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
Coords (max 500bp)
Coords 1  
Additional Coordinates
Coords 2 Optional
Coords 3 Optional
Coords 4 Optional


How was this calculated?

TGOLN2
ENST00000377386 (-) ENSG00000152291 (-)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 10-113 85327646-85327685 / 85327917-85327980 104 0.5974 50 0.32
2
 CDS 114-199 85327560-85327645 86 0.5741 50 0.22
3
 CDS 200-273 85327486-85327559 74 0.6452 50 0.23
4
 CDS 274-353 85327406-85327485 80 0.4843 50 0.21
5
 CDS 355-436 85327323-85327404 82 0.5107 50 0.19
6
 CDS 437-519 85327240-85327322 83 0.4872 50 0.21
7
 CDS 520-605 85327154-85327239 86 0.6027 50 0.23
8
 CDS 606-691 85327068-85327153 86 0.4686 50 0.21
9
 CDS 692-777 85326982-85327067 86 0.6571 50 0.26
10
 CDS 778-856 85326903-85326981 79 0.4450 50 0.24
11
 CDS 857-946 85326813-85326902 90 0.7207 50 0.29
12
 CDS 947-1042 85326717-85326812 96 0.6911 50 0.29
13
 CDS 1043-1135 85326624-85326716 93 0.6899 50 0.26
14
 CDS 1139-1241 85326518-85326620 103 0.7650 50 0.29
15
 CDS 1242-1331 85324919-85324998 / 85326508-85326517 90 0.6551 50 0.28
16
 CDS,3'UTR 1333-1441 85322636-85322741 / 85324915-85324917 109 0.7980 50 0.31
17
 3'UTR 1442-1544 85322533-85322635 103 0.5898 50 0.30
18
 3'UTR 1550-1680 85322397-85322527 131 0.8120 50 0.39
19
 3'UTR 1681-1791 85322286-85322396 111 0.8321 50 0.37
20
 3'UTR 1794-1901 85322176-85322283 108 0.8139 50 0.34
21
 3'UTR 1902-1976 85322101-85322175 75 0.6434 50 0.37
22
 3'UTR 1979-2092 85321985-85322098 114 0.6384 50 0.22
23
 3'UTR 2093-2189 85321888-85321984 97 0.8073 50 0.33
24
 3'UTR 2191-2309 85321768-85321886 119 0.6805 50 0.27
25
 3'UTR 2312-2409 85321668-85321765 98 0.8291 50 0.40
26
 3'UTR 2410-2512 85321565-85321667 103 0.6947 50 0.24
27
 3'UTR 2514-2631 85321446-85321563 118 0.6939 50 0.28
28
 3'UTR 2632-2734 85321343-85321445 103 0.6648 50 0.23
29
 3'UTR 2735-2842 85321235-85321342 108 0.7229 50 0.28
30
 3'UTR 2846-2941 85321136-85321231 96 0.7357 50 0.25
31
 3'UTR 2944-3044 85321033-85321133 101 0.9106 50 0.36
32
 3'UTR 3046-3154 85320923-85321031 109 0.6360 50 0.28
33
 3'UTR 3158-3249 85320828-85320919 92 0.4452 50 0.30
34
 3'UTR 3250-3355 85320722-85320827 106 0.5996 50 0.36
35
 3'UTR 3357-3452 85320625-85320720 96 0.6181 50 0.30
36
 3'UTR 3456-3561 85320516-85320621 106 0.7092 50 0.29
37
 3'UTR 3562-3654 85320423-85320515 93 0.7228 50 0.25
38
 3'UTR 3655-3771 85320306-85320422 117 0.8745 50 0.38
39
 3'UTR 3773-3885 85320192-85320304 113 0.8345 50 0.33
40
 3'UTR 3889-3988 85320089-85320188 100 0.8730 50 0.36
41
 3'UTR 3989-4095 85319982-85320088 107 0.8348 50 0.32
42
 3'UTR 4097-4175 85319902-85319980 79 0.5814 50 0.32
43
 3'UTR 4176-4281 85319796-85319901 106 0.4100 50 0.31
44
 3'UTR 4282-4391 85319686-85319795 110 0.7775 50 0.43
45
 3'UTR 4396-4505 85319572-85319681 110 0.7089 50 0.38
46
 3'UTR 4507-4618 85319459-85319570 112 0.6517 50 0.24
47
 3'UTR 4620-4713 85319364-85319457 94 0.8239 50 0.52
48
 3'UTR 4715-4810 85319267-85319362 96 0.7891 50 0.52
49
 3'UTR 4813-4893 85319184-85319264 81 0.9228 50 0.76
50
 3'UTR 4894-4984 85319093-85319183 91 0.5230 50 0.30
51
 3'UTR 4986-5108 85318969-85319091 123 0.6188 50 0.32
52
 3'UTR 5109-5228 85318849-85318968 120 0.8760 50 0.40
53
 3'UTR 5229-5329 85318748-85318848 101 0.7611 50 0.32
54
 3'UTR 5331-5434 85318643-85318746 104 0.6379 50 0.29
55
 3'UTR 5435-5538 85318539-85318642 104 0.5485 50 0.25
56
 3'UTR 5539-5659 85318418-85318538 121 0.6555 50 0.26
57
 3'UTR 5662-5766 85318311-85318415 105 0.7481 50 0.37
58
 3'UTR 5767-5892 85318185-85318310 126 0.5583 50 0.25
59
 3'UTR 5893-6035 85318042-85318184 143 0.4405 59 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.

Recently Visualized

TGOLN2
Chr Coords Strand
2 85319129 - 85319628
500 bp
66s
completed
production / 362c1546a7 / 2025-05-20 12:06