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?

MPP1
ENST00000369534 (-) ENSG00000130830 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 306-402 154791804-154791847 / 154792142-154792194 97 0.3563 50 0.33
2
 CDS 403-495 154791011-154791068 / 154791769-154791803 93 0.1576 50 0.31
3
 CDS 498-578 154789968-154790022 / 154790983-154791008 81 0.2389 50 0.33
4
 CDS 581-681 154786312-154786400 / 154789954-154789965 101 0.2068 50 0.34
5
 CDS 682-779 154786214-154786311 98 0.5682 50 0.32
6
 CDS 782-873 154785074-154785157 / 154786204-154786211 92 0.4704 50 0.29
7
 CDS 874-997 154783488-154783507 / 154784028-154784108 / 154785051-154785073 124 0.3754 50 0.36
8
 CDS 998-1116 154781745-154781802 / 154783427-154783487 119 0.2567 50 0.32
9
 CDS 1117-1213 154781648-154781744 97 0.3705 50 0.33
10
 CDS 1214-1438 154779252-154779353 / 154781600-154781647 225 0.2762 50 0.38
11
 CDS,3'UTR 1439-1540 154779150-154779251 102 0.4616 50 0.38
12
 3'UTR 1543-1745 154778945-154779147 203 0.4188 50 0.40
13
 3'UTR 1754-1813 154778877-154778936 60 0.0891 30 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.

Recently Visualized

MPP1
Chr Coords Strand
X 154779252 - 154779353
154781600 - 154781647
150 bp
10s
completed
MPP1
Chr Coords Strand
X 154791011 - 154791068
154791769 - 154791803
93 bp
7s
completed
MPP1
Chr Coords Strand
X 154781745 - 154781802
154783427 - 154783487
119 bp
5s
completed
production / 8daaec85cb / 2026-01-15 03:43