TF Info Page for HOXD1 (Homeodomain)

Conclusion

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

Description

Description: homeobox D1 [Source:HGNC Symbol;Acc:HGNC:5132]
Entrez Summary microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
Ensembl ID: ENSG00000128645
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; IPR020479;
Protein Domain: ENSP00000328598
Domain:
Protein: ENSP00000328598DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene Candidate_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:11775067
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
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-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
PBMBerger08Inferred - Hoxd1 (98% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA1 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA1 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA1 (85% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa1 (85% AA Identity, Mus musculus)
PBMZoo_01Inferred - O76842_CUPSA (85% AA Identity, Cupiennius salei)
MiscHocoMocoInferred - HOXA1 (85% AA Identity, Homo sapiens)
B1HJASPARInferred - lab (84% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - lab (84% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - HOXB1 (82% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB1 (82% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXB1 (82% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXB1 (82% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxc5 (68% AA Identity, Mus musculus)
HT-SELEXYin2017Inferred - HOXA4 (66% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - HOXA4 (66% AA Identity, Homo sapiens)
PBMBerger08Inferred - Hoxa4 (66% AA Identity, Mus musculus)
PBMBerger08Inferred - Hoxc6 (66% AA Identity, Mus musculus)
B1HJASPARInferred - ind (66% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - Q7M3U4_ACRFO (66% AA Identity, Acropora formosa)
B1HJASPARInferred - zen2 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - zen2 (66% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - zen2 (66% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - zen2 (66% AA Identity, Drosophila melanogaster)
TransfacTransfacLicense requiredInferred - HOXA4 (66% AA Identity, Homo sapiens)
MiscHocoMocoInferred - HOXC6 (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