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?

TGFB1
ENST00000221930 (-) ENSG00000105329 (-)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 2-80 41353843-41353921 79 0.4355 50 0.24
2
 5'UTR 86-182 41353741-41353837 97 0.8089 50 0.46
3
 5'UTR 183-287 41353636-41353740 105 0.7965 50 0.29
4
 5'UTR 288-393 41353530-41353635 106 0.8048 50 0.29
5
 5'UTR 394-480 41353443-41353529 87 0.7807 50 0.30
6
 5'UTR 482-559 41353364-41353441 78 0.8961 50 0.34
7
 5'UTR 561-640 41353283-41353362 80 0.9068 50 0.29
8
 5'UTR 642-725 41353198-41353281 84 0.5374 50 0.21
9
 5'UTR 726-808 41353115-41353197 83 0.8620 50 0.43
10
 5'UTR,CDS 813-903 41353020-41353110 91 0.7158 50 0.38
11
 CDS 906-1009 41352914-41353017 104 0.7549 50 0.34
12
 CDS 1011-1099 41352824-41352912 89 0.9075 50 0.42
13
 CDS 1100-1190 41352733-41352823 91 0.8324 50 0.25
14
 CDS 1192-1271 41348418-41348455 / 41352690-41352731 80 0.6402 50 0.18
15
 CDS 1273-1372 41348317-41348416 100 0.6373 50 0.21
16
 CDS 1374-1455 41344804-41344864 / 41348295-41348315 82 0.7463 50 0.25
17
 CDS 1456-1575 41342185-41342247 / 41344747-41344803 120 0.8103 50 0.34
18
 CDS 1576-1667 41341954-41342030 / 41342170-41342184 92 0.7510 50 0.28
19
 CDS 1668-1750 41332270-41332281 / 41341883-41341953 83 0.7698 50 0.29
20
 CDS 1752-1845 41332175-41332268 94 0.8019 50 0.33
21
 CDS 1847-1933 41331170-41331210 / 41332128-41332173 87 0.7475 50 0.34
22
 CDS,3'UTR 1936-2064 41331039-41331167 129 0.8078 65 0.31
Download CSV

Custom Gene Windows

TGFB1
Chr Coords Strand
19 41353344 - 41353843
500 bp
64s
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
TGFB1

Aoi: Chr: Coords Strand:
TGFB1 19 41353344 - 41353843 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TGFB1(-)
  • Length Length of region: 500 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 20 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 5 6 7 8 9 10 11 12 13 14 15 16 17
production / 362c1546a7 / 2025-05-20 03:45