Currently, this page only shows the annotations for a motif if it:
+ has a discovery p-value < 0.1
Filters based on species and motif discovery algorithms are not applied to the contents of this page.
The annotation score for a cisRED motif is based on an edit distance calculated between the motif's sequence on the target genome and each site sequence for a known transcription factor in JASPAR or TRANSFAC. In calculating an edit distance, the distance value for each base is normalized by the information content of the JASPAR or TRANSFAC transciption factor at that position. A best match motif position and score is identified by translating the cisRED and known sequence past each other, and considering both forward and reverse complement sequences. A best score is converted into an annotation p-value via a distribution of scores from a large set of random sequences.
The strand information in the table below indicates whether the best score was based on the motif's forward sequence (+), or on its reverse complement (-).For JASPAR annotations only, you can:
- export the list of the known site sequences that were used for a particular annotation by clicking on the 'Export List' button in that row of the table below. The exported data will indicate which of the known sites was most similar to the cisRED motif, and whether this closest match was to the forward or reverse complement cisRED sequence.
- visit the Jaspar database, where you can search by ID, using the ID shown in the last column of the table below, to see the sequence logo associated with that transcription factor.
|Strand||Source||Transcription Factor (TF)||JasparID /
species: mouse, Mus musculus
species: cat, Felis sivestris catus
species: Rattus norvegicus
species: human, Homo sapiens