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?

TEX2
ENST00000584379 (-) ENSG00000136478 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 11-110 64214226-64214242 / 64263168-64263250 100 0.4952 50 0.41
2
 5'UTR,CDS 111-189 64214147-64214225 79 0.4350 50 0.34
3
 CDS 190-304 64214032-64214146 115 0.4395 50 0.30
4
 CDS 305-390 64213946-64214031 86 0.5359 50 0.35
5
 CDS 392-489 64213847-64213944 98 0.5330 50 0.41
6
 CDS 490-592 64213744-64213846 103 0.5121 50 0.34
7
 CDS 593-676 64213660-64213743 84 0.3584 50 0.38
8
 CDS 677-761 64213575-64213659 85 0.2551 50 0.38
9
 CDS 762-850 64213486-64213574 89 0.7135 50 0.49
10
 CDS 851-929 64213407-64213485 79 0.4007 50 0.36
11
 CDS 930-1043 64213293-64213406 114 0.4283 50 0.41
12
 CDS 1045-1138 64213198-64213291 94 0.4854 50 0.38
13
 CDS 1139-1228 64213108-64213197 90 0.4422 50 0.37
14
 CDS 1229-1326 64213010-64213107 98 0.6973 50 0.39
15
 CDS 1328-1442 64212894-64213008 115 0.5722 50 0.31
16
 CDS 1445-1558 64212778-64212891 114 0.6211 50 0.37
17
 CDS 1559-1675 64212661-64212777 117 0.4539 50 0.33
18
 CDS 1676-1753 64212583-64212660 78 0.2211 50 0.33
19
 CDS 1754-1855 64195003-64195095 / 64212574-64212582 102 0.5966 50 0.36
20
 CDS 1856-1930 64194928-64195002 75 0.5485 50 0.33
21
 CDS 1931-2016 64193837-64193889 / 64194895-64194927 86 0.3337 50 0.36
22
 CDS 2017-2115 64193738-64193836 99 0.3691 50 0.38
23
 CDS 2118-2201 64193652-64193735 84 0.5503 50 0.35
24
 CDS 2203-2309 64188401-64188415 / 64193559-64193650 107 0.6370 50 0.36
25
 CDS 2310-2390 64188320-64188400 81 0.6677 50 0.45
26
 CDS 2391-2486 64188224-64188319 96 0.4205 50 0.43
27
 CDS 2488-2575 64177439-64177471 / 64188168-64188222 88 0.6257 50 0.42
28
 CDS 2576-2682 64177332-64177438 107 0.6401 50 0.38
29
 CDS 2683-2772 64171117-64171199 / 64177325-64177331 90 0.4698 50 0.37
30
 CDS 2775-2873 64160850-64160933 / 64171100-64171114 99 0.6284 50 0.42
31
 CDS 2874-2980 64154910-64154967 / 64160801-64160849 107 0.5584 50 0.41
32
 CDS 2982-3071 64153132-64153154 / 64154842-64154908 90 0.7867 50 0.40
33
 CDS 3074-3160 64153043-64153129 87 0.3781 50 0.26
34
 CDS 3162-3242 64152961-64153041 81 0.6014 50 0.31
35
 CDS 3243-3343 64150877-64150961 / 64152945-64152960 101 0.3776 50 0.31
36
 CDS 3345-3442 64149029-64149091 / 64150841-64150875 98 0.4493 50 0.34
37
 CDS,3'UTR 3443-3545 64148926-64149028 103 0.4975 50 0.41
38
 3'UTR 3557-3658 64148813-64148914 102 0.6115 50 0.46
39
 3'UTR 3664-3768 64148703-64148807 105 0.5382 50 0.40
40
 3'UTR 3769-3853 64148618-64148702 85 0.4927 50 0.35
41
 3'UTR 3855-3956 64148515-64148616 102 0.5058 50 0.40
42
 3'UTR 3957-4078 64148393-64148514 122 0.6742 50 0.35
43
 3'UTR 4079-4161 64148310-64148392 83 0.5172 50 0.33
44
 3'UTR 4162-4254 64148217-64148309 93 0.5347 50 0.31
45
 3'UTR 4255-4364 64148107-64148216 110 0.6558 50 0.37
46
 3'UTR 4372-4466 64148005-64148099 95 0.5436 50 0.32
47
 3'UTR 4472-4581 64147890-64147999 110 0.5356 50 0.33
48
 3'UTR 4582-4689 64147782-64147889 108 0.6423 50 0.40
49
 3'UTR 4690-4779 64147692-64147781 90 0.2085 50 0.33
50
 3'UTR 4782-4907 64147564-64147689 126 0.3915 50 0.44
51
 3'UTR 4910-5010 64147461-64147561 101 0.5112 50 0.40
52
 3'UTR 5011-5098 64147373-64147460 88 0.1211 50 0.69
53
 3'UTR 5099-5185 64147286-64147372 87 0.0457 50 0.75
54
 3'UTR 5186-5244 64147227-64147285 59 0.3522 36 0.81
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
5
TEX2

Aoi: Chr: Coords Strand:
TEX2 17 64213847 - 64213944 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TEX2(-)
  • Length Length of region: 98 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 5 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 / bdd4f6bb6e / 2025-10-21 09:37