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
Coords (max 500bp)
Coords 1  
Additional Coordinates
Coords 2 Optional
Coords 3 Optional
Coords 4 Optional


How was this calculated?

CTSZ
ENST00000681011 (-) ENSG00000101160 (-)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 118-209 59006394-59006485 92 0.8366 50 0.31
2
 CDS 211-290 59001636-59001644 / 59006322-59006392 80 0.8478 50 0.32
3
 CDS 291-390 59001536-59001635 100 0.9149 50 0.33
4
 CDS 391-471 58997744-58997753 / 59001465-59001535 81 0.9383 50 0.33
5
 CDS 476-564 58997651-58997739 89 0.8833 50 0.28
6
 CDS 569-659 58996755-58996801 / 58997603-58997646 91 0.8688 50 0.23
7
 CDS 661-771 58996643-58996753 111 0.8096 50 0.18
8
 CDS 772-875 58995660-58995759 / 58996639-58996642 104 0.8769 50 0.22
9
 CDS,3'UTR 876-981 58995554-58995659 106 0.9506 50 0.40
10
 3'UTR 982-1097 58995438-58995553 116 0.9364 50 0.33
11
 3'UTR 1100-1205 58995330-58995435 106 0.9253 50 0.32
12
 3'UTR 1206-1326 58995209-58995329 121 0.6922 50 0.45
13
 3'UTR 1328-1509 58995026-58995207 182 0.2615 50 0.54
14
 3'UTR 1510-1620 58994915-58995025 111 0.2856 50 0.56
15
 3'UTR 1623-1729 58994806-58994912 107 0.3326 50 0.56
16
 3'UTR 1732-1821 58994714-58994803 90 0.1539 50 0.60
17
 3'UTR 1825-2337 58994198-58994710 513 0.2258 50 0.55
Error
18
 3'UTR 2342-2635 58993900-58994193 294 0.6242 50 0.59
19
 3'UTR 2636-2720 58993815-58993899 85 0.2705 50 0.58
20
 3'UTR 2721-2813 58993722-58993814 93 0.3220 50 0.65
21
 3'UTR 2816-2903 58993632-58993719 88 0.2339 50 0.50
22
 3'UTR 2904-3082 58993453-58993631 179 0.2688 50 0.59
23
 3'UTR 3085-3513 58993022-58993450 429 0.3541 50 0.41
24
 3'UTR 3514-4580 58991955-58993021 1067 0.3005 50 0.59
Error
25
 3'UTR 4581-5122 58991413-58991954 542 0.2345 50 0.59
Error
26
 3'UTR 5124-5475 58991060-58991411 352 0.3813 50 0.58
27
 3'UTR 5480-5591 58990944-58991055 112 0.3550 50 0.59
28
 3'UTR 5592-6611 58989924-58990943 1020 0.0911 50 0.65
Error
29
 3'UTR 6612-6932 58989603-58989923 321 0.4078 50 0.66
30
 3'UTR 6933-7030 58989505-58989602 98 0.2604 50 0.67
31
 3'UTR 7031-7594 58988941-58989504 564 0.2200 50 0.58
Error
32
 3'UTR 7595-8795 58987740-58988940 1201 0.3987 50 0.60
Error
33
 3'UTR 8796-9733 58986802-58987739 938 0.3788 50 0.59
Error
34
 3'UTR 9735-10379 58986156-58986800 645 0.2429 50 0.58
Error
35
 3'UTR 10383-10440 58986095-58986152 58 0.2231 34 0.55
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

CTSZ
Chr Coords Strand
20 58989482 - 58989981
500 bp
65s
completed
production / 362c1546a7 / 2025-05-20 14:27