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?

ADAR
ENST00000680270 (-) ENSG00000160710 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 39-123 154602538-154602622 85 0.6971 50 0.29
2
 5'UTR 124-212 154602449-154602537 89 0.5629 50 0.22
3
 5'UTR 213-301 154602360-154602448 89 0.7193 50 0.35
4
 5'UTR 302-405 154602256-154602359 104 0.8522 50 0.36
5
 5'UTR 409-495 154602166-154602252 87 0.7867 50 0.34
6
 5'UTR 498-589 154602072-154602163 92 0.4879 50 0.21
7
 5'UTR 590-676 154601838-154601888 / 154602036-154602071 87 0.6875 50 0.28
8
 5'UTR,CDS 678-765 154601749-154601836 88 0.5280 50 0.25
9
 CDS 767-860 154601654-154601747 94 0.6974 50 0.29
10
 CDS 862-954 154601560-154601652 93 0.6792 50 0.28
11
 CDS 956-1032 154601482-154601558 77 0.6249 50 0.21
12
 CDS 1033-1113 154601401-154601481 81 0.7228 50 0.23
13
 CDS 1114-1188 154601326-154601400 75 0.8038 50 0.23
14
 CDS 1192-1281 154601233-154601322 90 0.7989 50 0.34
15
 CDS 1282-1377 154601137-154601232 96 0.5967 50 0.27
16
 CDS 1379-1467 154601047-154601135 89 0.6424 50 0.23
17
 CDS 1468-1562 154598497-154598585 / 154601041-154601046 95 0.8332 50 0.29
18
 CDS 1563-1639 154598420-154598496 77 0.7811 50 0.24
19
 CDS 1641-1720 154597914-154597976 / 154598402-154598418 80 0.6544 50 0.24
20
 CDS 1721-1806 154597828-154597913 86 0.6125 50 0.24
21
 CDS 1810-1901 154597173-154597264 92 0.7758 50 0.31
22
 CDS 1904-2000 154596947-154596995 / 154597123-154597170 97 0.5148 50 0.26
23
 CDS 2001-2101 154596846-154596946 101 0.6895 50 0.27
24
 CDS 2104-2197 154590355-154590409 / 154596805-154596843 94 0.6801 50 0.30
25
 CDS 2198-2295 154590257-154590354 98 0.7407 50 0.27
26
 CDS 2296-2372 154589925-154589928 / 154590184-154590256 77 0.7603 50 0.30
27
 CDS 2373-2454 154589843-154589924 82 0.5403 50 0.25
28
 CDS 2455-2560 154589443-154589462 / 154589757-154589842 106 0.7081 50 0.33
29
 CDS 2562-2654 154588654-154588673 / 154589369-154589441 93 0.5113 50 0.26
30
 CDS 2657-2740 154588568-154588651 84 0.5241 50 0.23
31
 CDS 2743-2835 154588181-154588258 / 154588551-154588565 93 0.5851 50 0.27
32
 CDS 2836-2917 154586338-154586363 / 154588125-154588180 82 0.6471 50 0.29
33
 CDS 2918-3026 154586229-154586337 109 0.7062 50 0.30
34
 CDS 3032-3130 154585810-154585865 / 154586181-154586223 99 0.6834 50 0.25
35
 CDS 3132-3226 154585306-154585344 / 154585753-154585808 95 0.7633 50 0.26
36
 CDS 3230-3335 154585024-154585043 / 154585217-154585302 106 0.7413 50 0.27
37
 CDS 3340-3433 154584926-154585019 94 0.8227 50 0.27
38
 CDS 3435-3522 154584837-154584924 88 0.7467 50 0.25
39
 CDS,3'UTR 3525-3636 154584723-154584834 112 0.7647 50 0.27
40
 3'UTR 3641-3768 154584591-154584718 128 0.7752 50 0.32
41
 3'UTR 3769-3858 154584501-154584590 90 0.6939 50 0.26
42
 3'UTR 3859-3992 154584367-154584500 134 0.5152 50 0.25
43
 3'UTR 3993-4096 154584263-154584366 104 0.7412 50 0.35
44
 3'UTR 4097-4193 154584166-154584262 97 0.7886 50 0.44
45
 3'UTR 4194-4296 154584063-154584165 103 0.8410 50 0.36
46
 3'UTR 4297-4388 154583971-154584062 92 0.6741 50 0.29
47
 3'UTR 4389-4474 154583885-154583970 86 0.7944 50 0.34
48
 3'UTR 4476-4566 154583793-154583883 91 0.7067 50 0.30
49
 3'UTR 4567-4668 154583691-154583792 102 0.8282 50 0.31
50
 3'UTR 4671-4775 154583584-154583688 105 0.7704 50 0.24
51
 3'UTR 4779-4889 154583470-154583580 111 0.6313 50 0.23
52
 3'UTR 4893-5014 154583345-154583466 122 0.7463 50 0.36
53
 3'UTR 5015-5142 154583217-154583344 128 0.7995 50 0.42
54
 3'UTR 5144-5234 154583125-154583215 91 0.7812 50 0.42
55
 3'UTR 5235-5328 154583031-154583124 94 0.8765 50 0.46
56
 3'UTR 5333-5425 154582934-154583026 93 0.6273 50 0.30
57
 3'UTR 5426-5530 154582829-154582933 105 0.7933 50 0.35
58
 3'UTR 5535-5628 154582731-154582824 94 0.8481 50 0.42
59
 3'UTR 5631-5736 154582623-154582728 106 0.8869 50 0.39
60
 3'UTR 5737-5826 154582533-154582622 90 0.6808 50 0.26
61
 3'UTR 5827-5910 154582449-154582532 84 0.8125 50 0.41
62
 3'UTR 5912-6040 154582319-154582447 129 0.5772 50 0.27
63
 3'UTR 6041-6161 154582198-154582318 121 0.7988 50 0.45
64
 3'UTR 6162-6264 154582095-154582197 103 0.6458 48 0.34
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
27
ADAR

Aoi: Chr: Coords Strand:
ADAR 1 154589843 - 154589924 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: ADAR(-)
  • Length Length of region: 82 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 2 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
1 2
production / 19ff247cc9 / 2026-03-16 18:03