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?

ACLY
ENST00000590151 (-) ENSG00000131473 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 1-118 41913866-41913900 / 41918880-41918962 118 0.7948 50 0.25
2
 CDS 119-202 41913782-41913865 84 0.7112 50 0.18
3
 CDS 205-292 41912520-41912542 / 41913715-41913779 88 0.7696 50 0.26
4
 CDS 294-399 41910278-41910284 / 41912420-41912518 106 0.8921 50 0.27
5
 CDS 400-491 41909665-41909700 / 41910222-41910277 92 0.8643 50 0.29
6
 CDS 493-606 41909550-41909663 114 0.7969 50 0.23
7
 CDS 607-697 41909018-41909068 / 41909510-41909549 91 0.7757 50 0.24
8
 CDS 698-791 41907508-41907572 / 41908989-41909017 94 0.7544 50 0.22
9
 CDS 792-886 41906618-41906646 / 41907442-41907507 95 0.8958 50 0.23
10
 CDS 887-995 41905640-41905658 / 41906528-41906617 109 0.8443 50 0.22
11
 CDS 1004-1086 41905549-41905631 83 0.8419 50 0.23
12
 CDS 1088-1168 41904736-41904790 / 41905522-41905547 81 0.7527 50 0.20
13
 CDS 1172-1261 41901728-41901813 / 41904729-41904732 90 0.8632 50 0.26
14
 CDS 1263-1370 41898709-41898785 / 41901696-41901726 108 0.8696 50 0.23
15
 CDS 1371-1434 41898645-41898708 64 0.8651 50 0.26
16
 CDS 1436-1525 41897763-41897839 / 41898631-41898643 90 0.8313 50 0.28
17
 CDS 1528-1599 41893145-41893174 / 41896620-41896649 / 41897749-41897760 72 0.6547 50 0.22
18
 CDS 1600-1704 41893040-41893144 105 0.7305 50 0.22
19
 CDS 1705-1800 41892359-41892447 / 41893033-41893039 96 0.7016 50 0.24
20
 CDS 1801-1890 41887694-41887703 / 41892279-41892358 90 0.7061 50 0.21
21
 CDS 1892-1977 41887607-41887692 86 0.7391 50 0.21
22
 CDS 1978-2075 41886219-41886308 / 41887599-41887606 98 0.8439 50 0.25
23
 CDS 2076-2181 41886113-41886218 106 0.8998 50 0.22
24
 CDS 2185-2294 41883203-41883232 / 41884193-41884272 110 0.8359 50 0.20
25
 CDS 2295-2405 41878895-41878924 / 41883122-41883202 111 0.8328 50 0.25
26
 CDS 2406-2510 41878190-41878196 / 41878797-41878894 105 0.7886 50 0.23
27
 CDS 2512-2612 41873951-41873965 / 41878103-41878188 101 0.8104 50 0.25
28
 CDS 2613-2704 41873859-41873950 92 0.8689 50 0.28
29
 CDS 2705-2819 41872116-41872182 / 41873811-41873858 115 0.8616 50 0.21
30
 CDS 2822-2924 41871812-41871832 / 41872032-41872113 103 0.9410 50 0.28
31
 CDS 2929-3033 41871703-41871807 105 0.7397 50 0.19
32
 CDS 3034-3114 41869521-41869587 / 41871689-41871702 81 0.8622 50 0.20
33
 CDS 3115-3214 41869073-41869125 / 41869474-41869520 100 0.8108 50 0.21
34
 CDS 3215-3336 41867890-41867904 / 41868709-41868785 / 41869043-41869072 122 0.6673 50 0.18
35
 CDS,3'UTR 3337-3437 41867789-41867889 101 0.8640 50 0.27
36
 3'UTR 3438-3531 41867695-41867788 94 0.8466 50 0.28
37
 3'UTR 3532-3602 41867624-41867694 71 0.8297 50 0.23
38
 3'UTR 3605-3706 41867520-41867621 102 0.8179 50 0.23
39
 3'UTR 3709-3831 41867395-41867517 123 0.8788 50 0.27
40
 3'UTR 3833-3961 41867265-41867393 129 0.8003 50 0.30
41
 3'UTR 3962-4073 41867153-41867264 112 0.8298 50 0.32
42
 3'UTR 4079-4194 41867032-41867147 116 0.8401 50 0.27
43
 3'UTR 4196-4300 41866926-41867030 105 0.6171 56 0.29
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
1
ACLY

Aoi: Chr: Coords Strand:
ACLY 17 41913866 - 41913900, 41918880 - 41918962 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: ACLY(-)
  • Length Length of region: 118 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 14 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 / 6f779e32bc / 2026-02-04 17:40