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?

IQGAP1
ENST00000268182 (+) ENSG00000140575 (+)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 14-108 90388255-90388349 95 0.5335 50 0.28
2
 CDS 109-214 90388350-90388396 / 90390774-90390832 106 0.6877 50 0.21
3
 CDS 219-330 90390837-90390873 / 90426110-90426184 112 0.7723 50 0.20
4
 CDS 331-414 90426185-90426266 / 90429589-90429590 84 0.8137 50 0.28
5
 CDS 416-517 90429592-90429666 / 90433719-90433745 102 0.7772 50 0.25
6
 CDS 519-610 90433747-90433795 / 90439332-90439374 92 0.5293 50 0.21
7
 CDS 611-702 90439375-90439399 / 90440502-90440568 92 0.6889 50 0.23
8
 CDS 704-813 90440570-90440615 / 90441506-90441569 110 0.8042 50 0.24
9
 CDS 814-904 90441570-90441660 91 0.8653 50 0.24
10
 CDS 905-986 90441661-90441684 / 90443394-90443451 82 0.6686 50 0.23
11
 CDS 989-1080 90443454-90443478 / 90448573-90448639 92 0.5098 50 0.25
12
 CDS 1082-1172 90448641-90448731 91 0.7501 50 0.26
13
 CDS 1174-1270 90448733-90448736 / 90449559-90449643 / 90452775-90452782 97 0.7654 50 0.29
14
 CDS 1272-1374 90452784-90452886 103 0.5622 50 0.20
15
 CDS 1375-1456 90452887-90452938 / 90453132-90453161 82 0.6978 50 0.19
16
 CDS 1458-1572 90453163-90453277 115 0.7654 50 0.23
17
 CDS 1573-1666 90453278-90453292 / 90454428-90454506 94 0.8103 50 0.18
18
 CDS 1668-1776 90454508-90454552 / 90456152-90456215 109 0.8472 50 0.20
19
 CDS 1779-1868 90456218-90456307 90 0.7432 50 0.23
20
 CDS 1869-1960 90456308-90456315 / 90466001-90466084 92 0.6201 50 0.18
21
 CDS 1961-2073 90466085-90466091 / 90466269-90466374 113 0.6379 50 0.22
22
 CDS 2076-2171 90466377-90466436 / 90467450-90467485 96 0.7893 50 0.25
23
 CDS 2172-2275 90467486-90467589 104 0.7188 50 0.24
24
 CDS 2276-2377 90467590-90467592 / 90472840-90472938 102 0.8658 50 0.29
25
 CDS 2380-2467 90472941-90473010 / 90473715-90473732 88 0.7759 50 0.24
26
 CDS 2468-2557 90473733-90473798 / 90473896-90473919 90 0.7478 50 0.19
27
 CDS 2558-2646 90473920-90473967 / 90474064-90474104 89 0.8265 50 0.22
28
 CDS 2647-2741 90474105-90474133 / 90474485-90474550 95 0.7860 50 0.25
29
 CDS 2742-2843 90474551-90474652 102 0.5951 50 0.18
30
 CDS 2845-2929 90474654-90474693 / 90476663-90476707 85 0.8916 50 0.33
31
 CDS 2930-3038 90476708-90476816 109 0.6988 50 0.19
32
 CDS 3039-3118 90476817-90476818 / 90477067-90477144 80 0.7262 50 0.24
33
 CDS 3121-3200 90477147-90477226 80 0.4591 50 0.19
34
 CDS 3202-3305 90477228-90477230 / 90477665-90477765 104 0.7244 50 0.23
35
 CDS 3307-3399 90477767-90477859 93 0.5586 50 0.21
36
 CDS 3401-3491 90477861-90477889 / 90481960-90482021 91 0.7344 50 0.25
37
 CDS 3493-3591 90482023-90482100 / 90482197-90482217 99 0.8319 50 0.29
38
 CDS 3592-3707 90482218-90482281 / 90483361-90483412 116 0.6910 50 0.20
39
 CDS 3708-3794 90483413-90483499 87 0.8125 50 0.27
40
 CDS 3797-3887 90483502-90483592 91 0.6285 50 0.20
41
 CDS 3889-3987 90484220-90484318 99 0.7161 50 0.24
42
 CDS 3988-4072 90484319-90484352 / 90486030-90486080 85 0.4500 50 0.24
43
 CDS 4073-4161 90486081-90486132 / 90486954-90486990 89 0.7883 50 0.25
44
 CDS 4164-4255 90486993-90487084 92 0.7220 50 0.20
45
 CDS 4256-4340 90487085-90487089 / 90487495-90487574 85 0.7051 50 0.24
46
 CDS 4344-4422 90487578-90487582 / 90491333-90491406 79 0.6344 50 0.18
47
 CDS 4423-4500 90491407-90491484 78 0.8001 50 0.19
48
 CDS 4501-4586 90491485-90491545 / 90492545-90492569 86 0.7579 50 0.17
49
 CDS 4588-4680 90492571-90492663 93 0.8422 50 0.21
50
 CDS 4682-4761 90492665-90492711 / 90494713-90494745 80 0.7269 50 0.23
51
 CDS 4763-4848 90494747-90494832 86 0.6928 50 0.20
52
 CDS 4850-4951 90494834-90494835 / 90497232-90497331 102 0.8339 50 0.23
53
 CDS 4952-5050 90497332-90497340 / 90499995-90500084 99 0.7574 50 0.22
54
 CDS,3'UTR 5051-5140 90500085-90500174 90 0.8747 50 0.38
55
 3'UTR 5143-5220 90500177-90500254 78 0.7663 50 0.27
56
 3'UTR 5221-5341 90500255-90500375 121 0.7714 50 0.30
57
 3'UTR 5343-5473 90500377-90500507 131 0.6817 50 0.23
58
 3'UTR 5474-5561 90500508-90500595 88 0.7080 50 0.21
59
 3'UTR 5565-5678 90500599-90500712 114 0.8152 50 0.28
60
 3'UTR 5680-5783 90500714-90500817 104 0.8556 50 0.33
61
 3'UTR 5785-5885 90500819-90500919 101 0.8176 50 0.29
62
 3'UTR 5886-6010 90500920-90501044 125 0.6986 50 0.20
63
 3'UTR 6012-6103 90501046-90501137 92 0.8068 50 0.21
64
 3'UTR 6106-6195 90501140-90501229 90 0.6362 50 0.22
65
 3'UTR 6196-6303 90501230-90501337 108 0.7328 50 0.47
66
 3'UTR 6305-6392 90501339-90501426 88 0.8388 50 0.50
67
 3'UTR 6393-6502 90501427-90501536 110 0.6095 50 0.32
68
 3'UTR 6505-6611 90501539-90501645 107 0.5594 50 0.25
69
 3'UTR 6612-6723 90501646-90501757 112 0.5582 50 0.32
70
 3'UTR 6724-6805 90501758-90501839 82 0.5695 50 0.32
71
 3'UTR 6806-6895 90501840-90501929 90 0.3879 50 0.25
72
 3'UTR 6899-6998 90501933-90502032 100 0.3813 50 0.22
73
 3'UTR 7003-7111 90502037-90502145 109 0.4278 59 0.29
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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IQGAP1

Aoi: Chr: Coords Strand:
IQGAP1 15 90483413 - 90483499 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: IQGAP1(+)
  • Length Length of region: 87 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 / 2026-03-13 20:36