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?

CDC27
ENST00000066544 (-) ENSG00000004897 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 10-117 47189179-47189286 108 0.3715 50 0.30
2
 5'UTR,CDS 119-213 47181575-47181637 / 47189146-47189177 95 0.7859 50 0.27
3
 CDS 214-308 47171983-47172064 / 47181562-47181574 95 0.5009 50 0.19
4
 CDS 309-401 47170016-47170042 / 47171917-47171982 93 0.5661 50 0.23
5
 CDS 408-525 47158279-47158303 / 47169917-47170009 118 0.6292 50 0.20
6
 CDS 527-620 47157363-47157384 / 47158206-47158277 94 0.4887 50 0.21
7
 CDS 621-702 47157281-47157362 82 0.6111 50 0.24
8
 CDS 704-784 47157094-47157124 / 47157230-47157279 81 0.5768 50 0.23
9
 CDS 785-880 47156998-47157093 96 0.6609 50 0.28
10
 CDS 882-964 47156914-47156996 83 0.7307 50 0.27
11
 CDS 973-1059 47154693-47154779 87 0.7697 50 0.27
12
 CDS 1060-1145 47151854-47151918 / 47154672-47154692 86 0.6002 50 0.26
13
 CDS 1149-1222 47143954-47143982 / 47151806-47151850 74 0.6628 50 0.20
14
 CDS 1225-1300 47142430-47142436 / 47143883-47143951 76 0.6060 50 0.26
15
 CDS 1302-1366 47142364-47142428 65 0.6259 50 0.31
16
 CDS 1367-1449 47142281-47142363 83 0.5494 50 0.23
17
 CDS 1451-1541 47141986-47142025 / 47142229-47142279 91 0.7394 50 0.28
18
 CDS 1545-1641 47141886-47141982 97 0.6578 50 0.23
19
 CDS 1642-1746 47138820-47138891 / 47141853-47141885 105 0.5995 50 0.26
20
 CDS 1747-1846 47137342-47137360 / 47138739-47138819 100 0.6768 50 0.29
21
 CDS 1847-1941 47137247-47137341 95 0.6294 50 0.26
22
 CDS 1944-2057 47132354-47132374 / 47137152-47137244 114 0.5936 50 0.25
23
 CDS 2060-2143 47132268-47132351 84 0.6404 50 0.27
24
 CDS 2144-2228 47129448-47129521 / 47132257-47132267 85 0.5931 50 0.32
25
 CDS 2229-2316 47123928-47123960 / 47129393-47129447 88 0.5444 50 0.25
26
 CDS 2317-2417 47122542-47122600 / 47123886-47123927 101 0.3700 50 0.25
27
 CDS 2421-2504 47122455-47122538 84 0.5607 50 0.22
28
 CDS 2505-2591 47120942-47121017 / 47122444-47122454 87 0.6541 50 0.27
29
 CDS,3'UTR 2592-2714 47120819-47120941 123 0.7627 50 0.34
30
 3'UTR 2715-2813 47120720-47120818 99 0.8170 50 0.31
31
 3'UTR 2816-2944 47120589-47120717 129 0.7482 50 0.30
32
 3'UTR 2947-3070 47120463-47120586 124 0.7629 50 0.33
33
 3'UTR 3071-3154 47120379-47120462 84 0.6680 50 0.25
34
 3'UTR 3158-3258 47120275-47120375 101 0.7927 50 0.41
35
 3'UTR 3262-3380 47120153-47120271 119 0.5134 50 0.36
36
 3'UTR 3383-3462 47120071-47120150 80 0.6025 50 0.30
37
 3'UTR 3463-3556 47119977-47120070 94 0.3509 50 0.22
38
 3'UTR 3557-3684 47119849-47119976 128 0.7470 50 0.33
39
 3'UTR 3685-3814 47119719-47119848 130 0.6189 50 0.33
40
 3'UTR 3815-3912 47119621-47119718 98 0.7327 50 0.47
41
 3'UTR 3913-4027 47119506-47119620 115 0.5272 50 0.29
42
 3'UTR 4030-4137 47119396-47119503 108 0.5474 50 0.34
43
 3'UTR 4139-4245 47119288-47119394 107 0.4746 50 0.32
44
 3'UTR 4247-4334 47119199-47119286 88 0.5947 50 0.40
45
 3'UTR 4335-4451 47119082-47119198 117 0.5151 50 0.32
46
 3'UTR 4452-4553 47118980-47119081 102 0.3717 50 0.23
47
 3'UTR 4561-4682 47118851-47118972 122 0.8313 50 0.42
48
 3'UTR 4683-4823 47118710-47118850 141 0.5802 50 0.36
49
 3'UTR 4825-4909 47118624-47118708 85 0.5861 50 0.33
50
 3'UTR 4912-5024 47118509-47118621 113 0.8538 50 0.68
51
 3'UTR 5026-5142 47118391-47118507 117 0.4344 50 0.31
52
 3'UTR 5144-5242 47118291-47118389 99 0.5229 50 0.37
53
 3'UTR 5245-5335 47118198-47118288 91 0.4455 50 0.31
54
 3'UTR 5336-5464 47118069-47118197 129 0.7113 50 0.41
55
 3'UTR 5465-5529 47118004-47118068 65 0.5204 25 0.25
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.

Recently Visualized

CDC27-4709-5208
Chr Coords Strand
17 47118325 - 47118824
500 bp
65s
completed
production / b252b9f76a / 2025-07-17 17:18