TF Info Page for PDX1 (Homeodomain)

Conclusion

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

Description

Description: pancreatic and duodenal homeobox 1 [Source:HGNC Symbol;Acc:HGNC:6107]
Entrez Summary The protein encoded by this gene is a transcriptional activator of several genes, including insulin, somatostatin, glucokinase, islet amyloid polypeptide, and glucose transporter type 2. The encoded nuclear protein is involved in the early development of the pancreas and plays a major role in glucose-dependent regulation of insulin gene expression. Defects in this gene are a cause of pancreatic agenesis, which can lead to early-onset insulin-dependent diabetes mellitus (IDDM), as well as maturity onset diabetes of the young type 4 (MODY4). [provided by RefSeq, Aug 2017]
Ensembl ID: ENSG00000139515
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; IPR017995; IPR020479; ;
Protein Domain: ENSP00000370421
Domain:
Protein: ENSP00000370421DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding
Transactivation_
PMIDS:14704343
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
TAS - PMID:17941991
GO:0003705
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity
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-SELEXJolma2013Direct
HT-SELEXJolma2013Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
SELEXJASPARDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
PBMBerger08Inferred - Pdx1 (100% AA Identity, Mus musculus)
MiscHOMERInferred - Pdx1 (100% AA Identity, Mus musculus)
PBMZoo_01Inferred - SPU_026099 (92% AA Identity, Strongylocentrotus purpuratus)
PBMBadis09Inferred - Hoxa3 (78% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxa3 (78% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD3 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (78% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxd3 (78% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - HOXA3 (78% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb3 (77% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA5 (73% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA5 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa5 (73% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb4 (73% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB5 (73% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB5 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb5 (73% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD4 (73% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (73% AA Identity, Homo sapiens)
PBMZoo_01Inferred - Q0N4M8_NEMVE (73% AA Identity, Nematostella vectensis)
B1HJASPARInferred - Scr (73% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Scr (73% AA Identity, Drosophila melanogaster)
COMPILEDJASPARInferred - HOXA5 (73% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA5 (73% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXA5 (73% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxb4 (73% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXD4 (73% AA Identity, Homo sapiens)
B1HJASPARInferred - Antp (71% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Dfd (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Dfd (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Dfd (71% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXA2 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (71% AA Identity, Homo sapiens)
PBMZoo_01Inferred - HOXA2 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa2 (71% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA4 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA4 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa4 (71% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA7 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA7 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa7 (71% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxa7 (71% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB2 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB2 (71% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - HOXC4 (71% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXC4 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC4 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC4 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc4 (71% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxc5 (71% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Antp (71% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - Dfd (71% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXA4 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA7 (71% AA Identity, Homo sapiens)
MisciDMMPMMInferred - Antp (71% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - Dfd (71% AA Identity, Drosophila melanogaster)
MiscHOMERInferred - Hoxa2 (71% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXA7 (71% AA Identity, Homo sapiens)
B1HJASPARInferred - ftz (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - ftz (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXA6 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA6 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA6 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa6 (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXB7 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB7 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB7 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb7 (70% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXC4 (70% AA Identity, Homo sapiens)
B1HJASPARInferred - pb (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - pb (70% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - ftz (70% AA Identity, Drosophila melanogaster)
ChIP-seqmodENCODEInferred - lin-39 (70% AA Identity, Caenorhabditis elegans)
MisciDMMPMMInferred - ftz (70% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXB7 (70% AA Identity, Homo sapiens)
MiscHOMERInferred - lin-39 (70% AA Identity, Caenorhabditis elegans)
B1HJASPARInferred - abd-A (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - abd-A (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - abd-A (68% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXB6 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB6 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB6 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb6 (68% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXB7 (68% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - HOXB7 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc6 (68% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - abd-A (68% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - abd-A (68% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXB6 (68% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXC6 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA9 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa9 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB8 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB8 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB8 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb8 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXC9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXC9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC9 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc9 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD8 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD8 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD8 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxd8 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD9 (66% AA Identity, Homo sapiens)
PBMBusserDevelopment2012Inferred - Ubx (66% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Ubx (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Ubx (66% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXA9 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA9 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA9 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA9 (66% AA Identity, Homo sapiens)
ChIP-seqJASPARInferred - Hoxa9 (66% AA Identity, Mus musculus)
ChIP-seqJASPARInferred - Hoxc9 (66% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - HOXD9 (66% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Ubx (66% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXA9 (66% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXA9 (66% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxa9 (66% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXB8 (66% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxc9 (66% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXD9 (66% AA Identity, Homo sapiens)
MisciDMMPMMInferred - Ubx (66% AA Identity, Drosophila melanogaster)

Structure

Structure PDB 2H1K

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