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?

NORAD
ENST00000565493 (-) ENSG00000260032 (-)

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  Region Local Coords Chrom Coords Length R N Gini Action
1
 lncRNA 63-151 36050868-36050956 89 0.8570 50 0.45
2
 lncRNA 152-252 36050767-36050867 101 0.8556 50 0.31
3
 lncRNA 253-336 36050683-36050766 84 0.8311 50 0.33
4
 lncRNA 339-432 36050587-36050680 94 0.8323 50 0.38
5
 lncRNA 435-536 36050483-36050584 102 0.9126 50 0.43
6
 lncRNA 537-627 36050392-36050482 91 0.9156 50 0.41
7
 lncRNA 632-742 36050277-36050387 111 0.9397 50 0.44
8
 lncRNA 745-845 36050174-36050274 101 0.9632 50 0.44
9
 lncRNA 846-930 36050089-36050173 85 0.8735 50 0.25
10
 lncRNA 932-1037 36049982-36050087 106 0.8530 50 0.22
11
 lncRNA 1039-1148 36049871-36049980 110 0.8507 50 0.20
12
 lncRNA 1153-1280 36049739-36049866 128 0.8941 50 0.23
13
 lncRNA 1284-1402 36049617-36049735 119 0.9432 50 0.34
14
 lncRNA 1405-1523 36049496-36049614 119 0.9094 50 0.33
15
 lncRNA 1525-1633 36049386-36049494 109 0.9456 50 0.35
16
 lncRNA 1636-1760 36049259-36049383 125 0.8937 50 0.34
17
 lncRNA 1765-1864 36049155-36049254 100 0.9204 50 0.36
18
 lncRNA 1868-1972 36049047-36049151 105 0.8863 50 0.37
19
 lncRNA 1973-2102 36048917-36049046 130 0.8270 50 0.23
20
 lncRNA 2104-2207 36048812-36048915 104 0.9331 50 0.39
21
 lncRNA 2208-2320 36048699-36048811 113 0.8662 50 0.26
22
 lncRNA 2323-2424 36048595-36048696 102 0.9081 50 0.24
23
 lncRNA 2425-2546 36048473-36048594 122 0.9421 50 0.37
24
 lncRNA 2551-2675 36048344-36048468 125 0.8438 50 0.28
25
 lncRNA 2679-2783 36048236-36048340 105 0.9473 50 0.40
26
 lncRNA 2784-2887 36048132-36048235 104 0.9076 50 0.40
27
 lncRNA 2888-2995 36048024-36048131 108 0.8982 50 0.31
28
 lncRNA 3001-3108 36047911-36048018 108 0.9562 50 0.48
29
 lncRNA 3109-3227 36047792-36047910 119 0.8773 50 0.26
30
 lncRNA 3228-3347 36047672-36047791 120 0.9179 50 0.34
31
 lncRNA 3349-3444 36047575-36047670 96 0.8709 50 0.25
32
 lncRNA 3445-3536 36047483-36047574 92 0.8578 50 0.32
33
 lncRNA 3537-3656 36047363-36047482 120 0.7909 50 0.21
34
 lncRNA 3658-3756 36047263-36047361 99 0.9537 50 0.45
35
 lncRNA 3763-3847 36047172-36047256 85 0.8864 50 0.32
36
 lncRNA 3848-3957 36047062-36047171 110 0.9447 50 0.35
37
 lncRNA 3958-4045 36046974-36047061 88 0.8909 50 0.48
38
 lncRNA 4046-4185 36046834-36046973 140 0.5866 50 0.29
39
 lncRNA 4189-4312 36046707-36046830 124 0.7866 50 0.23
40
 lncRNA 4313-4431 36046588-36046706 119 0.8958 50 0.35
41
 lncRNA 4432-4550 36046469-36046587 119 0.8831 50 0.21
42
 lncRNA 4551-4660 36046359-36046468 110 0.8357 50 0.26
43
 lncRNA 4661-4774 36046245-36046358 114 0.8752 50 0.31
44
 lncRNA 4777-4883 36046136-36046242 107 0.8724 50 0.35
45
 lncRNA 4884-4999 36046020-36046135 116 0.8175 50 0.24
46
 lncRNA 5000-5117 36045902-36046019 118 0.7625 50 0.29
47
 lncRNA 5123-5240 36045779-36045896 118 0.8717 50 0.39
48
 lncRNA 5241-5388 36045631-36045778 148 0.7284 68 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

NORAD
Chr Coords Strand
20 36047911 - 36048018
108 bp
8s
completed
production / b252b9f76a / 2025-07-18 10:48