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?

URB2
ENST00000258243 (+) ENSG00000135763 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 247-374 229627757-229627759 / 229632269-229632393 128 0.2872 50 0.33
2
 CDS 376-472 229632395-229632445 / 229634917-229634962 97 0.3188 50 0.38
3
 CDS 474-687 229634964-229635177 214 0.4629 50 0.45
4
 CDS 688-793 229635178-229635283 106 0.1863 50 0.34
5
 CDS 794-905 229635284-229635395 112 0.3397 50 0.31
6
 CDS 907-1009 229635397-229635499 103 0.5790 50 0.43
7
 CDS 1010-1145 229635500-229635635 136 0.5715 50 0.40
8
 CDS 1148-1234 229635638-229635724 87 0.6074 50 0.37
9
 CDS 1235-1325 229635725-229635815 91 0.6212 50 0.38
10
 CDS 1326-1431 229635816-229635921 106 0.3211 50 0.34
11
 CDS 1433-1518 229635923-229636008 86 0.4913 50 0.36
12
 CDS 1522-1687 229636012-229636177 166 0.4883 50 0.41
13
 CDS 1688-1896 229636178-229636386 209 0.4623 50 0.42
14
 CDS 1899-2006 229636389-229636496 108 0.4195 50 0.39
15
 CDS 2007-2110 229636497-229636600 104 0.3234 50 0.31
16
 CDS 2111-2208 229636601-229636698 98 0.3381 50 0.35
17
 CDS 2210-2323 229636700-229636813 114 0.3225 50 0.38
18
 CDS 2324-2427 229636814-229636917 104 0.2428 50 0.33
19
 CDS 2428-2703 229636918-229637193 276 0.4236 50 0.40
20
 CDS 2704-2799 229637194-229637289 96 0.2724 50 0.31
21
 CDS 2800-2953 229637290-229637443 154 0.4550 50 0.39
22
 CDS 2954-3119 229637444-229637609 166 0.5348 50 0.45
23
 CDS 3120-3221 229637610-229637711 102 0.1569 50 0.35
24
 CDS 3222-3512 229637712-229638002 291 0.6462 50 0.40
25
 CDS 3514-3619 229638004-229638109 106 0.3905 50 0.38
26
 CDS 3620-3734 229638110-229638224 115 0.4017 50 0.41
27
 CDS 3737-3967 229638227-229638247 / 229643533-229643693 / 229645859-229645907 231 0.6471 50 0.42
28
 CDS 3969-4137 229645909-229645969 / 229647510-229647617 169 0.3570 50 0.37
29
 CDS 4138-4414 229647618-229647752 / 229651235-229651322 / 229654249-229654302 277 0.3210 50 0.30
30
 CDS 4418-4525 229654306-229654388 / 229659100-229659124 108 0.4370 50 0.32
31
 CDS 4528-4628 229659127-229659227 101 0.1993 50 0.30
32
 CDS,3'UTR 4631-4713 229659230-229659312 83 0.4464 50 0.31
33
 3'UTR 4717-4821 229659316-229659420 105 0.7075 50 0.36
34
 3'UTR 4822-4952 229659421-229659551 131 0.6588 50 0.35
35
 3'UTR 4953-5083 229659552-229659682 131 0.5359 50 0.39
36
 3'UTR 5084-5188 229659683-229659787 105 0.4318 50 0.38
37
 3'UTR 5189-5359 229659788-229659958 171 0.6304 60 0.59
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
17
URB2

Aoi: Chr: Coords Strand:
URB2 1 229636700 - 229636813 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: URB2(+)
  • Length Length of region: 114 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 1 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
1
production / 6f779e32bc / 2026-02-04 19:11