": 20, "href": "http://pfam.xfam.org/family/PF16493.3", "type": "pfama", "display": "true", "metadata": {"end": 55, "description": "Meis_PKNOX_N is a family found at the N-terminus of Meis, Myeloid ecotropic viral integration site, transcription regulators and PKNOX1 regulators, PBX/knotted 1 homeobox 1, homeobox proteins.", "database": "PfamA", "aliStart": 24, "scoreName": "E-value", "accession": "PF16493.3", "start": 20, "score": 7.7e-16, "identifier": "N-terminal of Homeobox Meis and PKNOX1", "type": "DBD", "aliEnd": 54}}], "length": 251}

{"regions": [{"startStyle": "jagged", "end": 366, "endStyle": "curved", "aliStart": 332, "text": "HD", "colour": "#228B22", "aliEnd": 365, "start": 329, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 366, "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": 332, "scoreName": "E-value", "accession": "PF00046.27", "start": 329, "score": 1.1e-07, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 365}}, {"startStyle": "straight", "end": 180, "endStyle": "straight", "aliStart": 96, "text": "Meis_PKNOX_N", "colour": "#9999ff", "aliEnd": 179, "start": 96, "href": "http://pfam.xfam.org/family/PF16493.3", "type": "pfama", "display": "true", "metadata": {"end": 180, "description": "Meis_PKNOX_N is a family found at the N-terminus of Meis, Myeloid ecotropic viral integration site, transcription regulators and PKNOX1 regulators, PBX/knotted 1 homeobox 1, homeobox proteins.", "database": "PfamA", "aliStart": 96, "scoreName": "E-value", "accession": "PF16493.3", "start": 96, "score": 2e-44, "identifier": "N-terminal of Homeobox Meis and PKNOX1", "type": "DBD", "aliEnd": 179}}], "length": 422}

{"regions": [{"startStyle": "curved", "end": 408, "endStyle": "curved", "aliStart": 353, "text": "HD", "colour": "#228B22", "aliEnd": 407, "start": 351, "href": "http://pfam.xfam.org/family/PF00046.27", "type": "pfama", "display": "true", "metadata": {"end": 408, "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": 353, "scoreName": "E-value", "accession": "PF00046.27", "start": 351, "score": 2.2000000000000002e-08, "identifier": "Homeobox domain", "type": "DBD", "aliEnd": 407}}, {"startStyle": "straight", "end": 268, "endStyle": "straight", "aliStart": 184, "text": "Meis_PKNOX_N", "colour": "#9999ff", "aliEnd": 267, "start": 184, "href": "http://pfam.xfam.org/family/PF16493.3", "type": "pfama", "display": "true", "metadata": {"end": 268, "description": "Meis_PKNOX_N is a family found at the N-terminus of Meis, Myeloid ecotropic viral integration site, transcription regulators and PKNOX1 regulators, PBX/knotted 1 homeobox 1, homeobox proteins.", "database": "PfamA", "aliStart": 184, "scoreName": "E-value", "accession": "PF16493.3", "start": 184, "score": 2.3e-44, "identifier": "N-terminal of Homeobox Meis and PKNOX1", "type": "DBD", "aliEnd": 267}}], "length": 464}

TF Info Page for MEIS3 (Homeodomain)