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?

SAMD4A
ENST00000392067 (+) ENSG00000020577 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 1-120 54567612-54567731 120 0.6447 50 0.25
2
 5'UTR 121-202 54567732-54567813 82 0.6513 50 0.26
3
 5'UTR,CDS 203-317 54567814-54567928 115 0.6937 50 0.42
4
 CDS 319-430 54567930-54568041 112 0.8027 50 0.33
5
 CDS 432-515 54568043-54568112 / 54702062-54702075 84 0.7638 50 0.32
6
 CDS 519-605 54702079-54702165 87 0.6632 50 0.28
7
 CDS 607-696 54702167-54702256 90 0.6725 50 0.30
8
 CDS 698-794 54702258-54702354 97 0.5772 50 0.31
9
 CDS 797-881 54702357-54702441 85 0.6838 50 0.24
10
 CDS 883-982 54702443-54702542 100 0.7659 50 0.33
11
 CDS 983-1055 54702543-54702580 / 54737024-54737058 73 0.4949 50 0.23
12
 CDS 1056-1147 54737059-54737150 92 0.5317 50 0.38
13
 CDS 1148-1237 54737151-54737240 90 0.2894 50 0.35
14
 CDS 1239-1324 54737242-54737287 / 54748815-54748854 86 0.6043 50 0.31
15
 CDS 1327-1419 54748857-54748924 / 54751451-54751475 93 0.7271 50 0.33
16
 CDS 1420-1511 54751476-54751537 / 54760161-54760190 92 0.6988 50 0.27
17
 CDS 1512-1587 54760191-54760266 76 0.6025 50 0.30
18
 CDS 1589-1672 54760268-54760351 84 0.6931 50 0.36
19
 CDS 1673-1765 54760352-54760444 93 0.7823 50 0.42
20
 CDS 1766-1860 54760445-54760494 / 54764455-54764499 95 0.7531 50 0.30
21
 CDS 1864-1954 54764503-54764540 / 54770104-54770156 91 0.6441 50 0.25
22
 CDS 1956-2044 54770158-54770222 / 54774934-54774957 89 0.8769 50 0.23
23
 CDS 2045-2136 54774958-54775049 92 0.6532 50 0.27
24
 CDS 2141-2213 54775054-54775126 73 0.5676 50 0.28
25
 CDS 2216-2295 54775129-54775135 / 54776414-54776486 80 0.6173 50 0.27
26
 CDS 2297-2378 54776488-54776540 / 54784537-54784565 82 0.4769 50 0.25
27
 CDS,3'UTR 2379-2470 54784566-54784620 / 54788916-54788952 92 0.3255 50 0.25
28
 3'UTR 2472-2574 54788954-54789056 103 0.6121 50 0.37
29
 3'UTR 2575-2784 54789057-54789266 210 0.4497 50 0.33
30
 3'UTR 2785-2878 54789267-54789360 94 0.6649 50 0.36
31
 3'UTR 2881-2973 54789363-54789455 93 0.7395 50 0.42
32
 3'UTR 2974-3057 54789456-54789539 84 0.6269 50 0.32
33
 3'UTR 3062-3189 54789544-54789671 128 0.6548 50 0.35
34
 3'UTR 3195-3308 54789677-54789790 114 0.6483 50 0.29
35
 3'UTR 3311-3425 54789793-54789907 115 0.4264 50 0.32
36
 3'UTR 3428-3523 54789910-54790005 96 0.5845 50 0.43
37
 3'UTR 3524-3620 54790006-54790102 97 0.4921 50 0.39
38
 3'UTR 3621-3725 54790103-54790207 105 0.6513 50 0.29
39
 3'UTR 3726-3810 54790208-54790292 85 0.6854 50 0.26
40
 3'UTR 3811-3923 54790293-54790405 113 0.5458 50 0.23
41
 3'UTR 3925-4021 54790407-54790503 97 0.6211 50 0.29
42
 3'UTR 4023-4130 54790505-54790612 108 0.3609 50 0.24
43
 3'UTR 4133-4284 54790615-54790766 152 0.5504 50 0.28
44
 3'UTR 4285-4363 54790767-54790845 79 0.5434 50 0.32
45
 3'UTR 4364-4450 54790846-54790932 87 0.4853 50 0.37
46
 3'UTR 4452-4545 54790934-54791027 94 0.5101 50 0.43
47
 3'UTR 4547-4640 54791029-54791122 94 0.7520 50 0.50
48
 3'UTR 4641-4764 54791123-54791246 124 0.6119 50 0.26
49
 3'UTR 4765-4850 54791247-54791332 86 0.5384 50 0.36
50
 3'UTR 4851-4932 54791333-54791414 82 0.4530 50 0.32
51
 3'UTR 4934-5041 54791416-54791523 108 0.4842 50 0.30
52
 3'UTR 5045-5150 54791527-54791632 106 0.6017 50 0.28
53
 3'UTR 5162-5281 54791644-54791763 120 0.7363 50 0.37
54
 3'UTR 5283-5384 54791765-54791866 102 0.6432 50 0.33
55
 3'UTR 5385-5467 54791867-54791949 83 0.5095 50 0.33
56
 3'UTR 5468-5601 54791950-54792083 134 0.5897 50 0.39
57
 3'UTR 5602-5703 54792084-54792185 102 0.6543 50 0.32
58
 3'UTR 5705-5820 54792187-54792302 116 0.7899 50 0.47
59
 3'UTR 5821-5943 54792303-54792425 123 0.7728 50 0.39
60
 3'UTR 5944-6053 54792426-54792535 110 0.4599 50 0.34
61
 3'UTR 6058-6165 54792540-54792647 108 0.7803 50 0.46
62
 3'UTR 6166-6286 54792648-54792768 121 0.5444 50 0.28
63
 3'UTR 6287-6386 54792769-54792868 100 0.5089 50 0.35
64
 3'UTR 6388-6506 54792870-54792988 119 0.3204 50 0.34
65
 3'UTR 6508-6614 54792990-54793096 107 0.3970 50 0.32
66
 3'UTR 6618-6738 54793100-54793220 121 0.3424 54 0.40
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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SAMD4A

Aoi: Chr: Coords Strand:
SAMD4A 14 54791527 - 54791632 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: SAMD4A(+)
  • Length Length of region: 106 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 / 19ff247cc9 / 2026-03-17 08:50