TF Info Page for YBX3 (CSD)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer 100 perc ID - in vitro Identical DBD to YBX1. Might also bind RNA.

Description

Description: Y-box binding protein 3 [Source:HGNC Symbol;Acc:HGNC:2428]
Entrez Summary NA
Ensembl ID: ENSG00000060138
External Link: CisBP
Interpro IPR002059; IPR011129; IPR012340; IPR019844;
Protein Domain: ENSP00000228251
Protein Domain: ENSP00000279550
Protein Domain: ENSP00000485718
Domain:
Protein: ENSP00000228251DBD: Cold-shock protein, DNA-bindingOther:
Protein: ENSP00000279550DBD: Cold-shock protein, DNA-bindingOther: Herpes_LMP1
Protein: ENSP00000485718DBD: Cold-shock protein, DNA-bindingOther:

Previous Annotations

Source Annotation
TF-CAT classification Not a TF - Evidence that it is not a TF___
PMIDS:0
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:0001227
RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor
IEA - GO_REF:0000019
GO:0003700
sequence-specific DNA binding transcription factor activity
NAS - PMID:8710501
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
1a2, Orthologous HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source Annotation Motif Evidence
HT-SELEXYin2017Inferred - YBX1 (100% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - YBX1 (100% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - YBX1 (100% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - YBX1 (100% AA Identity, Homo sapiens)
MiscHocoMocoInferred - YBX1 (100% AA Identity, Homo sapiens)
PBMTF_EvolutionUnpublished DataInferred - NEMVEDRAFT_v1g104083 (81% AA Identity, Nematostella vectensis)
PBMZoo_01Inferred - cey-1 (77% AA Identity, Caenorhabditis elegans)

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