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?

TUBA1B
ENST00000336023 (-) ENSG00000123416 (-)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 1-107 49129714-49129722 / 49131298-49131395 107 0.9817 50 0.30
2
 CDS 108-205 49129616-49129713 98 0.9902 50 0.24
3
 CDS 206-310 49129511-49129615 105 0.9824 50 0.23
4
 CDS 311-395 49129317-49129390 / 49129500-49129510 85 0.9801 50 0.23
5
 CDS 396-492 49128917-49128938 / 49129242-49129316 97 0.9824 50 0.20
6
 CDS 493-612 49128797-49128916 120 0.9929 50 0.19
7
 CDS 613-685 49128724-49128796 73 0.9861 50 0.21
8
 CDS 686-774 49128635-49128723 89 0.9895 50 0.25
9
 CDS 777-869 49128540-49128632 93 0.9837 50 0.23
10
 CDS 870-951 49128458-49128539 82 0.9845 50 0.25
11
 CDS 955-1053 49128356-49128454 99 0.9679 50 0.23
12
 CDS 1060-1150 49128259-49128349 91 0.9831 50 0.18
13
 CDS 1157-1245 49128164-49128252 89 0.9799 50 0.22
14
 CDS 1249-1372 49128037-49128160 124 0.9843 50 0.19
15
 CDS,3'UTR 1375-1493 49127916-49128034 119 0.9845 50 0.22
16
 3'UTR 1494-1627 49127782-49127915 134 0.9280 63 0.26
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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TUBA1B

Aoi: Chr: Coords Strand:
TUBA1B 12 49129714 - 49129722, 49131298 - 49131395 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TUBA1B(-)
  • Length Length of region: 107 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 4 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 07:35