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?

POLRMT
ENST00000588649 (-) ENSG00000099821 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 30-130 632922-632938 / 633425-633508 101 0.6041 50 0.43
2
 CDS 133-224 630163-630168 / 632834-632919 92 0.4127 50 0.37
3
 CDS 225-347 630040-630162 123 0.6050 50 0.37
4
 CDS 348-450 629937-630039 103 0.5944 50 0.39
5
 CDS 452-788 629599-629935 337 0.6122 50 0.39
6
 CDS 789-918 625184-625254 / 629540-629598 130 0.4505 50 0.37
7
 CDS 919-1061 624823-624905 / 625124-625183 143 0.2653 50 0.37
8
 CDS 1062-1229 623540-623603 / 624719-624822 168 0.6369 50 0.46
9
 CDS 1230-1872 622153-622373 / 622821-622985 / 623454-623539 643 0.5542 50 0.43
Error
10
 CDS 1874-1967 621756-621846 / 622149-622151 94 0.4788 50 0.38
11
 CDS 1970-2982 619695-619765 / 619958-620080 / 621058-621753 1013 0.5863 50 0.41
Error
12
 CDS 2983-3097 619291-619296 / 619586-619694 115 0.5187 50 0.36
13
 CDS 3105-3200 619089-619110 / 619210-619283 96 0.6432 50 0.37
14
 CDS 3202-3294 618759-618760 / 618997-619087 93 0.3282 50 0.32
15
 CDS 3295-3628 617459-617480 / 618488-618586 / 618705-618758 334 0.3504 50 0.34
16
 CDS,3'UTR 3629-3750 617242-617323 / 617419-617458 122 0.5087 64 0.36
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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POLRMT

Aoi: Chr: Coords Strand:
POLRMT 19 630040 - 630162 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: POLRMT(-)
  • Length Length of region: 123 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 6 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 / 6f779e32bc / 2026-02-03 21:43