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?

MSRB1
ENST00000361871 (-) ENSG00000198736 (-)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 11-138 1941366-1941405 / 1943102-1943189 128 0.6303 50 0.30
2
 CDS 139-225 1941279-1941365 87 0.5840 50 0.30
3
 CDS 226-331 1940809-1940892 / 1941257-1941278 106 0.5017 50 0.32
4
 CDS,3'UTR 334-415 1939091-1939143 / 1940778-1940806 82 0.6457 50 0.42
5
 3'UTR 416-511 1938995-1939090 96 0.5733 50 0.39
6
 3'UTR 512-611 1938895-1938994 100 0.5551 50 0.38
7
 3'UTR 612-716 1938790-1938894 105 0.6693 50 0.48
8
 3'UTR 717-886 1938620-1938789 170 0.6176 50 0.49
9
 3'UTR 888-993 1938513-1938618 106 0.7772 50 0.57
10
 3'UTR 995-1085 1938421-1938511 91 0.5596 50 0.41
11
 3'UTR 1086-1201 1938305-1938420 116 0.4599 50 0.41
12
 3'UTR 1203-1250 1938256-1938303 48 0.5894 26 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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MSRB1

Aoi: Chr: Coords Strand:
MSRB1 16 1941366 - 1941405, 1943102 - 1943189 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: MSRB1(-)
  • Length Length of region: 128 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 12:32