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?

FOXRED2
ENST00000684868 (-) ENSG00000100350 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 182-309 36506913-36507040 128 0.4553 50 0.32
2
 5'UTR 316-409 36506813-36506906 94 0.4467 50 0.29
3
 5'UTR 410-522 36506700-36506812 113 0.6386 50 0.37
4
 5'UTR 523-630 36506592-36506699 108 0.5316 50 0.28
5
 5'UTR 631-735 36506487-36506591 105 0.5179 50 0.37
6
 5'UTR,CDS 740-848 36506374-36506482 109 0.5784 50 0.46
7
 CDS 852-950 36506272-36506370 99 0.7016 50 0.38
8
 CDS 952-1039 36506183-36506270 88 0.6596 50 0.31
9
 CDS 1040-1118 36506104-36506182 79 0.7149 50 0.24
10
 CDS 1119-1214 36506008-36506103 96 0.6617 50 0.28
11
 CDS 1219-1294 36505928-36506003 76 0.6536 50 0.30
12
 CDS 1295-1392 36504701-36504766 / 36505896-36505927 98 0.4737 50 0.28
13
 CDS 1393-1508 36504585-36504700 116 0.7327 50 0.31
14
 CDS 1509-1598 36504348-36504367 / 36504515-36504584 90 0.5918 50 0.33
15
 CDS 1602-1693 36504253-36504344 92 0.8353 50 0.36
16
 CDS 1694-1764 36504182-36504252 71 0.6563 50 0.39
17
 CDS 1765-1862 36501394-36501407 / 36504098-36504181 98 0.4743 50 0.30
18
 CDS 1863-1959 36501297-36501393 97 0.6573 50 0.32
19
 CDS 1960-2054 36498118-36498156 / 36501241-36501296 95 0.6501 50 0.26
20
 CDS 2056-2144 36498028-36498116 89 0.6494 50 0.30
21
 CDS 2149-2251 36496139-36496208 / 36497991-36498023 103 0.6648 50 0.28
22
 CDS 2255-2356 36496034-36496135 102 0.6337 50 0.28
23
 CDS 2357-2445 36493782-36493803 / 36495967-36496033 89 0.6270 50 0.26
24
 CDS 2448-2530 36493697-36493779 83 0.7571 50 0.33
25
 CDS 2531-2633 36490229-36490267 / 36493633-36493696 103 0.7351 50 0.31
26
 CDS 2634-2736 36490126-36490228 103 0.6053 50 0.36
27
 CDS 2737-2826 36490036-36490125 90 0.6945 50 0.37
28
 CDS,3'UTR 2827-2917 36489945-36490035 91 0.7238 50 0.36
29
 3'UTR 2918-2998 36489864-36489944 81 0.6621 50 0.36
30
 3'UTR 2999-3105 36489757-36489863 107 0.7887 50 0.49
31
 3'UTR 3106-3197 36489665-36489756 92 0.7741 50 0.40
32
 3'UTR 3199-3295 36489567-36489663 97 0.5956 50 0.33
33
 3'UTR 3296-3387 36489475-36489566 92 0.7458 50 0.37
34
 3'UTR 3389-3479 36489383-36489473 91 0.7382 50 0.40
35
 3'UTR 3481-3570 36489292-36489381 90 0.6627 50 0.35
36
 3'UTR 3572-3657 36489205-36489290 86 0.5950 50 0.32
37
 3'UTR 3658-3758 36489104-36489204 101 0.4834 50 0.32
38
 3'UTR 3760-3868 36488994-36489102 109 0.4282 50 0.30
39
 3'UTR 3869-3975 36488887-36488993 107 0.6625 50 0.29
40
 3'UTR 3976-4068 36488794-36488886 93 0.6374 50 0.40
41
 3'UTR 4070-4147 36488715-36488792 78 0.5146 50 0.59
42
 3'UTR 4148-4245 36488617-36488714 98 0.4254 50 0.54
43
 3'UTR 4246-4330 36488532-36488616 85 0.7243 50 0.35
44
 3'UTR 4332-4418 36488444-36488530 87 0.6987 50 0.41
45
 3'UTR 4420-4531 36488331-36488442 112 0.6756 50 0.50
46
 3'UTR 4533-4601 36488261-36488329 69 0.8556 50 0.46
47
 3'UTR 4603-4667 36488195-36488259 65 0.6450 50 0.44
48
 3'UTR 4670-4794 36488068-36488192 125 0.8227 50 0.53
49
 3'UTR 4795-4884 36487978-36488067 90 0.8810 50 0.71
50
 3'UTR 4889-4984 36487878-36487973 96 0.5239 50 0.70
51
 3'UTR 4986-5080 36487782-36487876 95 0.8495 50 0.49
52
 3'UTR 5081-5170 36487692-36487781 90 0.6841 50 0.27
53
 3'UTR 5171-5272 36487590-36487691 102 0.8170 50 0.38
54
 3'UTR 5275-5381 36487481-36487587 107 0.7911 50 0.27
55
 3'UTR 5382-5469 36487393-36487480 88 0.6797 50 0.28
56
 3'UTR 5470-5561 36487301-36487392 92 0.4727 50 0.34
57
 3'UTR 5562-5619 36487243-36487300 58 0.5134 30 0.38
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.

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FOXRED2

Aoi: Chr: Coords Strand:
FOXRED2 22 36487393 - 36487480 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: FOXRED2(-)
  • Length Length of region: 88 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 / 05e29e215d / 2026-05-09 19:13