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?

AGO1
ENST00000373204 (+) ENSG00000092847 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 239-333 35888427-35888521 95 0.6200 50 0.37
2
 CDS 334-434 35888522-35888610 / 35892557-35892568 101 0.5131 50 0.31
3
 CDS 435-528 35892569-35892662 94 0.4219 50 0.25
4
 CDS 529-638 35892663-35892677 / 35893097-35893191 110 0.3282 50 0.31
5
 CDS 641-744 35893194-35893278 / 35893674-35893692 104 0.5337 50 0.36
6
 CDS 746-855 35893694-35893803 110 0.4701 50 0.32
7
 CDS 856-955 35893804-35893810 / 35894037-35894129 100 0.7348 50 0.34
8
 CDS 957-1054 35894131-35894171 / 35894315-35894371 98 0.4784 50 0.27
9
 CDS 1055-1150 35894372-35894402 / 35895122-35895186 96 0.4931 50 0.31
10
 CDS 1151-1227 35895187-35895263 77 0.4617 50 0.32
11
 CDS 1228-1317 35895264-35895269 / 35901474-35901557 90 0.4963 50 0.33
12
 CDS 1319-1405 35901559-35901593 / 35901948-35901999 87 0.8107 50 0.38
13
 CDS 1406-1501 35902000-35902070 / 35902204-35902228 96 0.8055 50 0.36
14
 CDS 1502-1601 35902229-35902328 100 0.5808 50 0.29
15
 CDS 1606-1701 35902333-35902337 / 35906935-35907025 96 0.4427 50 0.24
16
 CDS 1703-1804 35907027-35907119 / 35913842-35913850 102 0.4959 50 0.32
17
 CDS 1805-1902 35913851-35913948 98 0.6561 50 0.28
18
 CDS 1903-1992 35913949-35914001 / 35914184-35914220 90 0.2957 50 0.28
19
 CDS 1994-2077 35914222-35914274 / 35915348-35915378 84 0.5910 50 0.36
20
 CDS 2079-2175 35915380-35915476 97 0.3383 50 0.25
21
 CDS 2176-2260 35915477-35915542 / 35917593-35917611 85 0.7744 50 0.29
22
 CDS 2264-2350 35917615-35917701 87 0.6130 50 0.30
23
 CDS 2355-2441 35917706-35917727 / 35918322-35918386 87 0.6818 50 0.29
24
 CDS 2447-2535 35918392-35918423 / 35919055-35919111 89 0.6605 50 0.32
25
 CDS 2537-2621 35919113-35919197 85 0.4101 50 0.31
26
 CDS 2624-2724 35919200-35919254 / 35919499-35919544 101 0.5458 50 0.32
27
 CDS,3'UTR 2725-2817 35919545-35919637 93 0.5737 50 0.33
28
 3'UTR 2818-2924 35919638-35919744 107 0.5155 50 0.34
29
 3'UTR 2933-3007 35919753-35919827 75 0.4827 50 0.32
30
 3'UTR 3009-3088 35919829-35919908 80 0.5552 50 0.34
31
 3'UTR 3090-3199 35919910-35920019 110 0.7033 50 0.30
32
 3'UTR 3203-3307 35920023-35920127 105 0.6148 50 0.25
33
 3'UTR 3308-3417 35920128-35920237 110 0.6916 50 0.33
34
 3'UTR 3420-3503 35920240-35920323 84 0.5871 50 0.38
35
 3'UTR 3504-3605 35920324-35920425 102 0.3906 50 0.37
36
 3'UTR 3606-3711 35920426-35920531 106 0.3647 50 0.34
37
 3'UTR 3714-3802 35920534-35920622 89 0.5803 50 0.28
38
 3'UTR 3803-3898 35920623-35920718 96 0.5755 50 0.37
39
 3'UTR 3902-4014 35920722-35920834 113 0.5105 50 0.37
40
 3'UTR 4015-4109 35920835-35920929 95 0.5005 50 0.32
41
 3'UTR 4111-4218 35920931-35921038 108 0.7096 50 0.43
42
 3'UTR 4220-4324 35921040-35921144 105 0.5984 50 0.34
43
 3'UTR 4325-4443 35921145-35921263 119 0.3517 50 0.33
44
 3'UTR 4457-4610 35921277-35921430 154 0.5410 50 0.48
45
 3'UTR 4611-4729 35921431-35921549 119 0.8172 50 0.60
46
 3'UTR 4734-4834 35921554-35921654 101 0.6138 50 0.36
47
 3'UTR 4835-4923 35921655-35921743 89 0.4876 50 0.39
48
 3'UTR 4924-5030 35921744-35921850 107 0.6479 50 0.50
49
 3'UTR 5033-5119 35921853-35921939 87 0.4958 50 0.34
50
 3'UTR 5121-5247 35921941-35922067 127 0.5406 50 0.36
51
 3'UTR 5248-5346 35922068-35922166 99 0.4484 50 0.34
52
 3'UTR 5348-5452 35922168-35922272 105 0.7393 50 0.39
53
 3'UTR 5454-5574 35922274-35922394 121 0.5179 50 0.31
54
 3'UTR 5575-5694 35922395-35922514 120 0.7146 50 0.38
55
 3'UTR 5695-5816 35922515-35922636 122 0.3096 50 0.36
56
 3'UTR 5818-5917 35922638-35922737 100 0.4034 50 0.33
57
 3'UTR 5918-6013 35922738-35922833 96 0.7741 50 0.40
58
 3'UTR 6017-6165 35922837-35922985 149 0.7121 50 0.35
59
 3'UTR 6169-6269 35922989-35923089 101 0.3470 50 0.27
60
 3'UTR 6271-6371 35923091-35923191 101 0.8087 50 0.44
61
 3'UTR 6372-6484 35923192-35923304 113 0.6434 50 0.31
62
 3'UTR 6486-6592 35923306-35923412 107 0.7105 50 0.31
63
 3'UTR 6594-6694 35923414-35923514 101 0.7723 50 0.34
64
 3'UTR 6696-6803 35923516-35923623 108 0.6762 50 0.34
65
 3'UTR 6805-6927 35923625-35923747 123 0.7574 50 0.41
66
 3'UTR 6928-7031 35923748-35923851 104 0.5630 50 0.35
67
 3'UTR 7033-7127 35923853-35923947 95 0.6156 50 0.32
68
 3'UTR 7132-7245 35923952-35924065 114 0.6803 50 0.38
69
 3'UTR 7246-7375 35924066-35924195 130 0.6548 50 0.43
70
 3'UTR 7376-7461 35924196-35924281 86 0.4302 50 0.37
71
 3'UTR 7466-10062 35924286-35926882 2597 0.3194 40 0.41
Error
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
37
AGO1

Aoi: Chr: Coords Strand:
AGO1 1 35920534 - 35920622 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: AGO1(+)
  • 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 / 6840c0a13a / 2026-06-08 09:57