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?

MAVS
ENST00000428216 (+) ENSG00000088888 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 107-197 3854594-3854684 91 0.1906 50 0.34
2
 CDS 198-290 3854685-3854741 / 3857635-3857670 93 0.3571 50 0.31
3
 CDS 291-403 3857671-3857783 113 0.3241 50 0.31
4
 CDS 404-496 3857784-3857809 / 3861332-3861398 93 0.5553 50 0.35
5
 CDS 497-986 3861399-3861504 / 3864256-3864479 490 0.3070 50 0.34
6
 CDS 988-1075 3864481-3864568 88 0.4421 50 0.42
7
 CDS 1078-1160 3864571-3864653 83 0.4842 50 0.31
8
 CDS 1161-1384 3864654-3864788 / 3865683-3865771 224 0.3101 50 0.43
9
 CDS 1387-1513 3865774-3865900 127 0.4927 50 0.41
10
 CDS,3'UTR 1516-2510 3865903-3866897 995 0.5790 50 0.40
Error
11
 3'UTR 2513-2643 3866900-3867030 131 0.4434 50 0.41
12
 3'UTR 2644-2739 3867031-3867126 96 0.4602 50 0.42
13
 3'UTR 2742-2835 3867129-3867222 94 0.3929 50 0.42
14
 3'UTR 2836-2960 3867223-3867347 125 0.3888 50 0.34
15
 3'UTR 2961-3060 3867348-3867447 100 0.5468 50 0.43
16
 3'UTR 3061-3177 3867448-3867564 117 0.6179 50 0.56
17
 3'UTR 3178-3266 3867565-3867653 89 0.7386 50 0.50
18
 3'UTR 3267-3382 3867654-3867769 116 0.4296 50 0.38
19
 3'UTR 3384-3605 3867771-3867992 222 0.4188 50 0.39
20
 3'UTR 3606-3692 3867993-3868079 87 0.6830 50 0.48
21
 3'UTR 3693-3774 3868080-3868161 82 0.5550 50 0.36
22
 3'UTR 3775-4215 3868162-3868602 441 0.5295 50 0.57
23
 3'UTR 4216-4431 3868603-3868818 216 0.5232 50 0.50
24
 3'UTR 4438-5084 3868825-3869471 647 0.2382 50 0.58
Error
25
 3'UTR 5085-6076 3869472-3870463 992 0.5390 50 0.45
Error
26
 3'UTR 6077-6212 3870464-3870599 136 0.4635 50 0.46
27
 3'UTR 6214-6513 3870601-3870900 300 0.2070 50 0.45
28
 3'UTR 6515-6864 3870902-3871251 350 0.5569 50 0.66
29
 3'UTR 6867-6973 3871254-3871360 107 0.4766 50 0.49
30
 3'UTR 6974-7167 3871361-3871554 194 0.2492 50 0.44
31
 3'UTR 7168-7291 3871555-3871678 124 0.2303 50 0.40
32
 3'UTR 7292-7607 3871679-3871994 316 0.5430 50 0.47
33
 3'UTR 7608-7711 3871995-3872098 104 0.3410 50 0.35
34
 3'UTR 7712-7817 3872099-3872204 106 0.4409 50 0.40
35
 3'UTR 7818-7901 3872205-3872288 84 0.2186 50 0.48
36
 3'UTR 7904-8021 3872291-3872408 118 0.4437 50 0.49
37
 3'UTR 8023-8109 3872410-3872496 87 0.2527 50 0.39
38
 3'UTR 8110-8205 3872497-3872592 96 0.3537 50 0.38
39
 3'UTR 8206-8308 3872593-3872695 103 0.5212 50 0.35
40
 3'UTR 8312-8414 3872699-3872801 103 0.5463 50 0.35
41
 3'UTR 8415-8505 3872802-3872892 91 0.3225 50 0.29
42
 3'UTR 8506-8607 3872893-3872994 102 0.7067 50 0.47
43
 3'UTR 8608-8707 3872995-3873094 100 0.3770 50 0.30
44
 3'UTR 8709-8826 3873096-3873213 118 0.4389 50 0.32
45
 3'UTR 8827-8940 3873214-3873327 114 0.4869 50 0.39
46
 3'UTR 8943-9032 3873330-3873419 90 0.3460 50 0.56
47
 3'UTR 9034-9133 3873421-3873520 100 0.8794 50 0.67
48
 3'UTR 9135-9246 3873522-3873633 112 0.5047 50 0.41
49
 3'UTR 9247-9350 3873634-3873737 104 0.5472 50 0.40
50
 3'UTR 9351-9460 3873738-3873847 110 0.6805 50 0.44
51
 3'UTR 9461-9540 3873848-3873927 80 0.5378 50 0.34
52
 3'UTR 9541-9617 3873928-3874004 77 0.5611 50 0.40
53
 3'UTR 9618-9696 3874005-3874083 79 0.2862 50 0.41
54
 3'UTR 9697-9795 3874084-3874182 99 0.2587 50 0.38
55
 3'UTR 9797-10025 3874184-3874412 229 0.6874 50 0.46
56
 3'UTR 10026-10414 3874413-3874801 389 0.4195 74 0.45
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
3
MAVS

Aoi: Chr: Coords Strand:
MAVS 20 3857671 - 3857783 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: MAVS(+)
  • Length Length of region: 113 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 3 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 / 8daaec85cb / 2026-01-15 03:51