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?

VHL
ENST00000256474 (+) ENSG00000134086 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 59-172 10141836-10141949 114 0.4043 50 0.34
2
 CDS 174-281 10141951-10142058 108 0.8125 50 0.42
3
 CDS 282-369 10142059-10142146 88 0.6080 50 0.32
4
 CDS 371-465 10142148-10142187 / 10146514-10146568 95 0.6840 50 0.26
5
 CDS 466-561 10146569-10146636 / 10149787-10149814 96 0.3308 50 0.31
6
 CDS 568-656 10149821-10149909 89 0.6290 50 0.31
7
 CDS,3'UTR 657-763 10149910-10150016 107 0.5996 50 0.28
8
 3'UTR 766-864 10150019-10150117 99 0.6786 50 0.30
9
 3'UTR 867-976 10150120-10150229 110 0.8704 50 0.50
10
 3'UTR 979-1096 10150232-10150349 118 0.7590 50 0.35
11
 3'UTR 1098-1206 10150351-10150459 109 0.6910 50 0.38
12
 3'UTR 1207-1332 10150460-10150585 126 0.8912 50 0.41
13
 3'UTR 1333-1455 10150586-10150708 123 0.6465 50 0.33
14
 3'UTR 1458-1560 10150711-10150813 103 0.4884 50 0.26
15
 3'UTR 1562-1721 10150815-10150974 160 0.7197 50 0.47
16
 3'UTR 1722-1834 10150975-10151087 113 0.3789 50 0.50
17
 3'UTR 1835-1934 10151088-10151187 100 0.5501 50 0.54
18
 3'UTR 1936-2040 10151189-10151293 105 0.6689 50 0.40
19
 3'UTR 2041-2149 10151294-10151402 109 0.4934 50 0.33
20
 3'UTR 2150-2224 10151403-10151477 75 0.4431 50 0.36
21
 3'UTR 2225-2336 10151478-10151589 112 0.5600 50 0.29
22
 3'UTR 2341-2444 10151594-10151697 104 0.6156 50 0.36
23
 3'UTR 2445-2561 10151698-10151814 117 0.7447 50 0.51
24
 3'UTR 2562-2652 10151815-10151905 91 0.5868 50 0.51
25
 3'UTR 2653-2996 10151906-10152249 344 0.2106 50 0.42
26
 3'UTR 2998-3096 10152251-10152349 99 0.2828 50 0.52
27
 3'UTR 3097-3424 10152350-10152677 328 0.4470 50 0.48
28
 3'UTR 3426-3526 10152679-10152779 101 0.3828 50 0.70
29
 3'UTR 3528-3654 10152781-10152907 127 0.4723 50 0.51
30
 3'UTR 3655-3739 10152908-10152992 85 0.4168 50 0.50
31
 3'UTR 3740-3839 10152993-10153092 100 0.4137 50 0.46
32
 3'UTR 3845-3941 10153098-10153194 97 0.5054 50 0.47
33
 3'UTR 3942-4044 10153195-10153297 103 0.5245 50 0.50
34
 3'UTR 4045-4148 10153298-10153401 104 0.5489 50 0.54
35
 3'UTR 4149-4220 10153402-10153473 72 0.6005 50 0.55
36
 3'UTR 4221-4311 10153474-10153564 91 0.4502 36 0.30
Download CSV

Custom Gene Windows

VHL
Chr Coords Strand
3 10152233 - 10152603
371 bp
15s
completed
VHL-4024-4173
Chr Coords Strand
3 10153277 - 10153426
150 bp
6s
completed
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
6
VHL

Aoi: Chr: Coords Strand:
VHL 3 10149821 - 10149909 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: VHL(+)
  • Length Length of region: 89 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 2 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 / bdd4f6bb6e / 2025-10-21 09:35