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?

HSP90AB1
ENST00000620073 (+) ENSG00000096384 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 180-277 44248630-44248727 98 0.9755 50 0.23
2
 CDS 280-385 44248730-44248776 / 44249377-44249435 106 0.9726 50 0.17
3
 CDS 386-469 44249436-44249519 84 0.9838 50 0.19
4
 CDS 471-587 44249521-44249583 / 44249675-44249728 117 0.9774 50 0.22
5
 CDS 589-702 44249730-44249834 / 44250021-44250029 114 0.9879 50 0.25
6
 CDS 707-796 44250034-44250123 90 0.9892 50 0.16
7
 CDS 798-895 44250125-44250154 / 44250291-44250358 98 0.9700 50 0.11
8
 CDS 898-987 44250361-44250450 90 0.9760 50 0.13
9
 CDS 988-1064 44250451-44250527 77 0.9831 50 0.17
10
 CDS 1065-1156 44250528-44250599 / 44251048-44251067 92 0.9871 50 0.12
11
 CDS 1162-1253 44251073-44251164 92 0.9727 50 0.16
12
 CDS 1254-1365 44251165-44251213 / 44251418-44251480 112 0.9429 50 0.16
13
 CDS 1366-1457 44251481-44251572 92 0.9809 50 0.20
14
 CDS 1458-1542 44251573-44251608 / 44251737-44251785 85 0.9830 50 0.21
15
 CDS 1545-1638 44251788-44251881 94 0.9659 50 0.20
16
 CDS 1639-1752 44251882-44251884 / 44251999-44252109 114 0.9740 50 0.17
17
 CDS 1754-1863 44252111-44252220 110 0.9600 50 0.13
18
 CDS 1864-1959 44252221-44252267 / 44253045-44253093 96 0.9762 50 0.16
19
 CDS 1961-2047 44253095-44253181 87 0.9744 50 0.20
20
 CDS 2048-2134 44253182-44253268 87 0.9649 50 0.16
21
 CDS 2137-2232 44253271-44253366 96 0.9832 50 0.21
22
 CDS 2233-2337 44253367-44253378 / 44253489-44253581 105 0.9750 50 0.13
23
 CDS,3'UTR 2341-2444 44253585-44253688 104 0.9863 50 0.24
24
 3'UTR 2446-2563 44253690-44253807 118 0.9859 50 0.32
25
 3'UTR 2573-2639 44253817-44253883 67 0.9322 30 0.28
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.

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HSP90AB1

Aoi: Chr: Coords Strand:
HSP90AB1 6 44251165 - 44251213, 44251418 - 44251480 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: HSP90AB1(+)
  • Length Length of region: 112 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 / 2026-04-03 22:51