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
Coords (max 500bp)
Coords 1  
Additional Coordinates
Coords 2 Optional
Coords 3 Optional
Coords 4 Optional


How was this calculated?

TP53
ENST00000269305 (-) ENSG00000141510 (-)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 4-115 7676622-7676622 / 7687377-7687487 112 0.3946 50 0.27
2
 5'UTR,CDS 116-206 7676531-7676621 91 0.7159 50 0.27
3
 CDS 208-298 7676213-7676272 / 7676382-7676403 / 7676521-7676529 91 0.6241 50 0.32
4
 CDS 304-383 7676128-7676207 80 0.6625 50 0.30
5
 CDS 384-462 7676049-7676127 79 0.5064 50 0.31
6
 CDS 463-562 7675192-7675236 / 7675994-7676048 100 0.6397 50 0.34
7
 CDS 565-647 7675107-7675189 83 0.6076 50 0.34
8
 CDS 650-762 7674911-7674971 / 7675053-7675104 113 0.3401 50 0.32
9
 CDS 765-859 7674246-7674290 / 7674859-7674908 95 0.6270 50 0.31
10
 CDS 860-949 7673813-7673837 / 7674181-7674245 90 0.3813 50 0.26
11
 CDS 954-1051 7673711-7673808 98 0.5773 50 0.32
12
 CDS 1052-1122 7673548-7673608 / 7673701-7673710 71 0.5975 50 0.30
13
 CDS 1126-1235 7670616-7670715 / 7673535-7673544 110 0.5674 50 0.28
14
 CDS 1236-1311 7669622-7669690 / 7670609-7670615 76 0.5157 50 0.29
15
 CDS,3'UTR 1314-1406 7669527-7669619 93 0.7019 50 0.35
16
 3'UTR 1407-1531 7669402-7669526 125 0.7487 50 0.41
17
 3'UTR 1532-1650 7669283-7669401 119 0.8679 50 0.48
18
 3'UTR 1651-1743 7669190-7669282 93 0.8552 50 0.47
19
 3'UTR 1745-1859 7669074-7669188 115 0.8336 50 0.44
20
 3'UTR 1871-1975 7668958-7669062 105 0.8338 50 0.49
21
 3'UTR 1978-2078 7668855-7668955 101 0.8170 50 0.42
22
 3'UTR 2097-2222 7668711-7668836 126 0.7623 50 0.44
23
 3'UTR 2223-2327 7668606-7668710 105 0.6271 50 0.34
24
 3'UTR 2328-2419 7668514-7668605 92 0.8455 50 0.43
25
 3'UTR 2420-2483 7668450-7668513 64 0.7438 35 0.41
Download CSV

Custom Gene Windows

TP53
Chr Coords Strand
17 7674255 - 7674290
7674859 - 7674971
7675053 - 7675236
7675994 - 7676160
500 bp
69s
completed
TP53
Chr Coords Strand
17 7668949 - 7669448
500 bp
66s
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
17
TP53

Aoi: Chr: Coords Strand:
TP53 17 7669283 - 7669401 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TP53(-)
  • Length Length of region: 119 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 7 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 / 362c1546a7 / 2025-05-20 09:57