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


How was this calculated?

SEPTIN5
ENST00000455784 (+) ENSG00000184702 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 142-228 19719603-19719689 87 0.6620 50 0.30
2
 CDS 235-333 19719696-19719698 / 19719806-19719892 / 19720115-19720123 99 0.7549 50 0.30
3
 CDS 335-430 19720125-19720220 96 0.6635 50 0.23
4
 CDS 434-521 19720224-19720238 / 19720320-19720392 88 0.6668 50 0.26
5
 CDS 522-621 19720393-19720454 / 19720549-19720586 100 0.6235 50 0.29
6
 CDS 622-720 19720587-19720666 / 19720768-19720786 99 0.8303 50 0.31
7
 CDS 721-825 19720787-19720869 / 19721640-19721661 105 0.6940 50 0.29
8
 CDS 827-939 19721663-19721736 / 19721822-19721860 113 0.7757 50 0.31
9
 CDS 940-1022 19721861-19721943 83 0.8015 50 0.29
10
 CDS 1023-1096 19721944-19721957 / 19722237-19722296 74 0.6998 50 0.34
11
 CDS,3'UTR 1099-1197 19722299-19722339 / 19722428-19722485 99 0.6960 50 0.23
12
 3'UTR 1199-1278 19722487-19722566 80 0.8014 50 0.30
13
 3'UTR 1280-1371 19722568-19722659 92 0.7591 50 0.32
14
 3'UTR 1372-1476 19722660-19722764 105 0.5672 50 0.43
15
 3'UTR 1478-1619 19722766-19722907 142 0.5739 50 0.46
16
 3'UTR 1621-1722 19722909-19723010 102 0.6561 50 0.44
17
 3'UTR 1723-1813 19723011-19723101 91 0.9928 50 0.60
18
 3'UTR 1818-1914 19723106-19723202 97 0.7992 50 0.44
19
 3'UTR 1916-2028 19723204-19723316 113 0.4110 40 0.36
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
18
SEPTIN5

Aoi: Chr: Coords Strand:
SEPTIN5 22 19723106 - 19723202 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: SEPTIN5(+)
  • Length Length of region: 97 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 11 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 / b252b9f76a / 2025-07-17 03:16