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?

DVL1
ENST00000378891 (-) ENSG00000107404 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 1-91 1349022-1349112 91 0.6064 50 0.43
2
 CDS 93-179 1348934-1349020 87 0.6569 50 0.42
3
 CDS 181-288 1342484-1342484 / 1342689-1342758 / 1348896-1348932 108 0.5784 50 0.33
4
 CDS 293-389 1342383-1342479 97 0.6218 50 0.40
5
 CDS 391-475 1342091-1342156 / 1342363-1342381 85 0.6116 50 0.38
6
 CDS 476-571 1341748-1341805 / 1342053-1342090 96 0.4993 50 0.38
7
 CDS 572-664 1340492-1340503 / 1341667-1341747 93 0.7392 50 0.40
8
 CDS 665-748 1340315-1340316 / 1340410-1340491 84 0.6836 50 0.35
9
 CDS 749-823 1340171-1340177 / 1340247-1340314 75 0.6357 50 0.33
10
 CDS 825-930 1340064-1340169 106 0.6354 50 0.38
11
 CDS 932-1040 1339643-1339649 / 1339736-1339812 / 1340038-1340062 109 0.6183 50 0.31
12
 CDS 1041-1125 1339416-1339439 / 1339582-1339642 85 0.5559 50 0.39
13
 CDS 1126-1218 1338615-1338653 / 1339362-1339415 93 0.3498 50 0.39
14
 CDS 1220-1315 1338433-1338436 / 1338522-1338613 96 0.5837 50 0.37
15
 CDS 1318-1420 1338328-1338430 103 0.6717 50 0.39
16
 CDS 1424-1508 1338155-1338183 / 1338269-1338324 85 0.6901 50 0.32
17
 CDS 1510-1598 1338065-1338153 89 0.6934 50 0.42
18
 CDS 1599-1719 1336483-1336515 / 1337977-1338064 121 0.5476 50 0.41
19
 CDS 1721-1839 1336363-1336481 119 0.5133 50 0.40
20
 CDS 1840-1915 1336287-1336362 76 0.5255 50 0.50
21
 CDS 1916-2017 1336185-1336286 102 0.6268 50 0.44
22
 CDS,3'UTR 2020-2137 1336065-1336182 118 0.3631 50 0.42
23
 3'UTR 2138-2244 1335958-1336064 107 0.4904 50 0.41
24
 3'UTR 2246-2364 1335838-1335956 119 0.2804 50 0.48
25
 3'UTR 2365-2458 1335744-1335837 94 0.7131 50 0.46
26
 3'UTR 2459-2564 1335638-1335743 106 0.7365 50 0.39
27
 3'UTR 2566-2661 1335541-1335636 96 0.6556 50 0.41
28
 3'UTR 2662-2773 1335429-1335540 112 0.7266 50 0.39
29
 3'UTR 2774-2903 1335299-1335428 130 0.5989 61 0.39
Download CSV

Custom Gene Windows

miR-212-5p A
Chr Coords Strand
1 1335569 - 1335552
-16 bp
2s
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

Aoi: Chr: Coords Strand:
miR-212-5p A 1 1335569 - 1335552 -
Download Data & Images
Structures
production / bdd4f6bb6e / 2025-10-21 00:58