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?

XBP1
ENST00000216037 (-) ENSG00000100219 (-)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 41-153 28800445-28800557 113 0.7449 50 0.37
2
 CDS 154-248 28800350-28800444 95 0.7493 50 0.36
3
 CDS 250-330 28799124-28799153 / 28800298-28800348 81 0.8091 50 0.27
4
 CDS 333-422 28797181-28797205 / 28799057-28799121 90 0.5685 50 0.22
5
 CDS 423-534 28796185-28796192 / 28797077-28797180 112 0.7281 50 0.26
6
 CDS 535-628 28796091-28796184 94 0.8717 50 0.36
7
 CDS 629-735 28795670-28795732 / 28796047-28796090 107 0.6869 50 0.25
8
 CDS 736-827 28795578-28795669 92 0.9716 50 0.25
9
 CDS,3'UTR 828-913 28795492-28795577 86 0.8368 50 0.38
10
 3'UTR 914-1003 28795402-28795491 90 0.7133 50 0.32
11
 3'UTR 1004-1093 28795312-28795401 90 0.6417 50 0.25
12
 3'UTR 1095-1206 28795199-28795310 112 0.7179 50 0.45
13
 3'UTR 1210-1312 28795093-28795195 103 0.6265 50 0.27
14
 3'UTR 1313-1404 28795001-28795092 92 0.6300 50 0.35
15
 3'UTR 1405-1512 28794893-28795000 108 0.7836 50 0.47
16
 3'UTR 1513-1625 28794780-28794892 113 0.6732 50 0.32
17
 3'UTR 1626-1737 28794668-28794779 112 0.6767 50 0.32
18
 3'UTR 1738-1834 28794571-28794667 97 0.6495 45 0.40
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.

completed

Aoi: Chr: Coords Strand:
XBP1_splice_site 22 28796102 - 28796174 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: XBP1(-)
  • Length Length of region: 73 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 3 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 02:20