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?

IRAK1
ENST00000369980 (-) ENSG00000184216 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 5-95 154019808-154019898 91 0.8647 50 0.42
2
 CDS 96-198 154019705-154019807 103 0.8602 50 0.35
3
 CDS 199-297 154019528-154019598 / 154019677-154019704 99 0.8499 50 0.26
4
 CDS 298-387 154019438-154019527 90 0.8819 50 0.27
5
 CDS 388-460 154019263-154019328 / 154019431-154019437 73 0.8986 50 0.33
6
 CDS 461-544 154019061-154019078 / 154019197-154019262 84 0.8184 50 0.31
7
 CDS 545-629 154018976-154019060 85 0.9779 50 0.38
8
 CDS 631-723 154018695-154018787 93 0.8070 50 0.35
9
 CDS 726-853 154018322-154018355 / 154018599-154018692 128 0.9004 50 0.30
10
 CDS 855-965 154018040-154018120 / 154018291-154018320 111 0.8343 50 0.31
11
 CDS 966-1048 154017019-154017067 / 154018006-154018039 83 0.7740 50 0.27
12
 CDS 1054-1139 154016624-154016644 / 154016949-154017013 86 0.8604 50 0.37
13
 CDS 1141-1235 154016528-154016622 95 0.9025 50 0.38
14
 CDS 1237-1341 154016083-154016097 / 154016437-154016526 105 0.8813 50 0.39
15
 CDS 1346-1453 154014218-154014278 / 154016032-154016078 108 0.8479 50 0.33
16
 CDS 1454-1541 154014130-154014217 88 0.9376 50 0.46
17
 CDS 1542-1639 154013424-154013433 / 154014042-154014129 98 0.9068 50 0.38
18
 CDS 1642-1740 154013323-154013421 99 0.8285 50 0.35
19
 CDS 1741-1830 154013233-154013322 90 0.9212 50 0.43
20
 CDS 1833-1923 154013140-154013230 91 0.9023 50 0.49
21
 CDS 1924-2019 154013044-154013139 96 0.9150 50 0.42
22
 CDS 2022-2107 154012592-154012677 86 0.8691 50 0.29
23
 CDS 2111-2208 154011880-154011917 / 154012529-154012588 98 0.8727 50 0.35
24
 CDS,3'UTR 2209-2309 154011779-154011879 101 0.8420 50 0.28
25
 3'UTR 2311-2426 154011662-154011777 116 0.9178 50 0.39
26
 3'UTR 2428-2560 154011528-154011660 133 0.8002 50 0.31
27
 3'UTR 2561-2657 154011431-154011527 97 0.9046 50 0.43
28
 3'UTR 2660-2766 154011322-154011428 107 0.9443 50 0.52
29
 3'UTR 2768-2858 154011230-154011320 91 0.9486 50 0.43
30
 3'UTR 2860-2978 154011110-154011228 119 0.9702 50 0.48
31
 3'UTR 2979-3072 154011016-154011109 94 0.8738 50 0.27
32
 3'UTR 3074-3170 154010918-154011014 97 0.9132 50 0.42
33
 3'UTR 3171-3260 154010828-154010917 90 0.9143 50 0.36
34
 3'UTR 3265-3350 154010738-154010823 86 0.9242 50 0.34
35
 3'UTR 3351-3449 154010639-154010737 99 0.9073 50 0.32
36
 3'UTR 3450-3579 154010509-154010638 130 0.8977 60 0.35
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
12
IRAK1

Aoi: Chr: Coords Strand:
IRAK1 X 154016624 - 154016644, 154016949 - 154017013 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: IRAK1(-)
  • Length Length of region: 86 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
1
production / 05e29e215d / 2026-04-03 19:22