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?

TUBA1A
ENST00000301071 (-) ENSG00000167552 (-)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 8-92 49188989-49189073 85 0.6521 50 0.28
2
 5'UTR,CDS 94-192 49186746-49186833 / 49188977-49188987 99 0.9194 50 0.26
3
 CDS 193-291 49186647-49186745 99 0.8076 50 0.24
4
 CDS 295-383 49186403-49186458 / 49186611-49186643 89 0.7910 50 0.22
5
 CDS 386-474 49186312-49186400 89 0.7294 50 0.19
6
 CDS 478-596 49185871-49185989 119 0.8792 50 0.21
7
 CDS 597-679 49185788-49185870 83 0.8136 50 0.21
8
 CDS 680-774 49185693-49185787 95 0.8660 50 0.25
9
 CDS 775-872 49185595-49185692 98 0.8970 50 0.30
10
 CDS 873-954 49185513-49185594 82 0.8454 50 0.31
11
 CDS 955-1057 49185410-49185512 103 0.7142 50 0.27
12
 CDS 1058-1155 49185312-49185409 98 0.9058 50 0.24
13
 CDS 1156-1250 49185217-49185311 95 0.8638 50 0.24
14
 CDS 1251-1374 49185093-49185216 124 0.8157 50 0.22
15
 CDS,3'UTR 1378-1496 49184971-49185089 119 0.7933 50 0.20
16
 3'UTR 1499-1659 49184808-49184968 161 0.6316 71 0.46
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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TUBA1A

Aoi: Chr: Coords Strand:
TUBA1A 12 49186746 - 49186833, 49188977 - 49188987 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TUBA1A(-)
  • Length Length of region: 99 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 8 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 06:56