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?

CLOCK
ENST00000513440 (-) ENSG00000134852 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 129-234 55509960-55510065 106 0.3491 50 0.28
2
 5'UTR 235-336 55489412-55489465 / 55509912-55509959 102 0.3140 50 0.27
3
 5'UTR,CDS 337-428 55482775-55482828 / 55489374-55489411 92 0.7014 50 0.20
4
 CDS 429-536 55478952-55478963 / 55479640-55479699 / 55482739-55482774 108 0.4608 50 0.21
5
 CDS 537-627 55478861-55478951 91 0.5309 50 0.28
6
 CDS 629-719 55476009-55476054 / 55478815-55478859 91 0.6239 50 0.29
7
 CDS 720-832 55470740-55470806 / 55475963-55476008 113 0.5521 50 0.23
8
 CDS 833-932 55463729-55463805 / 55470717-55470739 100 0.6499 50 0.30
9
 CDS 934-1023 55459215-55459261 / 55463685-55463727 90 0.8640 50 0.31
10
 CDS 1025-1108 55458993-55459010 / 55459148-55459213 84 0.5098 50 0.35
11
 CDS 1109-1211 55456299-55456300 / 55458892-55458992 103 0.5927 50 0.34
12
 CDS 1212-1306 55455990-55456003 / 55456218-55456298 95 0.7224 50 0.27
13
 CDS 1308-1415 55453809-55453824 / 55455897-55455988 108 0.6411 50 0.26
14
 CDS 1416-1517 55453707-55453808 102 0.4939 50 0.25
15
 CDS 1522-1624 55450232-55450232 / 55453054-55453129 / 55453677-55453702 103 0.6244 50 0.27
16
 CDS 1626-1713 55450143-55450230 88 0.6493 50 0.31
17
 CDS 1715-1790 55449472-55449496 / 55450091-55450141 76 0.6611 50 0.28
18
 CDS 1792-1878 55448857-55448868 / 55449396-55449470 87 0.4895 50 0.22
19
 CDS 1879-1972 55444770-55444785 / 55448779-55448856 94 0.5535 50 0.31
20
 CDS 1973-2051 55444691-55444769 79 0.4611 50 0.33
21
 CDS 2052-2151 55443855-55443896 / 55444633-55444690 100 0.4155 50 0.32
22
 CDS 2155-2240 55443766-55443851 86 0.7845 50 0.34
23
 CDS 2241-2318 55443688-55443765 78 0.6214 50 0.30
24
 CDS 2320-2396 55442558-55442634 77 0.4923 50 0.28
25
 CDS 2397-2482 55442472-55442557 86 0.5671 50 0.33
26
 CDS 2486-2583 55438477-55438537 / 55442432-55442468 98 0.6347 50 0.38
27
 CDS 2586-2680 55438380-55438474 95 0.6366 50 0.32
28
 CDS 2681-2759 55438301-55438379 79 0.6156 50 0.30
29
 CDS 2760-2846 55435527-55435594 / 55438282-55438300 87 0.4963 50 0.32
30
 CDS 2848-2918 55435455-55435525 71 0.3167 50 0.28
31
 CDS,3'UTR 2921-3009 55435364-55435452 89 0.6527 50 0.38
32
 3'UTR 3011-3124 55435249-55435362 114 0.7081 50 0.32
33
 3'UTR 3125-3233 55435140-55435248 109 0.5753 50 0.30
34
 3'UTR 3234-3335 55435038-55435139 102 0.5178 50 0.28
35
 3'UTR 3336-3425 55434948-55435037 90 0.5769 50 0.38
36
 3'UTR 3426-3533 55434840-55434947 108 0.4841 50 0.33
37
 3'UTR 3534-3630 55434743-55434839 97 0.5515 50 0.30
38
 3'UTR 3631-3770 55434603-55434742 140 0.7495 50 0.44
39
 3'UTR 3781-3898 55434475-55434592 118 0.3223 50 0.32
40
 3'UTR 3905-4015 55434358-55434468 111 0.5305 50 0.32
41
 3'UTR 4016-4127 55434246-55434357 112 0.6075 50 0.40
42
 3'UTR 4130-4237 55434136-55434243 108 0.7509 50 0.40
43
 3'UTR 4240-4348 55434025-55434133 109 0.5876 50 0.40
44
 3'UTR 4350-4444 55433929-55434023 95 0.5468 50 0.30
45
 3'UTR 4446-4541 55433832-55433927 96 0.3589 50 0.32
46
 3'UTR 4543-4626 55433747-55433830 84 0.5251 50 0.32
47
 3'UTR 4630-4719 55433654-55433743 90 0.4997 50 0.34
48
 3'UTR 4720-4815 55433558-55433653 96 0.3729 50 0.32
49
 3'UTR 4816-4914 55433459-55433557 99 0.5983 50 0.38
50
 3'UTR 4917-5013 55433360-55433456 97 0.4644 50 0.31
51
 3'UTR 5014-5100 55433273-55433359 87 0.4340 50 0.33
52
 3'UTR 5101-5189 55433184-55433272 89 0.5477 50 0.40
53
 3'UTR 5190-5307 55433066-55433183 118 0.4327 50 0.34
54
 3'UTR 5309-5398 55432975-55433064 90 0.5582 50 0.33
55
 3'UTR 5399-5485 55432888-55432974 87 0.3627 50 0.30
56
 3'UTR 5486-5582 55432791-55432887 97 0.4623 50 0.42
57
 3'UTR 5583-5699 55432674-55432790 117 0.6075 50 0.43
58
 3'UTR 5700-5811 55432562-55432673 112 0.6944 50 0.50
59
 3'UTR 5812-5968 55432405-55432561 157 0.2104 50 0.37
60
 3'UTR 5970-6081 55432292-55432403 112 0.2326 50 0.32
61
 3'UTR 6082-6183 55432190-55432291 102 0.2925 50 0.32
62
 3'UTR 6185-6295 55432078-55432188 111 0.4075 50 0.32
63
 3'UTR 6299-6413 55431960-55432074 115 0.4061 50 0.28
64
 3'UTR 6415-6507 55431866-55431958 93 0.4054 50 0.32
65
 3'UTR 6511-6604 55431769-55431862 94 0.5529 50 0.29
66
 3'UTR 6605-6729 55431644-55431768 125 0.6112 50 0.36
67
 3'UTR 6733-6841 55431532-55431640 109 0.7156 50 0.34
68
 3'UTR 6848-6956 55431417-55431525 109 0.5181 50 0.32
69
 3'UTR 6959-7054 55431319-55431414 96 0.4231 50 0.26
70
 3'UTR 7055-7155 55431218-55431318 101 0.5467 50 0.40
71
 3'UTR 7156-7238 55431135-55431217 83 0.4409 50 0.29
72
 3'UTR 7239-7334 55431039-55431134 96 0.4934 50 0.35
73
 3'UTR 7335-7440 55430933-55431038 106 0.5524 50 0.32
74
 3'UTR 7443-7556 55430817-55430930 114 0.4900 50 0.25
75
 3'UTR 7559-7665 55430708-55430814 107 0.2891 50 0.23
76
 3'UTR 7666-7776 55430597-55430707 111 0.5330 50 0.34
77
 3'UTR 7777-7895 55430478-55430596 119 0.6585 50 0.43
78
 3'UTR 7896-7993 55430380-55430477 98 0.6007 50 0.42
79
 3'UTR 7994-8120 55430253-55430379 127 0.4381 50 0.31
80
 3'UTR 8124-8223 55430150-55430249 100 0.1730 50 0.29
81
 3'UTR 8224-8342 55430031-55430149 119 0.3590 50 0.32
82
 3'UTR 8346-8474 55429899-55430027 129 0.3470 50 0.33
83
 3'UTR 8477-8561 55429812-55429896 85 0.6210 50 0.48
84
 3'UTR 8565-8678 55429695-55429808 114 0.2441 50 0.40
85
 3'UTR 8680-8778 55429595-55429693 99 0.4354 50 0.46
86
 3'UTR 8779-8888 55429485-55429594 110 0.3259 50 0.39
87
 3'UTR 8889-8974 55429399-55429484 86 0.3877 50 0.50
88
 3'UTR 8975-9059 55429314-55429398 85 0.4961 50 0.38
89
 3'UTR 9060-9151 55429222-55429313 92 0.3647 50 0.37
90
 3'UTR 9153-9270 55429103-55429220 118 0.3180 50 0.44
91
 3'UTR 9276-9516 55428857-55429097 241 0.2738 50 0.44
92
 3'UTR 9518-9818 55428555-55428855 301 0.3377 50 0.42
93
 3'UTR 9819-9913 55428460-55428554 95 0.4091 50 0.33
94
 3'UTR 9914-10037 55428336-55428459 124 0.4648 50 0.39
95
 3'UTR 10038-10150 55428223-55428335 113 0.7337 50 0.45
96
 3'UTR 10153-10297 55428076-55428220 145 0.5556 72 0.49
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
14
CLOCK

Aoi: Chr: Coords Strand:
CLOCK 4 55453707 - 55453808 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: CLOCK(-)
  • Length Length of region: 102 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 4 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 / 2026-02-04 02:42