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?

HNRNPC
ENST00000554455 (-) ENSG00000092199 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 1-101 21269325-21269425 101 0.9476 50 0.27
2
 5'UTR,CDS 103-201 21234183-21234229 / 21263311-21263336 / 21269298-21269323 99 0.9047 50 0.23
3
 CDS 202-295 21234089-21234182 94 0.8982 50 0.17
4
 CDS 296-421 21233963-21234088 126 0.9156 50 0.19
5
 CDS 422-519 21230985-21231072 / 21233953-21233962 98 0.9417 50 0.18
6
 CDS 520-613 21213099-21213117 / 21230319-21230366 / 21230958-21230984 94 0.9505 50 0.19
7
 CDS 614-710 21213002-21213098 97 0.9789 50 0.21
8
 CDS 711-804 21211872-21211923 / 21212960-21213001 94 0.9697 50 0.21
9
 CDS 805-888 21211545-21211566 / 21211810-21211871 84 0.9680 50 0.22
10
 CDS 889-1002 21211431-21211544 114 0.9435 50 0.14
11
 CDS 1004-1107 21211227-21211306 / 21211406-21211429 104 0.9349 50 0.16
12
 3'UTR 1110-1209 21211125-21211224 100 0.9593 50 0.31
13
 3'UTR 1210-1303 21211031-21211124 94 0.9579 50 0.29
14
 3'UTR 1305-1416 21210918-21211029 112 0.9285 50 0.38
15
 3'UTR 1418-1525 21210809-21210916 108 0.9212 50 0.33
16
 3'UTR 1530-1643 21210691-21210804 114 0.9454 50 0.36
17
 3'UTR 1645-1784 21210550-21210689 140 0.8312 63 0.33
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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HNRNPC

Aoi: Chr: Coords Strand:
HNRNPC 14 21234183 - 21234229, 21263311 - 21263336, 21269298 - 21269323 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: HNRNPC(-)
  • 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 / 2026-03-20 19:34