TF Info Page for ATF5 (bZIP)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 2 Obligate heteromer In vivo/Misc source Only known motifs are from Transfac or HocoMoco - origin is uncertain Transfac motifs dont correspond to canonical bZIP binding sites. Annotated as obligate heteromer based on peptide array studies (PMID:12805554).

Description

Description: activating transcription factor 5 [Source:HGNC Symbol;Acc:HGNC:790]
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: ENSG00000169136
External Link: CisBP
Interpro IPR004827; ;
Protein Domain: ENSP00000396954
Protein Domain: ENSP00000470633
Protein Domain: ENSP00000470464
Protein Domain: ENSP00000471162
Protein Domain: ENSP00000470978
Domain:
Protein: ENSP00000396954DBD: bZIPOther:
Protein: ENSP00000470633DBD: bZIPOther:
Protein: ENSP00000470464DBD: bZIPOther:
Protein: ENSP00000471162DBD: bZIPOther:
Protein: ENSP00000470978DBD: bZIPOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding_
PMIDS:15735663 16164412
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:0000981
sequence-specific DNA binding RNA polymerase II transcription factor activity
IBA - GO_REF:0000033
GO:0001228
RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor
IC - GO_REF:0000036
GO:0003700
sequence-specific DNA binding transcription factor activity
IDA - PMID:20654631 | ISS - GO_REF:0000024
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
2a1, Lower confidence direct evidence
TF has conditional DNA-binding requirements Obligate_Multimer

DNA-Binding

Published Motif Data

Source Annotation Motif Evidence
TransfacTransfacLicense requiredDirect
MiscHocoMocoDirect
HT-SELEXYin2017Inferred - ATF4 (60% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - ATF4 (60% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - ATF4 (60% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - ATF4 (60% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - ATF4 (60% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - ATF4 (60% AA Identity, Homo sapiens)
PBMDREAM_contestInferred - Atf4 (59% AA Identity, Mus musculus)
MiscHOMERInferred - Atf4 (59% AA Identity, Mus musculus)

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