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?

MLLT6
ENST00000621332 (+) ENSG00000275023 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 381-494 38705653-38705741 / 38706950-38706974 114 0.4909 50 0.38
2
 CDS 495-598 38706975-38707029 / 38707486-38707534 104 0.6456 50 0.33
3
 CDS 599-701 38707535-38707540 / 38707763-38707859 103 0.7472 50 0.41
4
 CDS 703-799 38707861-38707872 / 38709173-38709257 97 0.6646 50 0.35
5
 CDS 800-899 38709258-38709276 / 38709482-38709562 100 0.6140 50 0.34
6
 CDS 900-1020 38709563-38709575 / 38711847-38711954 121 0.7418 50 0.35
7
 CDS 1022-1093 38711956-38712014 / 38712691-38712703 72 0.6946 50 0.33
8
 CDS 1094-1168 38712704-38712778 75 0.6675 50 0.37
9
 CDS 1169-1255 38712779-38712789 / 38715612-38715687 87 0.6936 50 0.43
10
 CDS 1256-1353 38715688-38715785 98 0.4574 50 0.34
11
 CDS 1355-1447 38715787-38715828 / 38716367-38716417 93 0.6625 50 0.38
12
 CDS 1448-1574 38716418-38716544 127 0.3989 50 0.36
13
 CDS 1575-1817 38716545-38716787 243 0.4166 50 0.44
14
 CDS 1818-1914 38716788-38716884 97 0.4773 50 0.43
15
 CDS 1915-2021 38716885-38716981 / 38717432-38717441 107 0.7384 50 0.43
16
 CDS 2022-2109 38717442-38717529 88 0.5267 50 0.42
17
 CDS 2113-2188 38717533-38717608 76 0.4270 50 0.37
18
 CDS 2189-2587 38717609-38717613 / 38717845-38717953 / 38720372-38720443 399 0.5240 50 0.39
19
 CDS 2590-2679 38720446-38720535 90 0.6299 50 0.47
20
 CDS 2680-2763 38720536-38720569 / 38720659-38720708 84 0.3501 50 0.36
21
 CDS 2764-3136 38720709-38720747 / 38721878-38722211 373 0.5234 50 0.44
22
 CDS 3137-3215 38722212-38722227 / 38722678-38722740 79 0.4910 50 0.38
23
 CDS 3217-3310 38722742-38722768 / 38724620-38724686 94 0.5077 50 0.42
24
 CDS 3311-3407 38724687-38724783 97 0.4642 50 0.41
25
 CDS 3410-3497 38724786-38724873 88 0.6669 50 0.45
26
 CDS 3498-3588 38724874-38724964 91 0.4117 50 0.37
27
 CDS,3'UTR 3589-3688 38724965-38724976 / 38725557-38725644 100 0.5902 50 0.45
28
 3'UTR 3689-3801 38725645-38725757 113 0.3318 50 0.44
29
 3'UTR 3802-3897 38725758-38725853 96 0.6120 50 0.36
30
 3'UTR 3898-4004 38725854-38725960 107 0.6156 50 0.34
31
 3'UTR 4005-4118 38725961-38726074 114 0.7024 50 0.44
32
 3'UTR 4122-4216 38726078-38726172 95 0.7717 50 0.50
33
 3'UTR 4218-4324 38726174-38726280 107 0.7717 50 0.42
34
 3'UTR 4325-4485 38726281-38726441 161 0.8033 50 0.41
35
 3'UTR 4486-4573 38726442-38726529 88 0.6441 50 0.31
36
 3'UTR 4574-4681 38726530-38726637 108 0.5855 50 0.38
37
 3'UTR 4684-4763 38726640-38726719 80 0.5171 50 0.46
38
 3'UTR 4768-4865 38726724-38726821 98 0.6970 50 0.37
39
 3'UTR 4866-4934 38726822-38726890 69 0.4786 50 0.37
40
 3'UTR 4935-5035 38726891-38726991 101 0.7132 50 0.38
41
 3'UTR 5037-5204 38726993-38727160 168 0.5707 50 0.38
42
 3'UTR 5206-5323 38727162-38727279 118 0.4725 50 0.36
43
 3'UTR 5324-5501 38727280-38727457 178 0.1691 50 0.34
44
 3'UTR 5504-5611 38727460-38727567 108 0.4317 50 0.43
45
 3'UTR 5614-5708 38727570-38727664 95 0.7279 50 0.57
46
 3'UTR 5709-5809 38727665-38727765 101 0.9083 50 0.67
47
 3'UTR 5811-5899 38727767-38727855 89 0.7385 50 0.46
48
 3'UTR 5900-5997 38727856-38727953 98 0.5274 50 0.33
49
 3'UTR 6001-6075 38727957-38728031 75 0.5014 50 0.44
50
 3'UTR 6076-6311 38728032-38728267 236 0.5782 50 0.46
51
 3'UTR 6312-6420 38728268-38728376 109 0.4104 50 0.42
52
 3'UTR 6422-6560 38728378-38728516 139 0.7108 50 0.44
53
 3'UTR 6561-6679 38728517-38728635 119 0.5517 50 0.37
54
 3'UTR 6680-6770 38728636-38728726 91 0.6549 50 0.50
55
 3'UTR 6771-6899 38728727-38728855 129 0.3602 50 0.41
56
 3'UTR 6901-7030 38728857-38728986 130 0.4567 50 0.43
57
 3'UTR 7033-7130 38728989-38729086 98 0.4133 50 0.40
58
 3'UTR 7131-7217 38729087-38729173 87 0.5132 50 0.38
59
 3'UTR 7218-7346 38729174-38729302 129 0.3840 50 0.37
60
 3'UTR 7347-7449 38729303-38729405 103 0.4499 50 0.41
61
 3'UTR 7450-7558 38729406-38729514 109 0.5194 50 0.49
62
 3'UTR 7560-7668 38729516-38729624 109 0.4349 56 0.44
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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MLLT6

Aoi: Chr: Coords Strand:
MLLT6 17 38705653 - 38705741, 38706950 - 38706974 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: MLLT6(+)
  • Length Length of region: 114 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 5 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 / b252b9f76a / 2025-07-17 08:30