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?

MYH10
ENST00000687178 (-) ENSG00000133026 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 498-603 8623172-8623277 106 0.7901 50 0.31
2
 CDS 604-703 8623072-8623171 100 0.5824 50 0.26
3
 CDS 710-803 8622972-8623065 94 0.4489 50 0.26
4
 CDS 804-908 8604948-8604982 / 8622902-8622971 105 0.4756 50 0.27
5
 CDS 911-1001 8604855-8604945 91 0.4011 50 0.26
6
 CDS 1004-1102 8577295-8577338 / 8589081-8589108 / 8604826-8604852 99 0.5649 50 0.26
7
 CDS 1105-1223 8569778-8569812 / 8577236-8577292 119 0.7645 50 0.28
8
 CDS 1224-1333 8553967-8554018 / 8569720-8569777 110 0.3803 50 0.26
9
 CDS 1334-1434 8552056-8552144 / 8553955-8553966 101 0.4131 50 0.30
10
 CDS 1435-1529 8548703-8548787 / 8552046-8552055 95 0.5988 50 0.31
11
 CDS 1533-1630 8548367-8548408 / 8548644-8548699 98 0.4519 50 0.33
12
 CDS 1634-1732 8546615-8546662 / 8548313-8548363 99 0.5039 50 0.30
13
 CDS 1733-1818 8545586-8545600 / 8546544-8546614 86 0.6579 50 0.34
14
 CDS 1820-1913 8545491-8545584 94 0.5291 50 0.26
15
 CDS 1917-2017 8542220-8542280 / 8545448-8545487 101 0.3843 50 0.25
16
 CDS 2018-2109 8542128-8542219 92 0.4390 50 0.27
17
 CDS 2110-2199 8535863-8535931 / 8542107-8542127 90 0.5085 50 0.25
18
 CDS 2207-2290 8535772-8535855 84 0.4431 50 0.28
19
 CDS 2291-2388 8535418-8535501 / 8535758-8535771 98 0.5408 50 0.22
20
 CDS 2390-2499 8521206-8521285 / 8535387-8535416 110 0.4948 50 0.24
21
 CDS 2500-2584 8521121-8521205 85 0.3135 50 0.27
22
 CDS 2590-2683 8520930-8520999 / 8521092-8521115 94 0.3988 50 0.32
23
 CDS 2685-2780 8518906-8518950 / 8520878-8520928 96 0.2351 50 0.30
24
 CDS 2785-2884 8518713-8518791 / 8518881-8518901 100 0.5686 50 0.28
25
 CDS 2885-2978 8513883-8513894 / 8518631-8518712 94 0.5459 50 0.33
26
 CDS 2980-3079 8513666-8513669 / 8513786-8513881 100 0.6721 50 0.30
27
 CDS 3080-3176 8513569-8513665 97 0.7750 50 0.24
28
 CDS 3178-3270 8512595-8512657 / 8513538-8513567 93 0.5850 50 0.29
29
 CDS 3272-3367 8512498-8512593 96 0.4173 50 0.25
30
 CDS 3368-3440 8509924-8509949 / 8512451-8512497 73 0.4416 50 0.30
31
 CDS 3443-3535 8509829-8509921 93 0.4073 50 0.26
32
 CDS 3536-3625 8508605-8508677 / 8509812-8509828 90 0.5214 50 0.29
33
 CDS 3626-3711 8506455-8506489 / 8508554-8508604 86 0.6302 50 0.24
34
 CDS 3712-3798 8506368-8506454 87 0.7641 50 0.29
35
 CDS 3799-3888 8504867-8504906 / 8506318-8506367 90 0.4575 50 0.29
36
 CDS 3895-3977 8504778-8504860 83 0.6233 50 0.29
37
 CDS 3978-4065 8500967-8500970 / 8504694-8504777 88 0.6613 50 0.34
38
 CDS 4066-4149 8500883-8500966 84 0.5531 50 0.29
39
 CDS 4150-4229 8499454-8499476 / 8500826-8500882 80 0.5859 50 0.28
40
 CDS 4230-4329 8499354-8499453 100 0.6111 50 0.29
41
 CDS 4331-4431 8495224-8495241 / 8499270-8499352 101 0.5086 50 0.27
42
 CDS 4433-4528 8493876-8493885 / 8495137-8495222 96 0.4128 50 0.30
43
 CDS 4529-4619 8493785-8493875 91 0.3896 50 0.25
44
 CDS 4622-4713 8492983-8493024 / 8493733-8493782 92 0.6062 50 0.32
45
 CDS 4714-4807 8492889-8492982 94 0.7177 50 0.33
46
 CDS 4811-4890 8492806-8492885 80 0.5066 50 0.29
47
 CDS 4895-4988 8492442-8492509 / 8492776-8492801 94 0.5358 50 0.25
48
 CDS 4989-5075 8492355-8492441 87 0.6751 50 0.28
49
 CDS 5077-5157 8490529-8490552 / 8492297-8492353 81 0.5296 50 0.30
50
 CDS 5158-5256 8490430-8490528 99 0.6102 50 0.30
51
 CDS 5257-5344 8490342-8490429 88 0.4703 50 0.27
52
 CDS 5345-5448 8487493-8487594 / 8490340-8490341 104 0.4164 50 0.29
53
 CDS 5449-5540 8484235-8484266 / 8487433-8487492 92 0.3336 50 0.28
54
 CDS 5541-5633 8484142-8484234 93 0.3703 50 0.29
55
 CDS 5636-5724 8481324-8481410 / 8484138-8484139 89 0.6280 50 0.37
56
 CDS 5725-5826 8480426-8480525 / 8481322-8481323 102 0.3391 50 0.29
57
 CDS 5827-5907 8480262-8480318 / 8480402-8480425 81 0.4364 50 0.31
58
 CDS 5908-5998 8480171-8480261 91 0.4308 50 0.27
59
 CDS 5999-6087 8478419-8478446 / 8480110-8480170 89 0.4674 50 0.29
60
 CDS 6088-6181 8477036-8477048 / 8478338-8478418 94 0.4150 50 0.25
61
 CDS 6182-6266 8476951-8477035 85 0.5798 50 0.28
62
 CDS 6268-6363 8475927-8475948 / 8476876-8476949 96 0.5865 50 0.30
63
 CDS 6365-6456 8475834-8475925 92 0.6226 50 0.30
64
 CDS,3'UTR 6457-6544 8475746-8475833 88 0.6477 50 0.34
65
 3'UTR 6546-6645 8475645-8475744 100 0.6580 50 0.32
66
 3'UTR 6646-6738 8475552-8475644 93 0.2800 50 0.32
67
 3'UTR 6741-6844 8475446-8475549 104 0.2361 50 0.36
68
 3'UTR 6845-6935 8475355-8475445 91 0.3882 50 0.36
69
 3'UTR 6937-7035 8475255-8475353 99 0.1437 50 0.31
70
 3'UTR 7037-7140 8475150-8475253 104 0.6579 50 0.47
71
 3'UTR 7142-7253 8475037-8475148 112 0.3537 50 0.39
72
 3'UTR 7254-7340 8474950-8475036 87 0.5458 50 0.43
73
 3'UTR 7341-7446 8474844-8474949 106 0.5220 50 0.36
74
 3'UTR 7449-7559 8474731-8474841 111 0.5710 50 0.34
75
 3'UTR 7560-7659 8474631-8474730 100 0.3834 50 0.28
76
 3'UTR 7660-7763 8474527-8474630 104 0.1593 50 0.29
77
 3'UTR 7766-7876 8474414-8474524 111 0.2604 50 0.36
78
 3'UTR 7877-7929 8474361-8474413 53 0.2206 31 0.33
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
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MYH10

Aoi: Chr: Coords Strand:
MYH10 17 8513569 - 8513665 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: MYH10(-)
  • Length Length of region: 97 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 00:45