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?

ODC1
ENST00000234111 (-) ENSG00000115758 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 3-86 10448242-10448325 84 0.9268 50 0.45
2
 5'UTR 90-206 10448122-10448238 117 0.7703 50 0.22
3
 5'UTR 208-322 10445045-10445049 / 10445155-10445264 115 0.9275 50 0.27
4
 5'UTR,CDS 323-415 10444952-10445044 93 0.9014 50 0.24
5
 CDS 416-522 10444562-10444647 / 10444931-10444951 107 0.9458 50 0.32
6
 CDS 523-617 10444261-10444267 / 10444474-10444561 95 0.9213 50 0.28
7
 CDS 619-722 10444156-10444259 104 0.9161 50 0.23
8
 CDS 725-833 10443787-10443836 / 10444095-10444153 109 0.9576 50 0.35
9
 CDS 839-943 10443547-10443571 / 10443702-10443781 105 0.9573 50 0.36
10
 CDS 945-1080 10443234-10443313 / 10443490-10443545 136 0.9727 50 0.40
11
 CDS 1081-1170 10442089-10442174 / 10443230-10443233 90 0.9477 50 0.26
12
 CDS 1176-1272 10441905-10441929 / 10442012-10442083 97 0.9237 50 0.22
13
 CDS 1273-1369 10441715-10441723 / 10441817-10441904 97 0.9548 50 0.29
14
 CDS 1370-1486 10441598-10441714 117 0.9398 50 0.29
15
 CDS 1487-1590 10440854-10440868 / 10441509-10441597 104 0.9425 50 0.27
16
 CDS 1591-1682 10440762-10440853 92 0.9415 50 0.25
17
 CDS,3'UTR 1683-1800 10440644-10440761 118 0.9310 50 0.20
18
 3'UTR 1807-1929 10440515-10440637 123 0.8727 50 0.24
19
 3'UTR 1930-2062 10440382-10440514 133 0.8835 67 0.31
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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ODC1

Aoi: Chr: Coords Strand:
ODC1 2 10444261 - 10444267, 10444474 - 10444561 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: ODC1(-)
  • Length Length of region: 95 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 2 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 / 2026-04-03 23:06