get eID ENSG00000139515 else done selects

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 TBA
Ensembl ID: ENSG00000139515
External Link: T093318_1.02
Interpro IPR001356; IPR009057; IPR017970; IPR017995; IPR020479; ;
Protein 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