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?

MALAT1
ENST00000619449 (+) ENSG00000251562 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 lncRNA 308-416 65499045-65499153 109 0.9358 50 0.24
2
 lncRNA 419-519 65499156-65499256 101 0.9797 50 0.26
3
 lncRNA 521-616 65499258-65499353 96 0.9807 50 0.23
4
 lncRNA 620-705 65499357-65499442 86 0.9697 50 0.22
5
 lncRNA 710-806 65499447-65499543 97 0.9805 50 0.24
6
 lncRNA 810-908 65499547-65499645 99 0.9826 50 0.23
7
 lncRNA 910-997 65499647-65499734 88 0.9765 50 0.20
8
 lncRNA 999-1073 65499736-65499810 75 0.9734 50 0.24
9
 lncRNA 1074-1157 65499811-65499894 84 0.9544 50 0.16
10
 lncRNA 1159-1237 65499896-65499974 79 0.9674 50 0.19
11
 lncRNA 1238-1337 65499975-65500074 100 0.9851 50 0.31
12
 lncRNA 1339-1430 65500076-65500167 92 0.9667 50 0.20
13
 lncRNA 1432-1535 65500169-65500272 104 0.9688 50 0.26
14
 lncRNA 1536-1644 65500273-65500381 109 0.9768 50 0.24
15
 lncRNA 1645-1739 65500382-65500476 95 0.9852 50 0.22
16
 lncRNA 1741-1844 65500478-65500581 104 0.9867 50 0.19
17
 lncRNA 1846-1957 65500583-65500694 112 0.9784 50 0.21
18
 lncRNA 1960-2072 65500697-65500809 113 0.9954 50 0.29
19
 lncRNA 2075-2217 65500812-65500954 143 0.9818 50 0.24
20
 lncRNA 2223-2331 65500960-65501068 109 0.9766 50 0.19
21
 lncRNA 2332-2466 65501069-65501203 135 0.9461 50 0.21
22
 lncRNA 2469-2593 65501206-65501330 125 0.9433 50 0.19
23
 lncRNA 2594-2690 65501331-65501427 97 0.9677 50 0.20
24
 lncRNA 2692-2798 65501429-65501535 107 0.9795 50 0.30
25
 lncRNA 2801-2918 65501538-65501655 118 0.9763 50 0.23
26
 lncRNA 2919-3021 65501656-65501758 103 0.9727 50 0.19
27
 lncRNA 3024-3135 65501761-65501872 112 0.9566 50 0.17
28
 lncRNA 3140-3256 65501877-65501993 117 0.9784 50 0.20
29
 lncRNA 3259-3371 65501996-65502108 113 0.9899 50 0.36
30
 lncRNA 3372-3495 65502109-65502232 124 0.9885 50 0.27
31
 lncRNA 3496-3616 65502233-65502353 121 0.9550 50 0.19
32
 lncRNA 3617-3747 65502354-65502484 131 0.9576 50 0.20
33
 lncRNA 3748-3894 65502485-65502631 147 0.9677 50 0.35
34
 lncRNA 3896-3994 65502633-65502731 99 0.9005 50 0.16
35
 lncRNA 3995-4086 65502732-65502823 92 0.8968 50 0.16
36
 lncRNA 4087-4172 65502824-65502909 86 0.9405 50 0.19
37
 lncRNA 4173-4253 65502910-65502990 81 0.9705 50 0.25
38
 lncRNA 4255-4347 65502992-65503084 93 0.9316 50 0.13
39
 lncRNA 4352-4458 65503089-65503195 107 0.9837 50 0.32
40
 lncRNA 4463-4574 65503200-65503311 112 0.9925 50 0.38
41
 lncRNA 4575-4692 65503312-65503429 118 0.9879 50 0.41
42
 lncRNA 4693-4796 65503430-65503533 104 0.9780 50 0.23
43
 lncRNA 4798-4896 65503535-65503633 99 0.9844 50 0.27
44
 lncRNA 4901-5022 65503638-65503759 122 0.9758 50 0.19
45
 lncRNA 5023-5118 65503760-65503855 96 0.9774 50 0.19
46
 lncRNA 5119-5167 65503856-65503904 49 0.9592 31 0.21
Download CSV

Custom Gene Windows

MALAT1-16-165
Chr Coords Strand
11 65497703 - 65497852
150 bp
3s
completed
MALAT1-5190-5339
Chr Coords Strand
11 65506281 - 65506430
150 bp
3s
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
MALAT1

Aoi: Chr: Coords Strand:
MALAT1-16-165 11 65497703 - 65497852 +
Download Data & Images
Structures
production / 6f779e32bc / 2026-02-03 20:18