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?

TUBB
ENST00000327892 (+) ENSG00000196230 (+)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 1-91 30720352-30720442 91 0.9228 50 0.28
2
 5'UTR,CDS 92-177 30720443-30720528 86 0.9772 50 0.32
3
 CDS 178-275 30720529-30720563 / 30722537-30722599 98 0.9765 50 0.14
4
 CDS 277-372 30722601-30722645 / 30722918-30722968 96 0.9838 50 0.21
5
 CDS 376-476 30722972-30723028 / 30723340-30723383 101 0.9699 50 0.19
6
 CDS 478-594 30723385-30723501 117 0.9818 50 0.17
7
 CDS 599-686 30723506-30723593 88 0.9768 50 0.19
8
 CDS 687-776 30723594-30723683 90 0.9732 50 0.18
9
 CDS 778-865 30723685-30723772 88 0.9794 50 0.20
10
 CDS 866-957 30723773-30723864 92 0.9861 50 0.25
11
 CDS 958-1045 30723865-30723952 88 0.9658 50 0.21
12
 CDS 1047-1150 30723954-30724057 104 0.9681 50 0.19
13
 CDS 1151-1236 30724058-30724143 86 0.9496 50 0.13
14
 CDS 1238-1326 30724145-30724233 89 0.9650 50 0.16
15
 CDS 1329-1423 30724236-30724330 95 0.9660 50 0.13
16
 CDS,3'UTR 1425-1517 30724332-30724424 93 0.9835 50 0.20
17
 3'UTR 1519-1640 30724426-30724547 122 0.9793 50 0.26
18
 3'UTR 1643-1760 30724550-30724667 118 0.9601 50 0.29
19
 3'UTR 1761-1841 30724668-30724748 81 0.8930 50 0.18
20
 3'UTR 1845-1943 30724752-30724850 99 0.9255 50 0.21
21
 3'UTR 1951-2048 30724858-30724955 98 0.9533 50 0.23
22
 3'UTR 2049-2134 30724956-30725041 86 0.9762 50 0.39
23
 3'UTR 2135-2233 30725042-30725140 99 0.9796 50 0.41
24
 3'UTR 2234-2322 30725141-30725229 89 0.9710 50 0.37
25
 3'UTR 2325-2432 30725232-30725339 108 0.9735 50 0.33
26
 3'UTR 2437-2506 30725344-30725413 70 0.7239 37 0.33
Download CSV

Custom Gene Windows

TUBB
Chr Coords Strand
6 30720352 - 30720394
30720507 - 30720563
30722596 - 30722645
150 bp
20s
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
TUBB

Aoi: Chr: Coords Strand:
TUBB 6 30720352 - 30720394, 30720507 - 30720563, 30722596 - 30722645 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TUBB(+)
  • Length Length of region: 150 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 14 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 / 362c1546a7 / 2025-05-20 04:33