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?

TAGLN2
ENST00000368097 (-) ENSG00000158710 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 1-86 159920510-159920537 / 159925450-159925507 86 0.8401 50 0.20
2
 CDS 87-186 159920410-159920509 100 0.9218 50 0.17
3
 CDS 188-281 159919821-159919835 / 159920330-159920408 94 0.9823 50 0.18
4
 CDS 282-367 159919735-159919820 86 0.9484 50 0.20
5
 CDS 369-462 159919356-159919376 / 159919661-159919733 94 0.9587 50 0.17
6
 CDS 463-568 159918918-159918941 / 159919274-159919355 106 0.9695 50 0.21
7
 CDS 569-669 159918817-159918917 101 0.9593 50 0.20
8
 CDS,3'UTR 670-758 159918728-159918816 89 0.9782 50 0.33
9
 3'UTR 759-859 159918627-159918727 101 0.9869 50 0.41
10
 3'UTR 860-941 159918545-159918626 82 0.9568 50 0.30
11
 3'UTR 946-1050 159918436-159918540 105 0.9538 50 0.26
12
 3'UTR 1053-1164 159918322-159918433 112 0.9490 50 0.33
13
 3'UTR 1167-1259 159918227-159918319 93 0.9550 50 0.35
14
 3'UTR 1260-1375 159918111-159918226 116 0.6786 39 0.26
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 / bdd4f6bb6e / 2025-10-19 01:10