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?

CD2BP2
ENST00000305596 (-) ENSG00000169217 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 58-148 30354657-30354707 / 30355212-30355251 91 0.4388 50 0.27
2
 CDS 149-260 30354264-30354322 / 30354604-30354656 112 0.6910 50 0.25
3
 CDS 266-368 30354031-30354058 / 30354184-30354258 103 0.6478 50 0.28
4
 CDS 379-473 30353926-30354020 95 0.6469 50 0.26
5
 CDS 474-572 30353727-30353800 / 30353901-30353925 99 0.7014 50 0.29
6
 CDS 573-685 30353614-30353726 113 0.6718 50 0.36
7
 CDS 686-786 30353513-30353613 101 0.9251 50 0.37
8
 CDS 787-881 30353418-30353512 95 0.6078 50 0.35
9
 CDS 884-992 30353227-30353287 / 30353368-30353415 109 0.4979 50 0.24
10
 CDS 998-1105 30353029-30353095 / 30353181-30353221 108 0.6127 50 0.32
11
 CDS,3'UTR 1106-1210 30352924-30353028 105 0.6784 50 0.37
12
 3'UTR 1215-1326 30352808-30352919 112 0.4678 50 0.40
13
 3'UTR 1327-1438 30352696-30352807 112 0.5105 50 0.45
14
 3'UTR 1443-1885 30352249-30352691 443 0.3640 50 0.40
15
 3'UTR 1886-1986 30352148-30352248 101 0.4596 50 0.40
16
 3'UTR 1987-2100 30352034-30352147 114 0.4715 50 0.44
17
 3'UTR 2101-2189 30351945-30352033 89 0.4332 50 0.41
18
 3'UTR 2190-2323 30351811-30351944 134 0.5381 50 0.45
19
 3'UTR 2324-2424 30351710-30351810 101 0.5430 50 0.47
20
 3'UTR 2434-2559 30351575-30351700 126 0.4989 50 0.34
21
 3'UTR 2560-2651 30351483-30351574 92 0.6223 50 0.39
22
 3'UTR 2652-2747 30351387-30351482 96 0.4185 50 0.33
23
 3'UTR 2748-2872 30351262-30351386 125 0.6881 50 0.44
24
 3'UTR 2873-2958 30351176-30351261 86 0.5517 50 0.40
25
 3'UTR 2959-3070 30351064-30351175 112 0.5456 50 0.38
26
 3'UTR 3073-3191 30350943-30351061 119 0.5908 50 0.46
27
 3'UTR 3197-3327 30350807-30350937 131 0.4696 70 0.42
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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CD2BP2

Aoi: Chr: Coords Strand:
CD2BP2 16 30354264 - 30354322, 30354604 - 30354656 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: CD2BP2(-)
  • Length Length of region: 112 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 / b252b9f76a / 2025-07-17 13:33