TF Info Page for HOXC4 (Homeodomain)

Conclusion

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

Description

Description: homeobox C4 [Source:HGNC Symbol;Acc:HGNC:5126]
Entrez Summary This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene, HOXC4, is one of several homeobox HOXC genes located in a cluster on chromosome 12. Three genes, HOXC5, HOXC4 and HOXC6, share a 5' non-coding exon. Transcripts may include the shared exon spliced to the gene-specific exons, or they may include only the gene-specific exons. Two alternatively spliced variants that encode the same protein have been described for HOXC4. Transcript variant one includes the shared exon, and transcript variant two includes only gene-specific exons. [provided by RefSeq, Jul 2008]
Ensembl ID: ENSG00000198353
External Link: CisBP
Interpro IPR001356; IPR001827; IPR009057; IPR017970; IPR017995; IPR020479;
Protein Domain: ENSP00000305973
Protein Domain: ENSP00000399808
Domain:
Protein: ENSP00000305973DBD: HomeodomainOther:
Protein: ENSP00000399808DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:15252056
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:0003700
sequence-specific DNA binding transcription factor activity
IEA - GO_REF:0000002
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
PBMBarrera2016Direct
PBMBarrera2016Direct
PBMBarrera2016Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
PBMBerger08Inferred - Hoxc4 (100% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB4 (96% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb4 (96% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD4 (96% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXD4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (96% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD4 (96% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxb4 (96% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXD4 (96% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA4 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA4 (94% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa4 (94% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - HOXA4 (94% AA Identity, Homo sapiens)
B1HJASPARInferred - Dfd (91% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Dfd (91% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Dfd (91% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXA5 (91% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA5 (91% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (91% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (91% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (91% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA5 (91% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa5 (91% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB5 (91% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB5 (91% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (91% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (91% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (91% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB5 (91% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb5 (91% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - Dfd (91% AA Identity, Drosophila melanogaster)
COMPILEDJASPARInferred - HOXA5 (91% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - HOXA5 (91% AA Identity, Homo sapiens)
MisciDMMPMMInferred - Dfd (91% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXA5 (91% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - HOXB7 (87% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB7 (87% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb7 (87% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxc5 (87% AA Identity, Mus musculus)
B1HJASPARInferred - Scr (87% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Scr (87% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXB7 (87% AA Identity, Homo sapiens)
B1HJASPARInferred - Antp (85% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXA7 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA7 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA7 (85% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa7 (85% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxa7 (85% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB6 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB6 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB6 (85% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb6 (85% AA Identity, Mus musculus)
PBMBarrera2016Inferred - HOXB7 (85% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - HOXB7 (85% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - Antp (85% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXA7 (85% AA Identity, Homo sapiens)
MisciDMMPMMInferred - Antp (85% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXA7 (85% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXB6 (85% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA6 (82% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA6 (82% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA6 (82% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa6 (82% AA Identity, Mus musculus)
B1HJASPARInferred - abd-A (80% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - abd-A (80% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - abd-A (80% AA Identity, Drosophila melanogaster)
PBMBerger08Inferred - Hoxc6 (80% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - abd-A (80% AA Identity, Drosophila melanogaster)
ChIP-seqmodENCODEInferred - lin-39 (80% AA Identity, Caenorhabditis elegans)
MisciDMMPMMInferred - abd-A (80% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXC6 (80% AA Identity, Homo sapiens)
MiscHOMERInferred - lin-39 (80% AA Identity, Caenorhabditis elegans)
B1HJASPARInferred - ftz (78% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - ftz (78% AA Identity, Drosophila melanogaster)
PBMBusserDevelopment2012Inferred - Ubx (78% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - Ubx (78% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - Ubx (78% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - ftz (78% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - Ubx (78% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - ftz (78% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - Ubx (78% AA Identity, Drosophila melanogaster)
PBMBerger08Inferred - Hoxb3 (75% AA Identity, Mus musculus)
PBMZoo_01Inferred - SPU_026099 (75% AA Identity, Strongylocentrotus purpuratus)
PBMBadis09Inferred - Hoxa3 (73% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxa3 (73% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD3 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD3 (73% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxd3 (73% AA Identity, Mus musculus)
PBMZoo_01Inferred - Q0N4M8_NEMVE (73% AA Identity, Nematostella vectensis)
TransfacTransfacLicense requiredInferred - HOXA3 (73% AA Identity, Homo sapiens)
B1HJASPARInferred - pb (71% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - pb (71% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - PDX1 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PDX1 (71% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - PDX1 (71% AA Identity, Homo sapiens)
PBMBerger08Inferred - Pdx1 (71% AA Identity, Mus musculus)
SELEXJASPARInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - PDX1 (71% AA Identity, Homo sapiens)
MiscHocoMocoInferred - PDX1 (71% AA Identity, Homo sapiens)
MiscHOMERInferred - Pdx1 (71% AA Identity, Mus musculus)
PBMTF_EvolutionUnpublished DataInferred - Cbr-mab-5 (70% AA Identity, Caenorhabditis briggsae)
HT-SELEXYin2017Inferred - HOXB8 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB8 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB8 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb8 (70% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXD8 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD8 (70% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXD8 (70% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxd8 (70% AA Identity, Mus musculus)
B1HJASPARInferred - zen (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - zen (70% AA Identity, Drosophila melanogaster)
MiscHocoMocoInferred - HOXB8 (70% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - GSX1 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - GSX1 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - GSX2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - GSX2 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Gsx2 (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA2 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA2 (68% AA Identity, Homo sapiens)
PBMZoo_01Inferred - HOXA2 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa2 (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB2 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXC8 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC8 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXC8 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc8 (68% AA Identity, Mus musculus)
B1HJASPARInferred - ind (68% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - lab (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - lab (68% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - O76842_CUPSA (68% AA Identity, Cupiennius salei)
B1HJASPARInferred - zen2 (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - zen2 (68% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXC8 (68% AA Identity, Homo sapiens)
MiscHOMERInferred - Hoxa2 (68% AA Identity, Mus musculus)
MiscHocoMocoInferred - HOXC8 (68% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXA1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA1 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA1 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa1 (66% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXB9 (66% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - HOXB9 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB9 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxb9 (66% AA Identity, Mus musculus)
PBMZoo_01Inferred - Q24782_9CNID (66% AA Identity, Eleutheria dichotoma)
MiscHocoMocoInferred - HOXA1 (66% AA Identity, Homo sapiens)

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