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?

DDX3X
ENST00000629496 (+) ENSG00000215301 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 388-487 41334161-41334260 100 0.8975 50 0.25
2
 CDS 493-590 41334266-41334297 / 41337408-41337465 / 41339036-41339043 98 0.9318 50 0.23
3
 CDS 592-689 41339045-41339083 / 41341484-41341542 98 0.8586 50 0.17
4
 CDS 690-824 41341543-41341616 / 41342495-41342555 135 0.9315 50 0.23
5
 CDS 830-921 41342561-41342652 92 0.9595 50 0.20
6
 CDS 922-1014 41342653-41342653 / 41342737-41342828 93 0.8865 50 0.20
7
 CDS 1018-1116 41342832-41342836 / 41343216-41343309 99 0.6771 50 0.17
8
 CDS 1119-1219 41343312-41343351 / 41343737-41343797 101 0.8153 50 0.20
9
 CDS 1220-1316 41343798-41343822 / 41344030-41344101 97 0.9740 50 0.22
10
 CDS 1319-1431 41344104-41344128 / 41344239-41344326 113 0.8528 50 0.18
11
 CDS 1432-1558 41344327-41344399 / 41345180-41345233 127 0.9276 50 0.23
12
 CDS 1560-1657 41345235-41345324 / 41345404-41345411 98 0.9141 50 0.20
13
 CDS 1659-1761 41345413-41345515 103 0.7991 50 0.17
14
 CDS 1765-1867 41345519-41345548 / 41346229-41346301 103 0.8909 50 0.23
15
 CDS 1870-1956 41346304-41346390 87 0.8748 50 0.18
16
 CDS 1957-2058 41346391-41346410 / 41346505-41346586 102 0.8677 50 0.16
17
 CDS 2059-2170 41346587-41346622 / 41346859-41346934 112 0.8949 50 0.18
18
 CDS 2171-2279 41346935-41347012 / 41347312-41347342 109 0.8912 50 0.20
19
 CDS 2281-2370 41347344-41347433 90 0.9065 50 0.26
20
 CDS,3'UTR 2372-2496 41347435-41347451 / 41347640-41347747 125 0.9625 50 0.33
21
 3'UTR 2497-2582 41347748-41347833 86 0.9405 50 0.30
22
 3'UTR 2585-2681 41347836-41347932 97 0.9205 50 0.26
23
 3'UTR 2685-2791 41347936-41348042 107 0.9101 50 0.29
24
 3'UTR 2793-2895 41348044-41348146 103 0.8485 50 0.24
25
 3'UTR 2896-2990 41348147-41348241 95 0.8692 50 0.21
26
 3'UTR 2991-3097 41348242-41348348 107 0.8325 50 0.26
27
 3'UTR 3101-3202 41348352-41348453 102 0.8395 50 0.24
28
 3'UTR 3203-3301 41348454-41348552 99 0.8902 50 0.21
29
 3'UTR 3303-3401 41348554-41348652 99 0.8804 50 0.24
30
 3'UTR 3402-3518 41348653-41348769 117 0.9414 50 0.35
31
 3'UTR 3521-3614 41348772-41348865 94 0.9228 50 0.29
32
 3'UTR 3615-3730 41348866-41348981 116 0.8735 50 0.28
33
 3'UTR 3736-3833 41348987-41349084 98 0.8993 50 0.35
34
 3'UTR 3834-3941 41349085-41349192 108 0.8640 50 0.31
35
 3'UTR 3942-4059 41349193-41349310 118 0.9504 50 0.36
36
 3'UTR 4064-4189 41349315-41349440 126 0.8870 50 0.25
37
 3'UTR 4192-4304 41349443-41349555 113 0.8015 50 0.21
38
 3'UTR 4305-4397 41349556-41349648 93 0.9414 50 0.37
39
 3'UTR 4399-4510 41349650-41349761 112 0.8162 50 0.23
40
 3'UTR 4511-4605 41349762-41349856 95 0.9256 50 0.31
41
 3'UTR 4606-4753 41349857-41350004 148 0.9079 50 0.33
42
 3'UTR 4754-4852 41350005-41350103 99 0.7128 50 0.26
43
 3'UTR 4855-4955 41350106-41350206 101 0.7340 44 0.41
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

DDX3X
Chr Coords Strand
X 41346935 - 41347012
41347312 - 41347342
109 bp
5s
completed
DDX3X
Chr Coords Strand
X 41342832 - 41342836
41343216 - 41343309
99 bp
5s
completed
DDX3X
Chr Coords Strand
X 41348352 - 41348453
102 bp
6s
completed
DDX3X
Chr Coords Strand
X 41349556 - 41349648
93 bp
5s
completed
DDX3X
Chr Coords Strand
X 41348866 - 41348981
116 bp
9s
completed
DDX3X
Chr Coords Strand
X 41349762 - 41349856
95 bp
6s
completed
production / 05e29e215d / 2026-04-03 22:48