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?

TNRC18
ENST00000430969 (-) ENSG00000182095 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 72-200 5423635-5423763 129 0.2774 50 0.28
2
 5'UTR 202-318 5423517-5423633 117 0.4277 50 0.35
3
 5'UTR 320-418 5421466-5421489 / 5423441-5423515 99 0.5032 50 0.33
4
 5'UTR 420-507 5421377-5421464 88 0.3506 50 0.39
5
 5'UTR 508-595 5421289-5421376 88 0.4949 50 0.34
6
 5'UTR,CDS 598-708 5421176-5421286 111 0.6457 50 0.49
7
 CDS 709-803 5421081-5421175 95 0.7009 50 0.43
8
 CDS 806-906 5394514-5394595 / 5421060-5421078 101 0.7805 50 0.35
9
 CDS 909-991 5390618-5390628 / 5394440-5394511 83 0.7216 50 0.33
10
 CDS 992-1070 5390539-5390617 79 0.5390 50 0.37
11
 CDS 1071-1168 5389293-5389336 / 5390485-5390538 98 0.4884 50 0.34
12
 CDS 1170-1257 5389204-5389291 88 0.4349 50 0.42
13
 CDS 1260-1371 5389090-5389201 112 0.5535 50 0.42
14
 CDS 1373-1467 5388994-5389088 95 0.4022 50 0.43
15
 CDS 1469-1586 5388875-5388992 118 0.4644 50 0.41
16
 CDS 1589-2082 5388379-5388872 494 0.6234 50 0.47
17
 CDS 2083-2163 5388298-5388378 81 0.5244 50 0.42
18
 CDS 2164-2247 5388214-5388297 84 0.4623 50 0.37
19
 CDS 2250-2349 5388112-5388211 100 0.5776 50 0.46
20
 CDS 2350-2455 5388006-5388111 106 0.7033 50 0.41
21
 CDS 2461-2549 5387912-5388000 89 0.5043 50 0.35
22
 CDS 2550-2649 5387812-5387911 100 0.8083 50 0.42
23
 CDS 2650-2766 5387695-5387811 117 0.8018 50 0.37
24
 CDS 2768-2870 5377944-5378024 / 5387672-5387693 103 0.6896 50 0.30
25
 CDS 2874-2962 5377507-5377576 / 5377922-5377940 89 0.7536 50 0.44
26
 CDS 2963-3060 5377409-5377506 98 0.7457 50 0.43
27
 CDS 3064-3152 5376940-5376993 / 5377371-5377405 89 0.6222 50 0.37
28
 CDS 3160-3254 5376216-5376224 / 5376847-5376932 95 0.6473 50 0.35
29
 CDS 3258-3335 5376135-5376212 78 0.5014 50 0.40
30
 CDS 3336-3428 5376042-5376134 93 0.5665 50 0.36
31
 CDS 3429-3539 5374382-5374484 / 5376034-5376041 111 0.7358 50 0.36
32
 CDS 3540-3624 5374297-5374381 85 0.8119 50 0.40
33
 CDS 3625-3708 5374213-5374296 84 0.7680 50 0.32
34
 CDS 3709-3772 5374149-5374212 64 0.5506 50 0.35
35
 CDS 3773-3865 5374056-5374148 93 0.6015 50 0.41
36
 CDS 3867-3946 5371285-5371364 80 0.6019 50 0.38
37
 CDS 3948-4036 5371195-5371283 89 0.5678 50 0.40
38
 CDS 4037-4141 5371090-5371194 105 0.6801 50 0.34
39
 CDS 4142-4242 5370989-5371089 101 0.7185 50 0.42
40
 CDS 4245-4347 5370884-5370986 103 0.7190 50 0.35
41
 CDS 4348-4460 5370771-5370883 113 0.8130 50 0.40
42
 CDS 4461-4554 5370677-5370770 94 0.7320 50 0.32
43
 CDS 4556-4649 5370582-5370675 94 0.7096 50 0.39
44
 CDS 4650-4748 5370483-5370581 99 0.7219 50 0.45
45
 CDS 4752-4855 5370376-5370479 104 0.7375 50 0.33
46
 CDS 4860-4970 5362712-5362822 111 0.7665 50 0.40
47
 CDS 4973-5067 5361999-5362033 / 5362650-5362709 95 0.8649 50 0.37
48
 CDS 5068-5172 5361720-5361722 / 5361897-5361998 105 0.8633 50 0.36
49
 CDS 5173-5256 5361636-5361719 84 0.8415 50 0.34
50
 CDS 5258-5351 5359517-5359569 / 5361594-5361634 94 0.8665 50 0.32
51
 CDS 5353-5449 5359419-5359515 97 0.7976 50 0.21
52
 CDS 5451-5537 5357210-5357276 / 5359398-5359417 87 0.8462 50 0.27
53
 CDS 5539-5639 5357108-5357208 101 0.8201 50 0.32
54
 CDS 5640-5728 5357019-5357107 89 0.8022 50 0.38
55
 CDS 5729-5823 5356924-5357018 95 0.7219 50 0.34
56
 CDS 5824-5903 5352023-5352094 / 5356916-5356923 80 0.6664 50 0.33
57
 CDS 5906-5997 5351929-5352020 92 0.6884 50 0.37
58
 CDS 5999-6094 5351832-5351927 96 0.8296 50 0.36
59
 CDS 6096-6214 5345704-5345810 / 5351819-5351830 119 0.6255 50 0.33
60
 CDS 6215-6317 5345601-5345703 103 0.8208 50 0.42
61
 CDS 6318-6413 5332993-5333049 / 5345562-5345600 96 0.6207 50 0.32
62
 CDS 6414-6506 5332900-5332992 93 0.7307 50 0.44
63
 CDS 6508-6606 5332800-5332898 99 0.6716 50 0.44
64
 CDS 6607-6694 5332712-5332799 88 0.7287 50 0.41
65
 CDS 6696-6776 5332630-5332710 81 0.8183 50 0.38
66
 CDS 6777-6870 5325163-5325248 / 5332622-5332629 94 0.7842 50 0.44
67
 CDS 6871-6958 5324335-5324355 / 5325096-5325162 88 0.7492 50 0.31
68
 CDS 6962-7062 5324231-5324331 101 0.7097 50 0.35
69
 CDS 7064-7154 5321116-5321190 / 5324214-5324229 91 0.7557 50 0.43
70
 CDS 7157-7257 5320548-5320607 / 5321073-5321113 101 0.6532 50 0.35
71
 CDS 7262-7354 5320346-5320426 / 5320532-5320543 93 0.6992 50 0.40
72
 CDS 7358-7462 5315993-5316072 / 5320318-5320342 105 0.6691 50 0.34
73
 CDS 7463-7550 5315098-5315148 / 5315956-5315992 88 0.6321 50 0.35
74
 CDS 7553-7651 5314997-5315095 99 0.6388 50 0.37
75
 CDS 7652-7736 5313792-5313863 / 5314984-5314996 85 0.8023 50 0.39
76
 CDS 7738-7813 5313715-5313790 76 0.6603 50 0.34
77
 CDS 7814-7887 5313641-5313714 74 0.4249 50 0.33
78
 CDS 7889-7956 5313572-5313639 68 0.6619 50 0.46
79
 CDS 7958-8059 5313469-5313570 102 0.5163 50 0.37
80
 CDS 8060-8160 5313368-5313468 101 0.7662 50 0.44
81
 CDS 8161-8247 5313281-5313367 87 0.6686 50 0.38
82
 CDS 8248-8335 5313193-5313280 88 0.6781 50 0.39
83
 CDS 8336-8434 5313094-5313192 99 0.6950 50 0.37
84
 CDS 8435-8515 5313013-5313093 81 0.5347 50 0.38
85
 CDS 8517-8602 5312926-5313011 86 0.4467 50 0.34
86
 CDS 8604-8715 5312813-5312924 112 0.4253 50 0.45
87
 CDS 8718-8793 5312735-5312810 76 0.4740 50 0.44
88
 CDS 8795-8866 5312662-5312733 72 0.4166 50 0.44
89
 CDS 8871-8946 5312582-5312657 76 0.2761 50 0.36
90
 CDS 8949-9039 5309355-5309368 / 5312503-5312579 91 0.5545 50 0.41
91
 CDS 9043-9138 5309256-5309351 96 0.5849 50 0.42
92
 CDS 9139-9233 5309161-5309255 95 0.6596 50 0.33
93
 CDS 9235-9318 5308894-5308949 / 5309132-5309159 84 0.6301 50 0.38
94
 CDS 9320-9428 5308222-5308312 / 5308875-5308892 109 0.6774 50 0.32
95
 CDS 9429-9514 5308136-5308221 86 0.4034 50 0.35
96
 CDS,3'UTR 9516-9608 5308042-5308134 93 0.5492 50 0.40
97
 3'UTR 9609-9738 5307912-5308041 130 0.5222 50 0.39
98
 3'UTR 9739-9821 5307829-5307911 83 0.5404 50 0.39
99
 3'UTR 9822-9933 5307717-5307828 112 0.7439 50 0.46
100
 3'UTR 9936-10010 5307640-5307714 75 0.7046 50 0.32
101
 3'UTR 10011-10106 5307544-5307639 96 0.8224 50 0.42
102
 3'UTR 10107-10200 5307450-5307543 94 0.8232 50 0.35
103
 3'UTR 10201-10283 5307367-5307449 83 0.8118 50 0.39
104
 3'UTR 10287-10378 5307272-5307363 92 0.6064 50 0.31
105
 3'UTR 10380-10488 5307162-5307270 109 0.8003 50 0.39
106
 3'UTR 10493-10563 5307087-5307157 71 0.5144 50 0.36
107
 3'UTR 10564-10658 5306992-5307086 95 0.5976 50 0.35
108
 3'UTR 10661-10814 5306836-5306989 154 0.6315 61 0.30
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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TNRC18

Aoi: Chr: Coords Strand:
TNRC18 7 5307162 - 5307270 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TNRC18(-)
  • Length Length of region: 109 nt.
  • Coverage 87.7% 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 / bf240190b0 / 2026-02-12 02:15