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?

CBX1
ENST00000225603 (-) ENSG00000108468 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 4-122 48101357-48101475 119 0.4650 50 0.24
2
 5'UTR 125-213 48077040-48077041 / 48101268-48101354 89 0.8989 50 0.27
3
 5'UTR,CDS 215-302 48076951-48077038 88 0.8618 50 0.21
4
 CDS 304-408 48076159-48076178 / 48076865-48076949 105 0.8217 50 0.17
5
 CDS 409-494 48076073-48076158 86 0.9334 50 0.28
6
 CDS 497-578 48075089-48075100 / 48076001-48076070 82 0.8085 50 0.19
7
 CDS 579-691 48071550-48071579 / 48075006-48075088 113 0.9309 50 0.30
8
 CDS 694-787 48071454-48071547 94 0.9421 50 0.27
9
 CDS,3'UTR 788-885 48071356-48071453 98 0.8946 50 0.30
10
 3'UTR 886-992 48071249-48071355 107 0.8603 50 0.31
11
 3'UTR 993-1091 48071150-48071248 99 0.9373 50 0.40
12
 3'UTR 1093-1181 48071060-48071148 89 0.9183 50 0.42
13
 3'UTR 1184-1333 48070908-48071057 150 0.9157 50 0.35
14
 3'UTR 1334-1424 48070817-48070907 91 0.8370 50 0.26
15
 3'UTR 1425-1518 48070723-48070816 94 0.8953 50 0.32
16
 3'UTR 1519-1629 48070612-48070722 111 0.9386 50 0.31
17
 3'UTR 1630-1737 48070504-48070611 108 0.9333 50 0.29
18
 3'UTR 1739-1845 48070396-48070502 107 0.9213 50 0.27
19
 3'UTR 1846-1948 48070293-48070395 103 0.9369 50 0.28
20
 3'UTR 1949-2021 48070220-48070292 73 0.7119 50 0.23
21
 3'UTR 2024-2179 48070062-48070217 156 0.7117 68 0.28
Download CSV

Custom Gene Windows

CBX1-791-890
Chr Coords Strand
17 48071351 - 48071437
48071438 - 48071450
100 bp
6s
completed
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
CBX1

Aoi: Chr: Coords Strand:
CBX1-791-890 17 48071351 - 48071437, 48071438 - 48071450 -
Download Data & Images
Structures
1 2
production / b252b9f76a / 2025-07-17 03:15