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?

KRAS
ENST00000311936 (-) ENSG00000133703 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 145-255 25245320-25245395 / 25250751-25250785 111 0.7630 50 0.37
2
 CDS 257-356 25227358-25227412 / 25245274-25245318 100 0.5353 50 0.21
3
 CDS 358-462 25227252-25227356 105 0.4752 50 0.22
4
 CDS 463-559 25225695-25225773 / 25227234-25227251 97 0.6669 50 0.25
5
 CDS 560-648 25209904-25209911 / 25225614-25225694 89 0.6233 50 0.23
6
 CDS 651-732 25209820-25209901 82 0.5485 50 0.25
7
 CDS,3'UTR 733-843 25209709-25209819 111 0.6442 50 0.32
8
 3'UTR 844-967 25209585-25209708 124 0.6483 50 0.34
9
 3'UTR 968-1085 25209467-25209584 118 0.7161 50 0.36
10
 3'UTR 1086-1196 25209356-25209466 111 0.7044 50 0.37
11
 3'UTR 1200-1307 25209245-25209352 108 0.7476 50 0.34
12
 3'UTR 1311-1437 25209115-25209241 127 0.5412 50 0.44
13
 3'UTR 1440-1539 25209013-25209112 100 0.3338 50 0.42
14
 3'UTR 1540-1637 25208915-25209012 98 0.5803 50 0.38
15
 3'UTR 1641-1758 25208794-25208911 118 0.5783 50 0.27
16
 3'UTR 1761-1879 25208673-25208791 119 0.4717 50 0.34
17
 3'UTR 1881-1974 25208578-25208671 94 0.5774 50 0.29
18
 3'UTR 1975-2095 25208457-25208577 121 0.3839 50 0.34
19
 3'UTR 2098-2179 25208373-25208454 82 0.4157 50 0.35
20
 3'UTR 2180-2296 25208256-25208372 117 0.5144 50 0.28
21
 3'UTR 2301-2407 25208145-25208251 107 0.4969 50 0.32
22
 3'UTR 2411-2506 25208046-25208141 96 0.4870 50 0.32
23
 3'UTR 2507-2611 25207941-25208045 105 0.4931 50 0.30
24
 3'UTR 2612-2707 25207845-25207940 96 0.3113 50 0.35
25
 3'UTR 2708-2812 25207740-25207844 105 0.4458 50 0.32
26
 3'UTR 2815-2905 25207647-25207737 91 0.4428 50 0.33
27
 3'UTR 2908-2999 25207553-25207644 92 0.5437 50 0.33
28
 3'UTR 3000-3105 25207447-25207552 106 0.7096 50 0.50
29
 3'UTR 3106-3217 25207335-25207446 112 0.6304 50 0.42
30
 3'UTR 3218-3311 25207241-25207334 94 0.7015 50 0.47
31
 3'UTR 3312-3394 25207158-25207240 83 0.7481 50 0.41
32
 3'UTR 3395-3517 25207035-25207157 123 0.6030 50 0.36
33
 3'UTR 3519-3631 25206921-25207033 113 0.4339 50 0.25
34
 3'UTR 3632-3737 25206815-25206920 106 0.5249 50 0.35
35
 3'UTR 3739-3826 25206726-25206813 88 0.5043 50 0.30
36
 3'UTR 3827-3929 25206623-25206725 103 0.5137 50 0.20
37
 3'UTR 3933-4060 25206492-25206619 128 0.7207 50 0.29
38
 3'UTR 4072-4167 25206385-25206480 96 0.5459 50 0.38
39
 3'UTR 4169-4275 25206277-25206383 107 0.5636 50 0.30
40
 3'UTR 4278-4370 25206182-25206274 93 0.5337 50 0.28
41
 3'UTR 4371-4503 25206049-25206181 133 0.6093 50 0.30
42
 3'UTR 4504-4607 25205945-25206048 104 0.2626 50 0.33
43
 3'UTR 4611-4707 25205845-25205941 97 0.4719 50 0.30
44
 3'UTR 4708-4849 25205703-25205844 142 0.5959 50 0.24
45
 3'UTR 4850-4944 25205608-25205702 95 0.6279 50 0.37
46
 3'UTR 4945-5066 25205486-25205607 122 0.4503 50 0.33
47
 3'UTR 5067-5160 25205392-25205485 94 0.4901 36 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
39
KRAS

Aoi: Chr: Coords Strand:
KRAS 12 25206277 - 25206383 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: KRAS(-)
  • Length Length of region: 107 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 4 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 / 6f779e32bc / 2026-02-04 02:28