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?

RUNX1
ENST00000344691 (-) ENSG00000159216 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 1-88 34888603-34888690 88 0.7015 50 0.32
2
 5'UTR 89-222 34888469-34888602 134 0.6225 50 0.28
3
 5'UTR 227-357 34888334-34888464 131 0.6149 50 0.25
4
 5'UTR 360-460 34888231-34888331 101 0.6726 50 0.30
5
 5'UTR 470-583 34888108-34888221 114 0.7423 50 0.27
6
 5'UTR 585-669 34888022-34888106 85 0.7431 50 0.25
7
 5'UTR 670-776 34887915-34888021 107 0.6486 50 0.26
8
 5'UTR 779-869 34887822-34887912 91 0.4437 50 0.20
9
 5'UTR 871-982 34887709-34887820 112 0.5313 50 0.26
10
 5'UTR 984-1094 34887597-34887707 111 0.7468 50 0.28
11
 5'UTR 1096-1196 34887495-34887595 101 0.6114 50 0.32
12
 5'UTR 1197-1288 34887403-34887494 92 0.6464 50 0.20
13
 5'UTR 1290-1388 34887303-34887401 99 0.7797 50 0.28
14
 5'UTR 1389-1520 34887171-34887302 132 0.6350 50 0.36
15
 5'UTR,CDS 1521-1625 34887066-34887170 105 0.4077 50 0.31
16
 CDS 1628-1723 34886968-34887063 96 0.6922 50 0.39
17
 CDS 1725-1821 34886870-34886966 97 0.3925 50 0.25
18
 CDS 1822-1925 34880637-34880713 / 34886843-34886869 104 0.5253 50 0.25
19
 CDS 1927-2024 34859560-34859578 / 34880557-34880635 98 0.7241 50 0.29
20
 CDS 2025-2097 34859487-34859559 73 0.6350 50 0.22
21
 CDS 2098-2188 34834524-34834601 / 34859474-34859486 91 0.6693 50 0.27
22
 CDS 2191-2260 34834452-34834521 70 0.6055 50 0.23
23
 CDS 2261-2339 34799426-34799462 / 34834410-34834451 79 0.5258 50 0.27
24
 CDS 2340-2425 34799340-34799425 86 0.5897 50 0.27
25
 CDS 2428-2506 34792569-34792610 / 34799301-34799337 79 0.5143 50 0.20
26
 CDS 2507-2582 34792493-34792568 76 0.5797 50 0.30
27
 CDS 2586-2669 34792406-34792489 84 0.3247 50 0.36
28
 CDS 2671-2764 34792311-34792404 94 0.3638 50 0.36
29
 CDS 2766-2839 34792236-34792309 74 0.6173 50 0.39
30
 CDS 2840-2929 34792146-34792235 90 0.4041 50 0.40
31
 CDS,3'UTR 2932-3025 34792050-34792143 94 0.6438 50 0.45
32
 3'UTR 3029-3123 34791952-34792046 95 0.5220 50 0.42
33
 3'UTR 3124-3214 34791861-34791951 91 0.6738 50 0.42
34
 3'UTR 3215-3311 34791764-34791860 97 0.4117 50 0.26
35
 3'UTR 3313-3441 34791634-34791762 129 0.5948 50 0.29
36
 3'UTR 3442-3564 34791511-34791633 123 0.6606 50 0.33
37
 3'UTR 3565-3713 34791362-34791510 149 0.6978 50 0.34
38
 3'UTR 3717-3831 34791244-34791358 115 0.6564 50 0.38
39
 3'UTR 3833-3928 34791147-34791242 96 0.5075 50 0.31
40
 3'UTR 3929-4027 34791048-34791146 99 0.3093 50 0.29
41
 3'UTR 4028-4134 34790941-34791047 107 0.3152 50 0.27
42
 3'UTR 4135-4224 34790851-34790940 90 0.7547 50 0.40
43
 3'UTR 4225-4318 34790757-34790850 94 0.5384 50 0.35
44
 3'UTR 4325-4419 34790656-34790750 95 0.5611 50 0.47
45
 3'UTR 4420-4523 34790552-34790655 104 0.6896 50 0.42
46
 3'UTR 4524-4636 34790439-34790551 113 0.5937 50 0.42
47
 3'UTR 4639-4751 34790324-34790436 113 0.5134 50 0.27
48
 3'UTR 4755-4864 34790211-34790320 110 0.6320 50 0.31
49
 3'UTR 4865-4964 34790111-34790210 100 0.5941 50 0.23
50
 3'UTR 4966-5060 34790015-34790109 95 0.8349 50 0.39
51
 3'UTR 5061-5154 34789921-34790014 94 0.6513 50 0.37
52
 3'UTR 5155-5247 34789828-34789920 93 0.6935 50 0.46
53
 3'UTR 5248-5362 34789713-34789827 115 0.5389 50 0.30
54
 3'UTR 5363-5492 34789583-34789712 130 0.8239 50 0.41
55
 3'UTR 5493-5593 34789482-34789582 101 0.8201 50 0.38
56
 3'UTR 5594-5705 34789370-34789481 112 0.7824 50 0.31
57
 3'UTR 5706-5787 34789288-34789369 82 0.6701 50 0.35
58
 3'UTR 5791-5935 34789140-34789284 145 0.4862 50 0.44
59
 3'UTR 5938-6018 34789057-34789137 81 0.6732 50 0.35
60
 3'UTR 6019-6121 34788954-34789056 103 0.7818 50 0.35
61
 3'UTR 6122-6268 34788807-34788953 147 0.7386 50 0.38
62
 3'UTR 6269-6412 34788663-34788806 144 0.8515 50 0.37
63
 3'UTR 6413-6534 34788541-34788662 122 0.4613 50 0.30
64
 3'UTR 6535-6649 34788426-34788540 115 0.7753 50 0.32
65
 3'UTR 6651-6776 34788299-34788424 126 0.4618 50 0.47
66
 3'UTR 6777-6838 34788237-34788298 62 0.3675 31 0.43
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
23
RUNX1

Aoi: Chr: Coords Strand:
RUNX1 21 34799426 - 34799462, 34834410 - 34834451 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: RUNX1(-)
  • Length Length of region: 79 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 / 6f779e32bc / 2026-02-04 17:39