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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?

HNRNPH2
ENST00000316594 (+) ENSG00000126945 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 2-106 101408223-101408319 / 101411936-101411943 105 0.4254 50 0.22
2
 5'UTR,CDS 107-202 101411944-101412039 96 0.6915 50 0.22
3
 CDS 203-298 101412040-101412135 96 0.6984 50 0.21
4
 CDS 300-397 101412137-101412234 98 0.7028 50 0.20
5
 CDS 402-506 101412239-101412343 105 0.7773 50 0.20
6
 CDS 507-630 101412344-101412467 124 0.6850 50 0.21
7
 CDS 633-720 101412470-101412557 88 0.7566 50 0.17
8
 CDS 721-820 101412558-101412657 100 0.8395 50 0.19
9
 CDS 821-966 101412658-101412803 146 0.8353 50 0.17
10
 CDS 969-1070 101412806-101412907 102 0.8839 50 0.23
11
 CDS 1071-1179 101412908-101413016 109 0.7151 50 0.20
12
 CDS 1180-1273 101413017-101413110 94 0.7367 50 0.18
13
 CDS 1274-1392 101413111-101413229 119 0.7235 50 0.22
14
 CDS,3'UTR 1394-1512 101413231-101413349 119 0.7800 50 0.21
15
 3'UTR 1514-1625 101413351-101413462 112 0.7030 50 0.20
16
 3'UTR 1628-1750 101413465-101413587 123 0.8770 50 0.33
17
 3'UTR 1753-1840 101413590-101413677 88 0.6457 50 0.25
18
 3'UTR 1841-1953 101413678-101413790 113 0.8260 50 0.31
19
 3'UTR 1954-2050 101413791-101413887 97 0.8696 50 0.33
20
 3'UTR 2051-2188 101413888-101414025 138 0.8360 50 0.28
21
 3'UTR 2189-2276 101414026-101414113 88 0.3823 35 0.31
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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HNRNPH2

Aoi: Chr: Coords Strand:
HNRNPH2 X 101411944 - 101412039 +
Download Data & Images


  • Annotation Based on canonical annotations, the following genes are in your area of interest: RPL36A-HNRNPH2(+), HNRNPH2(+)
  • Length Length of region: 96 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 6 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 / 2026-04-04 01:22