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?

GAPDH
ENST00000229239 (+) ENSG00000111640 (+)

Visualize entire gene
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500
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 2-100 6534518-6534569 / 6534810-6534856 99 0.9747 50 0.22
2
 CDS 101-211 6534857-6534861 / 6536494-6536593 / 6536684-6536689 111 0.9785 50 0.16
3
 CDS 212-299 6536690-6536777 88 0.9908 50 0.18
4
 CDS 300-396 6536778-6536790 / 6536920-6537003 97 0.9810 50 0.17
5
 CDS 399-502 6537006-6537010 / 6537101-6537199 104 0.9926 50 0.23
6
 CDS 503-577 6537200-6537216 / 6537309-6537366 75 0.9808 50 0.16
7
 CDS 584-676 6537373-6537390 / 6537584-6537658 93 0.9834 50 0.24
8
 CDS 681-775 6537663-6537757 95 0.9831 50 0.21
9
 CDS 776-867 6537758-6537849 92 0.9879 50 0.23
10
 CDS 870-955 6537852-6537937 86 0.9862 50 0.23
11
 CDS 956-1057 6537938-6537996 / 6538101-6538143 102 0.9791 50 0.19
12
 CDS,3'UTR 1058-1133 6538144-6538219 76 0.9821 50 0.25
13
 3'UTR 1134-1212 6538220-6538298 79 0.9866 50 0.39
14
 3'UTR 1213-1284 6538299-6538370 72 0.9457 38 0.31
Download CSV

Custom Gene Windows

GAPDH
Chr Coords Strand
12 6538204 - 6538353
150 bp
14s
completed
GAPDH
Chr Coords Strand
12 6537309 - 6537332
6537584 - 6537996
6538105 - 6538167
500 bp
68s
completed
GAPDH
Chr Coords Strand
12 6534833 - 6534858
6536494 - 6536593
6536684 - 6536790
6536920 - 6537010
6537101 - 6537216
6537331 - 6537390
500 bp
69s
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
GAPDH

Aoi: Chr: Coords Strand:
GAPDH 12 6537309 - 6537332, 6537584 - 6537996, 6538105 - 6538167 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: GAPDH(+)
  • 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
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production / 362c1546a7 / 2025-05-20 02:42