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?

CLASP1
ENST00000541377 (-) ENSG00000074054 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 50-146 121606140-121606180 / 121649372-121649427 97 0.3033 50 0.29
2
 5'UTR 148-234 121606052-121606138 87 0.3464 50 0.30
3
 5'UTR 235-323 121605963-121606051 89 0.5439 50 0.43
4
 5'UTR,CDS 324-448 121605838-121605962 125 0.7273 50 0.42
5
 CDS 450-545 121605741-121605836 96 0.3601 50 0.27
6
 CDS 549-657 121530254-121530325 / 121605701-121605737 109 0.4629 50 0.35
7
 CDS 660-751 121528694-121528780 / 121530247-121530251 92 0.5076 50 0.26
8
 CDS 752-846 121527813-121527890 / 121528677-121528693 95 0.4621 50 0.28
9
 CDS 848-929 121525852-121525920 / 121527799-121527811 82 0.5289 50 0.28
10
 CDS 930-1025 121515674-121515762 / 121525845-121525851 96 0.5769 50 0.32
11
 CDS 1026-1116 121469947-121469960 / 121503167-121503234 / 121515665-121515673 91 0.5728 50 0.30
12
 CDS 1118-1213 121469850-121469945 96 0.4530 50 0.26
13
 CDS 1214-1323 121462538-121462605 / 121469808-121469849 110 0.6081 50 0.27
14
 CDS 1326-1417 121461106-121461193 / 121462532-121462535 92 0.5495 50 0.26
15
 CDS 1418-1535 121460013-121460125 / 121461101-121461105 118 0.6893 50 0.35
16
 CDS 1537-1649 121458895-121458975 / 121459980-121460011 113 0.5081 50 0.29
17
 CDS 1650-1744 121457718-121457757 / 121458840-121458894 95 0.3940 50 0.28
18
 CDS 1745-1845 121450981-121450990 / 121451790-121451849 / 121457687-121457717 101 0.4150 50 0.25
19
 CDS 1848-1937 121449097-121449120 / 121450913-121450978 90 0.5338 50 0.25
20
 CDS 1938-2016 121449018-121449096 79 0.4948 50 0.30
21
 CDS 2018-2104 121448303-121448325 / 121448953-121449016 87 0.4477 50 0.28
22
 CDS 2107-2203 121447436-121447507 / 121448276-121448300 97 0.4439 50 0.30
23
 CDS 2204-2291 121447348-121447435 88 0.7461 50 0.32
24
 CDS 2292-2425 121430103-121430177 / 121447337-121447347 134 0.5689 50 0.30
25
 CDS 2428-2535 121425227-121425306 / 121430073-121430100 108 0.5440 50 0.37
26
 CDS 2536-2619 121425143-121425226 84 0.4691 50 0.33
27
 CDS 2622-2741 121409034-121409047 / 121410866-121410969 / 121425139-121425140 120 0.4701 50 0.26
28
 CDS 2742-2851 121407613-121407712 / 121409024-121409033 110 0.5670 50 0.29
29
 CDS 2854-2953 121407511-121407610 100 0.5201 50 0.30
30
 CDS 2958-3055 121404373-121404434 / 121407471-121407506 98 0.4759 50 0.23
31
 CDS 3056-3173 121401560-121401672 / 121401868-121401870 / 121404371-121404372 118 0.5058 50 0.28
32
 CDS 3177-3280 121398345-121398400 / 121401509-121401556 104 0.3956 50 0.29
33
 CDS 3281-3359 121397228-121397283 / 121398322-121398344 79 0.4744 50 0.29
34
 CDS 3360-3452 121387902-121387906 / 121397140-121397227 93 0.5551 50 0.28
35
 CDS 3453-3550 121387804-121387901 98 0.6915 50 0.33
36
 CDS 3552-3630 121387190-121387228 / 121387763-121387802 79 0.6198 50 0.32
37
 CDS 3631-3710 121377638-121377649 / 121387122-121387189 80 0.7207 50 0.40
38
 CDS 3713-3805 121377543-121377635 93 0.3945 50 0.25
39
 CDS 3808-3918 121367763-121367831 / 121377499-121377540 111 0.7701 50 0.44
40
 CDS 3919-3999 121367682-121367762 81 0.5698 50 0.30
41
 CDS 4000-4079 121367602-121367681 80 0.4250 50 0.27
42
 CDS 4081-4176 121365202-121365284 / 121367588-121367600 96 0.5724 50 0.27
43
 CDS 4178-4279 121365099-121365200 102 0.6214 50 0.28
44
 CDS 4280-4369 121363216-121363300 / 121365094-121365098 90 0.4937 50 0.28
45
 CDS 4370-4463 121348669-121348718 / 121363172-121363215 94 0.4516 50 0.30
46
 CDS 4464-4544 121348588-121348668 81 0.5108 50 0.36
47
 CDS 4546-4638 121347137-121347154 / 121348512-121348586 93 0.5549 50 0.28
48
 CDS 4639-4741 121340944-121340947 / 121347038-121347136 103 0.5499 50 0.29
49
 CDS 4742-4814 121340871-121340943 73 0.5019 50 0.28
50
 CDS,3'UTR 4816-4908 121340777-121340869 93 0.4765 50 0.35
51
 3'UTR 4909-5009 121340676-121340776 101 0.2231 50 0.31
52
 3'UTR 5010-5092 121340593-121340675 83 0.2355 50 0.26
53
 3'UTR 5095-5232 121340453-121340590 138 0.5822 50 0.29
54
 3'UTR 5234-5346 121340339-121340451 113 0.5795 50 0.33
55
 3'UTR 5347-5450 121340235-121340338 104 0.4976 50 0.31
56
 3'UTR 5456-5533 121340152-121340229 78 0.3840 50 0.34
57
 3'UTR 5534-5628 121340057-121340151 95 0.5216 50 0.42
58
 3'UTR 5630-5736 121339949-121340055 107 0.7373 50 0.36
59
 3'UTR 5738-5835 121339850-121339947 98 0.4617 50 0.35
60
 3'UTR 5838-5948 121339737-121339847 111 0.5858 50 0.33
61
 3'UTR 5949-6033 121339652-121339736 85 0.4988 50 0.28
62
 3'UTR 6034-6115 121339570-121339651 82 0.5995 50 0.39
63
 3'UTR 6116-6219 121339466-121339569 104 0.5648 50 0.33
64
 3'UTR 6226-6327 121339358-121339459 102 0.6376 50 0.35
65
 3'UTR 6328-6422 121339263-121339357 95 0.5492 50 0.37
66
 3'UTR 6423-6579 121339106-121339262 157 0.6475 50 0.38
67
 3'UTR 6580-6701 121338984-121339105 122 0.5431 50 0.33
68
 3'UTR 6704-6838 121338847-121338981 135 0.5803 50 0.34
69
 3'UTR 6839-6933 121338752-121338846 95 0.5718 50 0.40
70
 3'UTR 6934-7020 121338665-121338751 87 0.5652 50 0.31
71
 3'UTR 7024-7109 121338576-121338661 86 0.5179 50 0.38
72
 3'UTR 7110-7198 121338487-121338575 89 0.3991 50 0.41
73
 3'UTR 7199-7319 121338366-121338486 121 0.5287 50 0.51
74
 3'UTR 7322-7424 121338261-121338363 103 0.7770 50 0.46
75
 3'UTR 7428-7529 121338156-121338257 102 0.2363 50 0.35
76
 3'UTR 7530-7617 121338068-121338155 88 0.3925 50 0.37
77
 3'UTR 7619-7814 121337871-121338066 196 0.3179 73 0.42
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
11
CLASP1

Aoi: Chr: Coords Strand:
CLASP1 2 121469947 - 121469960, 121503167 - 121503234, 121515665 - 121515673 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: CLASP1(-)
  • Length Length of region: 91 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 / 6f779e32bc / 2026-02-03 20:19