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?

WDR82
ENST00000296490 (-) ENSG00000164091 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 17-115 52278535-52278633 99 0.6283 50 0.32
2
 5'UTR 116-201 52278449-52278534 86 0.6721 50 0.25
3
 5'UTR 203-287 52278363-52278447 85 0.6984 50 0.29
4
 5'UTR,CDS 288-383 52278267-52278362 96 0.6276 50 0.22
5
 CDS 384-472 52270787-52270809 / 52278201-52278266 89 0.6117 50 0.24
6
 CDS 473-560 52267006-52267018 / 52270712-52270786 88 0.4725 50 0.21
7
 CDS 561-665 52261429-52261479 / 52266952-52267005 105 0.7582 50 0.29
8
 CDS 667-776 52260440-52260501 / 52261380-52261427 110 0.7485 50 0.26
9
 CDS 779-891 52259813-52259872 / 52260385-52260437 113 0.7974 50 0.24
10
 CDS 894-996 52259258-52259266 / 52259717-52259810 103 0.6309 50 0.20
11
 CDS 997-1102 52258634-52258678 / 52259197-52259257 106 0.7325 50 0.24
12
 CDS 1104-1202 52257518-52257519 / 52258536-52258632 99 0.6566 50 0.20
13
 CDS,3'UTR 1203-1319 52257401-52257517 117 0.7335 50 0.23
14
 3'UTR 1324-1422 52257298-52257396 99 0.7665 50 0.27
15
 3'UTR 1424-1527 52257193-52257296 104 0.8625 50 0.34
16
 3'UTR 1528-1620 52257100-52257192 93 0.8000 50 0.32
17
 3'UTR 1621-1726 52256994-52257099 106 0.8191 50 0.37
18
 3'UTR 1732-1826 52256894-52256988 95 0.6789 50 0.31
19
 3'UTR 1830-1973 52256747-52256890 144 0.7474 50 0.30
20
 3'UTR 1979-2074 52256646-52256741 96 0.9559 50 0.38
21
 3'UTR 2076-2180 52256540-52256644 105 0.8059 50 0.27
22
 3'UTR 2182-2286 52256434-52256538 105 0.8675 50 0.32
23
 3'UTR 2297-2405 52256315-52256423 109 0.7909 50 0.34
24
 3'UTR 2406-2505 52256215-52256314 100 0.8242 50 0.34
25
 3'UTR 2509-2629 52256091-52256211 121 0.8711 50 0.38
26
 3'UTR 2630-2782 52255938-52256090 153 0.8636 50 0.30
27
 3'UTR 2783-2909 52255811-52255937 127 0.8081 50 0.36
28
 3'UTR 2910-2996 52255724-52255810 87 0.6010 50 0.18
29
 3'UTR 2998-3114 52255606-52255722 117 0.6913 50 0.22
30
 3'UTR 3117-3216 52255504-52255603 100 0.7866 50 0.26
31
 3'UTR 3217-3315 52255405-52255503 99 0.7767 50 0.28
32
 3'UTR 3317-3401 52255319-52255403 85 0.6731 50 0.28
33
 3'UTR 3402-3501 52255219-52255318 100 0.8969 50 0.44
34
 3'UTR 3505-3597 52255123-52255215 93 0.7901 50 0.39
35
 3'UTR 3599-3710 52255010-52255121 112 0.8250 50 0.45
36
 3'UTR 3712-3782 52254938-52255008 71 0.9089 50 0.73
37
 3'UTR 3783-3883 52254837-52254937 101 0.6822 50 0.29
38
 3'UTR 3886-4001 52254719-52254834 116 0.8242 50 0.35
39
 3'UTR 4004-4110 52254610-52254716 107 0.6698 50 0.25
40
 3'UTR 4111-4264 52254456-52254609 154 0.6888 65 0.33
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
38
WDR82

Aoi: Chr: Coords Strand:
WDR82 3 52254719 - 52254834 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: WDR82(-)
  • Length Length of region: 116 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 7 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 / 2025-07-19 09:35