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?

PLEKHM2
ENST00000375799 (+) ENSG00000116786 (+)

Visualize entire gene
100
150
300
500
+
-
Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 233-344 15684552-15684618 / 15716237-15716281 112 0.4319 50 0.31
2
 CDS 345-440 15716282-15716343 / 15716707-15716740 96 0.6575 50 0.37
3
 CDS 447-543 15716747-15716816 / 15717893-15717919 97 0.6870 50 0.41
4
 CDS 544-640 15717920-15717992 / 15718538-15718561 97 0.7494 50 0.33
5
 CDS 642-742 15718563-15718625 / 15719734-15719771 101 0.5880 50 0.29
6
 CDS 743-826 15719772-15719855 84 0.6138 50 0.30
7
 CDS 830-934 15719859-15719920 / 15721329-15721371 105 0.5498 50 0.37
8
 CDS 935-1014 15721372-15721388 / 15725317-15725379 80 0.6168 50 0.34
9
 CDS 1015-1092 15725380-15725457 78 0.6324 50 0.34
10
 CDS 1093-1176 15725458-15725541 84 0.5400 50 0.33
11
 CDS 1178-1255 15725543-15725545 / 15727014-15727088 78 0.6094 50 0.36
12
 CDS 1256-1344 15727089-15727177 89 0.6655 50 0.41
13
 CDS 1348-1439 15727181-15727272 92 0.5663 50 0.48
14
 CDS 1440-1533 15727273-15727366 94 0.6284 50 0.45
15
 CDS 1534-1633 15727367-15727466 100 0.6526 50 0.45
16
 CDS 1634-1728 15727467-15727561 95 0.6050 50 0.36
17
 CDS 1729-1828 15727562-15727661 100 0.7316 50 0.41
18
 CDS 1830-1933 15727663-15727766 104 0.7242 50 0.38
19
 CDS 1936-2043 15727769-15727832 / 15728079-15728122 108 0.4498 50 0.33
20
 CDS 2045-2135 15728124-15728148 / 15728267-15728332 91 0.4065 50 0.32
21
 CDS 2138-2241 15728335-15728357 / 15728669-15728733 / 15729102-15729117 104 0.7124 50 0.43
22
 CDS 2242-2360 15729118-15729190 / 15729797-15729842 119 0.6539 50 0.34
23
 CDS 2362-2449 15729844-15729929 / 15730532-15730533 88 0.6474 50 0.36
24
 CDS 2450-2539 15730534-15730623 90 0.6818 50 0.40
25
 CDS 2540-2619 15730624-15730703 80 0.3440 50 0.32
26
 CDS 2620-2726 15730704-15730722 / 15731192-15731257 / 15731889-15731910 107 0.3416 50 0.34
27
 CDS 2727-2812 15731911-15731996 86 0.7228 50 0.40
28
 CDS 2815-2909 15731999-15732048 / 15732350-15732394 95 0.5834 50 0.39
29
 CDS 2910-3007 15732395-15732492 98 0.5633 50 0.35
30
 CDS 3008-3101 15732493-15732529 / 15732612-15732668 94 0.4189 50 0.36
31
 CDS 3102-3193 15732669-15732728 / 15733797-15733828 92 0.5050 50 0.41
32
 CDS 3194-3280 15733829-15733915 87 0.5961 50 0.44
33
 CDS,3'UTR 3281-3391 15733916-15734026 111 0.4848 50 0.45
34
 3'UTR 3392-3479 15734027-15734114 88 0.6806 50 0.46
35
 3'UTR 3480-3583 15734115-15734218 104 0.6346 50 0.46
36
 3'UTR 3585-3668 15734220-15734303 84 0.6323 50 0.36
37
 3'UTR 3669-3783 15734304-15734418 115 0.5859 50 0.45
38
 3'UTR 3784-3878 15734419-15734513 95 0.4549 50 0.46
39
 3'UTR 3881-3981 15734516-15734616 101 0.5645 50 0.47
40
 3'UTR 3982-4120 15734617-15734755 139 0.5726 61 0.41
Download CSV

Custom Gene Windows

PLEKHM2-1508-1657
Chr Coords Strand
1 15727341 - 15727490
150 bp
10s
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
7
PLEKHM2

Aoi: Chr: Coords Strand:
PLEKHM2 1 15719859 - 15719920, 15721329 - 15721371 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: PLEKHM2(+)
  • Length Length of region: 105 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
1 2 3 4
production / bf240190b0 / 2026-02-20 18:58