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?

SON
ENST00000356577 (+) ENSG00000159140 (+)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 19-120 33543056-33543157 102 0.7597 50 0.27
2
 CDS 123-215 33543160-33543169 / 33546213-33546295 93 0.7747 50 0.23
3
 CDS 218-309 33546298-33546379 / 33549476-33549485 92 0.6957 50 0.17
4
 CDS 313-390 33549489-33549566 78 0.8614 50 0.27
5
 CDS 391-452 33549567-33549628 62 0.7368 50 0.30
6
 CDS 453-558 33549629-33549734 106 0.7229 50 0.25
7
 CDS 560-652 33549736-33549828 93 0.8173 50 0.31
8
 CDS 653-735 33549829-33549911 83 0.6136 50 0.25
9
 CDS 737-828 33549913-33550004 92 0.8668 50 0.36
10
 CDS 831-933 33550007-33550109 103 0.8700 50 0.29
11
 CDS 935-1020 33550111-33550196 86 0.8122 50 0.32
12
 CDS 1021-1113 33550197-33550289 93 0.6703 50 0.22
13
 CDS 1114-1215 33550290-33550391 102 0.8503 50 0.34
14
 CDS 1218-1319 33550394-33550495 102 0.6437 50 0.35
15
 CDS 1320-1416 33550496-33550592 97 0.4456 50 0.31
16
 CDS 1417-1516 33550593-33550692 100 0.8546 50 0.42
17
 CDS 1518-1616 33550694-33550792 99 0.7533 50 0.29
18
 CDS 1617-1722 33550793-33550898 106 0.7546 50 0.37
19
 CDS 1723-1850 33550899-33551026 128 0.8363 50 0.38
20
 CDS 1851-1979 33551027-33551155 129 0.6515 50 0.27
21
 CDS 1980-2091 33551156-33551267 112 0.8165 50 0.27
22
 CDS 2092-2193 33551268-33551369 102 0.7367 50 0.27
23
 CDS 2194-2271 33551370-33551447 78 0.6311 50 0.28
24
 CDS 2272-2355 33551448-33551531 84 0.7983 50 0.35
25
 CDS 2356-2443 33551532-33551619 88 0.5981 50 0.28
26
 CDS 2445-2525 33551621-33551701 81 0.7418 50 0.32
27
 CDS 2526-2610 33551702-33551786 85 0.3937 50 0.29
28
 CDS 2611-2708 33551787-33551884 98 0.7503 50 0.37
29
 CDS 2713-2818 33551889-33551994 106 0.6706 50 0.35
30
 CDS 2819-2920 33551995-33552096 102 0.6814 50 0.33
31
 CDS 2922-2999 33552098-33552175 78 0.6193 50 0.26
32
 CDS 3002-3100 33552178-33552276 99 0.7272 50 0.33
33
 CDS 3102-3209 33552278-33552385 108 0.7939 50 0.36
34
 CDS 3210-3318 33552386-33552494 109 0.6751 50 0.28
35
 CDS 3321-3432 33552497-33552608 112 0.7445 50 0.28
36
 CDS 3434-3522 33552610-33552698 89 0.6411 50 0.25
37
 CDS 3523-3602 33552699-33552778 80 0.7647 50 0.30
38
 CDS 3603-3690 33552779-33552866 88 0.6925 50 0.31
39
 CDS 3692-3801 33552868-33552977 110 0.6522 50 0.27
40
 CDS 3802-3886 33552978-33553062 85 0.8330 50 0.28
41
 CDS 3888-3982 33553064-33553158 95 0.6154 50 0.25
42
 CDS 3984-4081 33553160-33553257 98 0.5590 50 0.28
43
 CDS 4082-4198 33553258-33553374 117 0.7281 50 0.37
44
 CDS 4199-4321 33553375-33553497 123 0.7577 50 0.32
45
 CDS 4323-4427 33553499-33553603 105 0.7400 50 0.33
46
 CDS 4428-4518 33553604-33553694 91 0.7229 50 0.32
47
 CDS 4520-4615 33553696-33553791 96 0.8530 50 0.36
48
 CDS 4620-4718 33553796-33553894 99 0.6493 50 0.21
49
 CDS 4719-4822 33553895-33553998 104 0.7568 50 0.39
50
 CDS 4825-4925 33554001-33554101 101 0.7050 50 0.28
51
 CDS 4926-5033 33554102-33554209 108 0.7345 50 0.24
52
 CDS 5034-5123 33554210-33554299 90 0.7070 50 0.22
53
 CDS 5124-5204 33554300-33554380 81 0.7858 50 0.29
54
 CDS 5205-5309 33554381-33554485 105 0.7721 50 0.27
55
 CDS 5313-5416 33554489-33554592 104 0.8376 50 0.30
56
 CDS 5418-5504 33554594-33554680 87 0.8207 50 0.23
57
 CDS 5505-5589 33554681-33554765 85 0.7656 50 0.24
58
 CDS 5591-5677 33554767-33554853 87 0.8320 50 0.23
59
 CDS 5678-5754 33554854-33554930 77 0.7493 50 0.18
60
 CDS 5757-5834 33554933-33555010 78 0.7964 50 0.24
61
 CDS 5837-5932 33555013-33555108 96 0.9452 50 0.34
62
 CDS 5933-5997 33555109-33555173 65 0.8144 50 0.32
63
 CDS 5998-6080 33555174-33555256 83 0.6470 50 0.22
64
 CDS 6082-6166 33555258-33555342 85 0.6562 50 0.18
65
 CDS 6168-6255 33555344-33555391 / 33557156-33557195 88 0.6827 50 0.22
66
 CDS 6258-6341 33557198-33557281 84 0.7309 50 0.24
67
 CDS 6342-6430 33557282-33557316 / 33559230-33559283 89 0.4601 50 0.22
68
 CDS 6431-6522 33559284-33559375 92 0.7240 50 0.28
69
 CDS 6524-6599 33559587-33559662 76 0.4811 50 0.26
70
 CDS 6600-6699 33559663-33559762 100 0.5451 50 0.30
71
 CDS 6704-6797 33559767-33559775 / 33567157-33567241 94 0.7029 50 0.27
72
 CDS 6799-6898 33567243-33567267 / 33568971-33569045 100 0.7134 50 0.28
73
 CDS 6900-6999 33569047-33569087 / 33573308-33573366 100 0.7276 50 0.27
74
 CDS 7000-7086 33573367-33573453 87 0.5876 50 0.27
75
 CDS 7087-7196 33573454-33573455 / 33575596-33575667 / 33575778-33575813 110 0.5969 50 0.30
76
 CDS 7197-7328 33575814-33575893 / 33576365-33576416 132 0.7320 50 0.31
77
 CDS,3'UTR 7332-7419 33576420-33576507 88 0.7468 50 0.35
78
 3'UTR 7421-7523 33576509-33576611 103 0.8473 50 0.33
79
 3'UTR 7525-7629 33576613-33576717 105 0.5586 50 0.27
80
 3'UTR 7630-7749 33576718-33576837 120 0.5354 50 0.23
81
 3'UTR 7756-7863 33576844-33576951 108 0.6983 50 0.30
82
 3'UTR 7868-7966 33576956-33577054 99 0.6724 50 0.37
83
 3'UTR 7967-8074 33577055-33577162 108 0.7472 50 0.33
84
 3'UTR 8077-8193 33577165-33577281 117 0.5139 50 0.26
85
 3'UTR 8194-8334 33577282-33577422 141 0.3376 64 0.33
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.

Recently Visualized

SON
Chr Coords Strand
21 33554681 - 33554765
85 bp
5s
completed
SON
Chr Coords Strand
21 33553499 - 33553603
105 bp
8s
completed
SON
Chr Coords Strand
21 33551787 - 33551884
98 bp
6s
completed
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Chr Coords Strand
21 33553375 - 33553497
123 bp
77s
completed
production / 6f779e32bc / 2026-02-04 19:07