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?

DENR
ENST00000280557 (+) ENSG00000139726 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 18-156 122752841-122752950 / 122753693-122753721 139 0.7734 50 0.38
2
 CDS 157-255 122753722-122753807 / 122762187-122762199 99 0.7764 50 0.21
3
 CDS 256-354 122762200-122762206 / 122762845-122762929 / 122765304-122765310 99 0.7312 50 0.22
4
 CDS 355-444 122765311-122765387 / 122767488-122767500 90 0.7306 50 0.21
5
 CDS 445-512 122767501-122767568 68 0.8127 50 0.26
6
 CDS 513-613 122767569-122767604 / 122768782-122768846 101 0.7929 50 0.27
7
 CDS 618-720 122768851-122768921 / 122769034-122769065 103 0.7527 50 0.23
8
 CDS,3'UTR 721-825 122769066-122769170 105 0.8088 50 0.37
9
 3'UTR 827-923 122769172-122769268 97 0.7896 50 0.51
10
 3'UTR 925-1017 122769270-122769362 93 0.9761 50 0.62
11
 3'UTR 1022-1124 122769367-122769469 103 0.8507 50 0.33
12
 3'UTR 1125-1249 122769470-122769594 125 0.8199 50 0.37
13
 3'UTR 1250-1349 122769595-122769694 100 0.8554 50 0.32
14
 3'UTR 1358-1452 122769703-122769797 95 0.8575 50 0.38
15
 3'UTR 1453-1581 122769798-122769926 129 0.7672 50 0.31
16
 3'UTR 1582-1711 122769927-122770056 130 0.8729 50 0.32
17
 3'UTR 1712-1825 122770057-122770170 114 0.7782 50 0.25
18
 3'UTR 1826-1910 122770171-122770255 85 0.7502 50 0.31
19
 3'UTR 1914-2035 122770259-122770380 122 0.6374 50 0.23
20
 3'UTR 2036-2148 122770381-122770493 113 0.7189 50 0.29
21
 3'UTR 2151-2236 122770496-122770581 86 0.7239 50 0.28
22
 3'UTR 2237-2354 122770582-122770699 118 0.7892 50 0.28
23
 3'UTR 2356-2452 122770701-122770797 97 0.6691 50 0.29
24
 3'UTR 2453-2564 122770798-122770909 112 0.6712 50 0.39
25
 3'UTR 2567-2662 122770912-122771007 96 0.2502 43 0.39
Download CSV

Custom Gene Windows

DENR
Chr Coords Strand
12 122769156 - 122769655
500 bp
65s
completed
DENR-811-1310
Chr Coords Strand
12 122769156 - 122769655
500 bp
66s
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

Aoi: Chr: Coords Strand:
DENR 12 122769156 - 122769655 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: DENR(+)
  • Length Length of region: 500 nt.
  • Coverage 98.8% 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 20 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 / b252b9f76a / 2025-07-17 03:23