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?

UGP2
ENST00000337130 (+) ENSG00000169764 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 10-129 63841905-63842024 120 0.3742 50 0.31
2
 5'UTR 130-228 63842025-63842123 99 0.3517 50 0.25
3
 5'UTR,CDS 229-315 63842124-63842204 / 63856306-63856311 87 0.5126 50 0.44
4
 CDS 317-407 63856313-63856403 91 0.7717 50 0.21
5
 CDS 408-494 63856404-63856433 / 63857829-63857885 87 0.8556 50 0.24
6
 CDS 495-589 63857886-63857936 / 63882466-63882509 95 0.6704 50 0.18
7
 CDS 591-701 63882511-63882621 111 0.8243 50 0.21
8
 CDS 705-801 63882625-63882651 / 63883960-63884029 97 0.8113 50 0.24
9
 CDS 802-882 63884030-63884093 / 63885589-63885605 81 0.7708 50 0.25
10
 CDS 883-983 63885606-63885706 101 0.7515 50 0.21
11
 CDS 984-1095 63885707-63885818 112 0.8806 50 0.25
12
 CDS 1096-1179 63885819-63885886 / 63886341-63886356 84 0.7808 50 0.18
13
 CDS 1180-1272 63886357-63886449 93 0.7026 50 0.18
14
 CDS 1273-1360 63886450-63886537 88 0.8929 50 0.27
15
 CDS 1362-1475 63887402-63887515 114 0.7929 50 0.21
16
 CDS 1476-1568 63887516-63887608 93 0.8050 50 0.18
17
 CDS 1572-1676 63887612-63887644 / 63890081-63890152 105 0.7236 50 0.20
18
 CDS 1678-1777 63890154-63890185 / 63891120-63891187 100 0.8750 50 0.27
19
 CDS,3'UTR 1778-1876 63891188-63891286 99 0.7856 50 0.21
20
 3'UTR 1878-1989 63891288-63891399 112 0.8219 50 0.32
21
 3'UTR 1990-2088 63891400-63891498 99 0.8204 50 0.24
22
 3'UTR 2089-2141 63891499-63891551 53 0.4856 28 0.27
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
3
UGP2

Aoi: Chr: Coords Strand:
UGP2 2 63842124 - 63842204, 63856306 - 63856311 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: UGP2(+)
  • Length Length of region: 87 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 1 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 03:28