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?

EPS8
ENST00000646918 (-) ENSG00000151491 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 965-1381 15669493-15669536 / 15669664-15669825 / 15682893-15682958 417 0.2797 50 0.33
2
 CDS 1382-1480 15669394-15669492 99 0.5456 50 0.39
3
 CDS 1485-1575 15665888-15665892 / 15666440-15666522 / 15669387-15669389 91 0.3031 50 0.34
4
 CDS 1579-1661 15665802-15665884 83 0.3920 50 0.35
5
 CDS 1662-1759 15662048-15662099 / 15665756-15665801 98 0.4056 50 0.30
6
 CDS 1760-1844 15660678-15660740 / 15662026-15662047 85 0.4129 50 0.31
7
 CDS 1846-1936 15658558-15658585 / 15660614-15660676 91 0.2694 50 0.37
8
 CDS 1938-2028 15658123-15658153 / 15658497-15658556 91 0.4495 50 0.39
9
 CDS 2032-2176 15654190-15654293 / 15658079-15658119 145 0.2879 50 0.36
10
 CDS 2177-2274 15650954-15651006 / 15654145-15654189 98 0.4898 50 0.34
11
 CDS 2275-2368 15650860-15650953 94 0.5295 50 0.35
12
 CDS 2370-2456 15647210-15647260 / 15650823-15650858 87 0.4122 50 0.34
13
 CDS 2457-2640 15641730-15641830 / 15647127-15647209 184 0.4462 50 0.31
14
 CDS 2645-2753 15640742-15640846 / 15641722-15641725 109 0.3685 50 0.33
15
 CDS 2760-3085 15624338-15624407 / 15631442-15631664 / 15640703-15640735 326 0.4452 50 0.34
16
 CDS 3087-3174 15624249-15624336 88 0.4888 50 0.37
17
 CDS 3175-3274 15623210-15623287 / 15624227-15624248 100 0.4522 50 0.39
18
 CDS 3277-3369 15621388-15621430 / 15623158-15623207 93 0.3406 50 0.38
19
 CDS,3'UTR 3371-3486 15621271-15621386 116 0.4991 50 0.37
20
 3'UTR 3487-3803 15620954-15621270 317 0.5775 50 0.52
21
 3'UTR 3806-4135 15620622-15620951 330 0.5224 50 0.44
22
 3'UTR 4138-4235 15620522-15620619 98 0.3850 50 0.39
23
 3'UTR 4237-4322 15620435-15620520 86 0.3182 29 0.38
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
21
EPS8

Aoi: Chr: Coords Strand:
EPS8 12 15620622 - 15620951 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: EPS8(-)
  • Length Length of region: 330 nt.
  • Structures This region has 16 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.
  • Coverage 33.6% of the region's A/C bases included in the filtered DMS dataset. This is lower than the recommended 70%. While structure prediction is still possible even without any coverage, the structures will be based on the sequence alone, rather than based on experimental constraints.
Structures
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production / 05e29e215d / 2026-04-03 23:25