This track represents the genome-wide predicted binding sites for TF (transcription factor) binding profiles in the JASPAR database CORE collection.
Shaded boxes represent predicted binding sites for each of the TF profiles in the JASPAR CORE collection. The shading of the boxes indicates the p-value of the profile's match to that position (scaled between 0-1000 scores, where 0 corresponds to a p-value of 1 and 1000 to a p-value ≤ 10-10). Thus, the darker the shade, the lower (better) the p-value.
The default view shows only predicted binding sites with scores of 400 or greater but can be adjusted in the track settings. Multi-select filters allow viewing of particular transcription factors. At window sizes of greater than 10,000 base pairs, this track turns to density graph mode. Zoom to a smaller region and click into an item to see more detail.
From BED format documentation:
| shade | |||||||||
| score in range | ≤ 166 | 167-277 | 278-388 | 389-499 | 500-611 | 612-722 | 723-833 | 834-944 | ≥ 945 |
Conversion table:
| Item score | 0 | 100 | 131 | 200 | 300 | 400 | 500 | 600 | 700 | 800 | 900 | 1000 |
| p-value | 1 | 0.1 | 0.049 | 10-2 | 10-3 | 10-4 | 10-5 | 10-6 | 10-7 | 10-8 | 10-9 | ≤ 10-10 |
For each TF binding profile in the JASPAR database CORE collection, genomes were scanned for matches.
For the computation of relative scores and p-values, we used PWMScan (Ambrosini et al. 2018). We selected TFBS predictions with a PWM relative score ≥ 0.8 and a p-value < 0.05. P-values were scaled between 0 (corresponding to a p-value of 1) and 1000 (p-value ≤ 10-10) for colouring of the genome tracks and to allow for comparison of prediction confidence between different profiles.
Please refer to the supplementary information of the JASPAR 2020 manuscript for more details.
All data is freely available.
The JASPAR group provides TFBS predictions for many additional species and genomes. The 2026 release is available as a native track on the following genomes, and additionally on mm10 and araTha1 by connection to their Public Hub or by clicking the assembly links below:
| Species | Genome assembly versions |
| Human - Homo sapiens | hg38 |
| Mouse - Mus musculus | mm39 |
| Zebrafish - Danio rerio | danRer11 |
| Fruitfly - Drosophila melanogaster | dm6 |
| Nematode - Caenorhabditis elegans | ce11 |
| Vase tunicate - Ciona intestinalis | ci3 |
| Thale cress - Arabidopsis thaliana | araTha1 |
| Yeast - Saccharomyces cerevisiae | sacCer3 |
| Chicken - Gallus gallus | galGal6 |
The JASPAR database is a joint effort between several labs (please see the latest JASPAR paper, below). Binding site predictions and UCSC tracks were computed by the CBGR team at NCMBM using code developed at the Wasserman Lab. For enquiries about the data, please contact Anthony Mathelier ( ) or Ieva Rauluseviciute ( ).
CBGR
Computational Biology & Gene Regulation
Norwegian Centre for Molecular Biosciences and Medicine (NCMBM)
University of Oslo
Oslo, Norway
Wasserman Lab
Centre for Molecular Medicine and Therapeutics
BC Children's Hospital Research Institute
Department of Medical Genetics
University of British Columbia
Vancouver, Canada
Ovek Baydar D, Rauluseviciute I, Aronsen DR, Blanc-Mathieu R, Bonthuis I, de Beukelaer H, Ferenc K, Jegou A, Kumar V, Lemma RB et al. JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models. Nucleic Acids Res. 2026; PMID: 41325984; PMC: PMC12807658
Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2004;. PMID: 14681366