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?

PARP6
ENST00000569795 (-) ENSG00000137817 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 4-111 72272444-72272551 108 0.4981 50 0.46
2
 5'UTR 115-202 72271248-72271287 / 72272393-72272440 88 0.6042 50 0.39
3
 5'UTR 203-288 72271162-72271247 86 0.6107 50 0.39
4
 5'UTR 292-385 72271065-72271158 94 0.4905 50 0.32
5
 5'UTR 386-582 72267517-72267671 / 72271023-72271064 197 0.2176 50 0.31
6
 5'UTR,CDS 583-678 72266769-72266822 / 72267475-72267516 96 0.3623 50 0.35
7
 CDS 680-782 72265912-72265991 / 72266745-72266767 103 0.2713 50 0.30
8
 CDS 783-872 72265158-72265171 / 72265413-72265473 / 72265897-72265911 90 0.5247 50 0.44
9
 CDS 873-973 72264598-72264621 / 72265081-72265157 101 0.3451 50 0.35
10
 CDS 974-1075 72261649-72261707 / 72264555-72264597 102 0.5636 50 0.43
11
 CDS 1076-1164 72261560-72261648 89 0.6081 50 0.37
12
 CDS 1165-1258 72260597-72260688 / 72261558-72261559 94 0.4537 50 0.38
13
 CDS 1260-1439 72258125-72258132 / 72259608-72259661 / 72260478-72260595 180 0.5751 50 0.43
14
 CDS 1442-1549 72257419-72257440 / 72258037-72258122 108 0.5015 50 0.40
15
 CDS 1551-1673 72256538-72256590 / 72257348-72257417 123 0.6087 50 0.45
16
 CDS 1675-1768 72254499-72254520 / 72256465-72256536 94 0.2410 50 0.35
17
 CDS 1769-1868 72253449-72253504 / 72254455-72254498 100 0.6050 50 0.35
18
 CDS 1870-1952 72250932-72250954 / 72251207-72251255 / 72253437-72253447 83 0.3937 50 0.34
19
 CDS 1953-2046 72250086-72250092 / 72250845-72250931 94 0.4963 50 0.40
20
 CDS 2047-2203 72242679-72242699 / 72250020-72250085 157 0.3444 50 0.34
21
 CDS 2206-2287 72242196-72242220 / 72242620-72242676 82 0.5025 50 0.37
22
 CDS 2290-2391 72241921-72241985 / 72242157-72242193 102 0.3853 50 0.39
23
 CDS 2394-2493 72241476-72241557 / 72241901-72241918 100 0.2678 50 0.32
24
 CDS,3'UTR 2494-2618 72241351-72241475 125 0.3464 71 0.41
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
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PARP6

Aoi: Chr: Coords Strand:
PARP6 15 72265912 - 72265991, 72266745 - 72266767 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: PARP6(-)
  • Length Length of region: 103 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 / 2026-04-04 10:31