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?

HMCES
ENST00000383463 (+) ENSG00000183624 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 17-134 129278886-129278905 / 129279710-129279807 118 0.6461 50 0.32
2
 CDS 135-219 129279808-129279892 85 0.5417 50 0.32
3
 CDS 223-327 129279896-129279915 / 129288854-129288938 105 0.4002 50 0.25
4
 CDS 330-439 129288941-129288997 / 129290679-129290731 110 0.4897 50 0.23
5
 CDS 444-533 129290736-129290804 / 129298354-129298374 90 0.4540 50 0.22
6
 CDS 535-645 129298376-129298486 111 0.2796 50 0.21
7
 CDS 646-743 129298487-129298535 / 129301950-129301998 98 0.5413 50 0.28
8
 CDS 751-832 129302006-129302087 82 0.2669 50 0.27
9
 CDS 833-938 129302088-129302142 / 129304589-129304639 106 0.6028 50 0.38
10
 CDS 939-1017 129304640-129304718 79 0.6233 50 0.30
11
 CDS 1018-1105 129304719-129304806 88 0.7021 50 0.30
12
 CDS,3'UTR 1107-1226 129304808-129304927 120 0.6428 50 0.27
13
 3'UTR 1227-1359 129304928-129305060 133 0.7018 50 0.48
14
 3'UTR 1362-1474 129305063-129305175 113 0.5628 50 0.35
15
 3'UTR 1476-1557 129305177-129305258 82 0.4771 42 0.54
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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production / 6840c0a13a / 2026-05-29 12:24