How to predict by coordinate

Input the genomic coordinates of your region of interest, using hg38 as the reference genome. This input is the most flexible, and is unconstrained by sequencing coverage or any annotation. Be sure to double-check that the output sequence matches your expected region, and check that the output coverage of A/C bases is above the recommended 70%, which is reflective of DMS-modifiable bases meeting all coverage and quality filters.

For most users, only one set of coordinates will be used to define their region of interest. However, two sets of coordinates may be needed when joining two separate regions together, such as when crossing a splice junction.

When analyzing a region within a larger transcript, it is generally recommended to test “buffer” regions, where the region of interest should be extended by 20-50 nt on each end in order to reduce the likelihood of structures being arbitrarily interrupted by the region borders.

Due to computational and server constraints, users will be limited to a maximum input length of 500 nucleotides and a maximum output of 5 predicted structures, though some regions may yield fewer than that. If this does not suit your needs, consider downloading and running the data and code locally (see Download ).

Predict by Gene

Advanced Options
Chromosomal Coordinates (max 500bp)
Coords 1  
Additional Coordinates
Coords 2 Optional
Coords 3 Optional
Coords 4 Optional


How was this calculated?

PFKP
ENST00000381125 (+) ENSG00000067057 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 5-96 3067552-3067643 92 0.6102 50 0.35
2
 CDS 97-212 3067644-3067707 / 3082388-3082439 116 0.5879 50 0.31
3
 CDS 213-315 3082440-3082461 / 3099275-3099352 / 3101365-3101367 103 0.7078 50 0.28
4
 CDS 319-412 3101371-3101464 94 0.6584 50 0.31
5
 CDS 421-529 3101473-3101554 / 3103779-3103805 109 0.5836 50 0.33
6
 CDS 530-623 3103806-3103899 94 0.6130 50 0.34
7
 CDS 624-722 3103900-3103944 / 3105115-3105159 / 3105393-3105401 99 0.6253 50 0.36
8
 CDS 723-835 3105402-3105501 / 3107214-3107226 113 0.6916 50 0.30
9
 CDS 836-917 3107227-3107308 82 0.5995 50 0.28
10
 CDS 919-1018 3108701-3108793 / 3109355-3109361 100 0.6539 50 0.28
11
 CDS 1020-1114 3109363-3109457 95 0.7951 50 0.31
12
 CDS 1115-1226 3109458-3109480 / 3112222-3112286 / 3113119-3113142 112 0.5759 50 0.21
13
 CDS 1227-1311 3113143-3113188 / 3113372-3113410 85 0.7000 50 0.23
14
 CDS 1313-1418 3113412-3113517 106 0.7421 50 0.30
15
 CDS 1420-1521 3116776-3116846 / 3118782-3118812 102 0.5528 50 0.29
16
 CDS 1523-1612 3118814-3118869 / 3119892-3119925 90 0.5463 50 0.29
17
 CDS 1616-1717 3119929-3120030 102 0.5889 50 0.25
18
 CDS 1718-1795 3120031-3120044 / 3129819-3129882 78 0.6168 50 0.27
19
 CDS 1800-1901 3129887-3129983 / 3132380-3132384 102 0.6994 50 0.30
20
 CDS 1902-1986 3132385-3132441 / 3133203-3133230 85 0.5281 50 0.24
21
 CDS 1987-2088 3133231-3133314 / 3134483-3134500 102 0.5370 50 0.24
22
 CDS 2093-2178 3134505-3134582 / 3135736-3135743 86 0.7212 50 0.33
23
 CDS 2182-2278 3135747-3135838 / 3136450-3136454 97 0.3611 50 0.26
24
 CDS 2281-2367 3136457-3136543 87 0.5361 50 0.32
25
 CDS,3'UTR 2370-2475 3136546-3136651 106 0.6192 50 0.35
26
 3'UTR 2477-2581 3136653-3136757 105 0.5042 49 0.37
Download CSV

Custom Gene Windows

No custom gene windows have been created yet.
Gene Window Instructions/Interpretation
  1. Search for a gene by name. For each gene, only the canonical transcript (as defined by UCSC in GRCh38.106) is shown. Some gene names may correspond to multiple genomic locations.
  2. For the selected gene, a scatterplot showing the Gini indices, where a high Gini index corresponds to a highly-structured region, for small windows within the transcript. For small RNAs, these windows are sized 20 valid (coverage- and quality-filtered) A/C data points; for all other transcripts, these windows are sized 50 valid A/C data points, due to the ability of DMS to modify primarily A/C bases. In regions with sufficient coverage, these windows correspond to actual transcript lengths of roughly 40 and 100 nucleotides, respectively.
  3. Select a window of interest, either from the scatter plot or from the table below. Generally, windows with a high Gini will yield better results, where the DMS signal aligns more accurately with the predicted base-pais. Windows with high Gini indices relative to the rest of the transcript can also be used to find functional structural elements (ex: TFRC iron response elements).
  4. If previously-defined windows do not suit your needs, you can define a custom window either using (1) the slider below the scatterplot, which shows both a heatmap of previously-defined windows as well as the locations of each UTR and CDS; or (2) custom coordinate-based entry via Predict by Coordinates.
See About for more information on the dataset and for best practices in structure determination.

completed
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PFKP

Aoi: Chr: Coords Strand:
PFKP 10 3129887 - 3129983, 3132380 - 3132384 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: PFKP(+)
  • Length Length of region: 102 nt.
  • Coverage 100.0% of the region's A/C bases included in the filtered DMS dataset. Ideally, this number should be as high as possible for an experimenally-accurate prediction, and over 70% is recommended.
  • Structures This region has 4 maximum predicted structures. 5 is the maximum structures visible on this site. For up to 20 predictions per region, download and run the code locally.
Structures
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production / 05e29e215d / 2026-04-04 08:23