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?

TERF2
ENST00000254942 (-) ENSG00000132604 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 155-275 69385733-69385853 121 0.6321 50 0.39
2
 CDS 278-394 69385614-69385730 117 0.6183 50 0.26
3
 CDS 395-512 69384710-69384710 / 69385391-69385486 / 69385593-69385613 118 0.6755 50 0.31
4
 CDS 513-614 69384608-69384709 102 0.5153 50 0.25
5
 CDS 615-702 69372296-69372355 / 69384580-69384607 88 0.6513 50 0.38
6
 CDS 703-787 69370572-69370629 / 69372269-69372295 85 0.4581 50 0.31
7
 CDS 789-875 69370484-69370570 87 0.4912 50 0.33
8
 CDS 877-964 69368395-69368482 88 0.2666 50 0.30
9
 CDS 965-1042 69367141-69367199 / 69368376-69368394 78 0.3687 50 0.28
10
 CDS 1043-1136 69367047-69367140 94 0.5889 50 0.34
11
 CDS 1137-1218 69366965-69367046 82 0.3779 50 0.33
12
 CDS 1219-1303 69366880-69366964 85 0.5240 50 0.32
13
 CDS 1304-1376 69366807-69366879 73 0.4193 50 0.34
14
 CDS 1377-1476 69357548-69357561 / 69361404-69361489 100 0.4022 50 0.32
15
 CDS 1478-1567 69356996-69357056 / 69357518-69357546 90 0.2993 50 0.34
16
 CDS,3'UTR 1568-1665 69356898-69356995 98 0.3102 50 0.32
17
 3'UTR 1666-2375 69356188-69356897 710 0.2957 50 0.40
Error
18
 3'UTR 2382-2479 69356084-69356181 98 0.8472 50 0.51
19
 3'UTR 2483-2580 69355983-69356080 98 0.5620 50 0.48
20
 3'UTR 2581-2658 69355905-69355982 78 0.4208 31 0.34
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.

completed
10
TERF2

Aoi: Chr: Coords Strand:
TERF2 16 69367047 - 69367140 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TERF2(-)
  • Length Length of region: 94 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 7 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 16:54