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?

C9orf72
ENST00000619707 (-) ENSG00000147894 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 159-265 27567058-27567164 107 0.2785 50 0.26
2
 CDS 266-364 27566959-27567057 99 0.4849 50 0.32
3
 CDS 365-470 27566853-27566958 106 0.6101 50 0.31
4
 CDS 471-575 27566748-27566852 105 0.4796 50 0.28
5
 CDS 577-666 27565571-27565590 / 27566677-27566746 90 0.2408 50 0.30
6
 CDS 668-773 27562410-27562476 / 27565531-27565569 106 0.3949 50 0.28
7
 CDS 774-872 27560295-27560299 / 27561585-27561649 / 27562381-27562409 99 0.2197 50 0.25
8
 CDS 874-973 27558575-27558607 / 27560227-27560293 100 0.5377 50 0.36
9
 CDS,3'UTR 975-1782 27548102-27548422 / 27548557-27548666 / 27556561-27556796 / 27558491-27558573 808 0.4333 50 0.42
Error
10
 3'UTR 1783-1897 27547987-27548101 115 0.2600 50 0.35
11
 3'UTR 1901-2012 27547872-27547983 112 0.4108 50 0.39
12
 3'UTR 2013-2118 27547766-27547871 106 0.4240 50 0.37
13
 3'UTR 2120-2231 27547653-27547764 112 0.2432 50 0.30
14
 3'UTR 2232-2379 27547505-27547652 148 0.5124 50 0.33
15
 3'UTR 2380-2488 27547396-27547504 109 0.4542 50 0.37
16
 3'UTR 2489-2598 27547286-27547395 110 0.1243 50 0.32
17
 3'UTR 2600-2713 27547171-27547284 114 0.3258 50 0.36
18
 3'UTR 2716-2838 27547046-27547168 123 0.3609 50 0.34
19
 3'UTR 2840-2959 27546925-27547044 120 0.2834 52 0.37
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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C9orf72

Aoi: Chr: Coords Strand:
C9orf72 9 27560295 - 27560299, 27561585 - 27561649, 27562381 - 27562409 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: C9orf72(-)
  • 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 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 / 05e29e215d / 2026-03-24 16:55