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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?

CLK1
ENST00000321356 (-) ENSG00000013441 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 16-119 200861839-200861862 / 200864564-200864643 104 0.4765 50 0.32
2
 CDS 123-218 200861740-200861835 96 0.5054 50 0.30
3
 CDS 219-310 200861413-200861466 / 200861702-200861739 92 0.5657 50 0.28
4
 CDS 311-393 200861330-200861412 83 0.3868 50 0.25
5
 CDS 394-486 200860215-200860215 / 200861238-200861329 93 0.6507 50 0.25
6
 CDS 487-591 200859732-200859746 / 200860125-200860214 105 0.2599 50 0.22
7
 CDS 592-705 200858028-200858089 / 200859680-200859731 114 0.4808 50 0.26
8
 CDS 707-801 200857844-200857884 / 200857973-200858026 95 0.2823 50 0.30
9
 CDS 802-907 200857738-200857843 106 0.4056 50 0.32
10
 CDS 909-1003 200856910-200856985 / 200857718-200857736 95 0.4481 50 0.37
11
 CDS 1006-1094 200856740-200856811 / 200856891-200856907 89 0.4315 50 0.29
12
 CDS 1096-1193 200855046-200855086 / 200856682-200856738 98 0.2469 50 0.27
13
 CDS 1196-1294 200854637-200854695 / 200855004-200855043 99 0.3037 50 0.27
14
 CDS 1295-1384 200853925-200853993 / 200854616-200854636 90 0.3241 50 0.33
15
 CDS 1385-1485 200853371-200853449 / 200853903-200853924 101 0.5159 50 0.35
16
 CDS,3'UTR 1486-1578 200853278-200853370 93 0.3119 50 0.25
17
 3'UTR 1580-1692 200853164-200853276 113 0.5926 40 0.35
Download CSV

Custom Gene Windows

CLK1-121-270
Chr Coords Strand
2 200861453 - 200861466
200861702 - 200861837
150 bp
9s
completed
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
13
CLK1

Aoi: Chr: Coords Strand:
CLK1 2 200854637 - 200854695, 200855004 - 200855043 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: CLK1(-)
  • Length Length of region: 99 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 22:52