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?

QKI
ENST00000361752 (+) ENSG00000112531 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 307-410 163415024-163415127 104 0.6092 50 0.38
2
 5'UTR,CDS 412-515 163415129-163415232 104 0.8781 50 0.34
3
 CDS 516-597 163415233-163415314 82 0.8336 50 0.21
4
 CDS 599-688 163415316-163415335 / 163455279-163455348 90 0.6059 50 0.19
5
 CDS 689-801 163455349-163455421 / 163478780-163478819 113 0.7641 50 0.23
6
 CDS 802-883 163478820-163478896 / 163534982-163534986 82 0.8234 50 0.27
7
 CDS 885-971 163534988-163535074 87 0.7275 50 0.22
8
 CDS 972-1069 163535075-163535125 / 163561982-163562028 98 0.7978 50 0.23
9
 CDS 1071-1154 163562030-163562069 / 163563420-163563463 84 0.8438 50 0.26
10
 CDS 1155-1245 163563464-163563554 91 0.7772 50 0.23
11
 CDS 1246-1328 163563555-163563637 83 0.6045 50 0.21
12
 CDS 1330-1425 163563639-163563719 / 163566721-163566735 96 0.6546 50 0.19
13
 CDS,3'UTR 1426-1510 163566736-163566795 / 163570694-163570718 85 0.8793 50 0.31
14
 3'UTR 1511-1610 163570719-163570818 100 0.9206 50 0.43
15
 3'UTR 1612-1718 163570820-163570926 107 0.8374 50 0.31
16
 3'UTR 1725-1803 163570933-163571011 79 0.7647 50 0.27
17
 3'UTR 1804-1900 163571012-163571108 97 0.6989 50 0.31
18
 3'UTR 1902-2012 163571110-163571220 111 0.8346 50 0.36
19
 3'UTR 2015-2119 163571223-163571327 105 0.8317 50 0.29
20
 3'UTR 2120-2202 163571328-163571410 83 0.7759 50 0.20
21
 3'UTR 2206-2296 163571414-163571504 91 0.8375 50 0.31
22
 3'UTR 2306-2402 163571514-163571610 97 0.6543 50 0.25
23
 3'UTR 2403-2498 163571611-163571706 96 0.7050 50 0.29
24
 3'UTR 2502-2588 163571710-163571796 87 0.7469 50 0.33
25
 3'UTR 2589-2699 163571797-163571907 111 0.8269 50 0.24
26
 3'UTR 2701-2797 163571909-163572005 97 0.7799 50 0.26
27
 3'UTR 2800-2902 163572008-163572110 103 0.8389 50 0.34
28
 3'UTR 2903-3004 163572111-163572212 102 0.8338 50 0.22
29
 3'UTR 3005-3126 163572213-163572334 122 0.8721 50 0.29
30
 3'UTR 3133-3232 163572341-163572440 100 0.8916 50 0.32
31
 3'UTR 3233-3308 163572441-163572516 76 0.8163 50 0.40
32
 3'UTR 3309-3406 163572517-163572614 98 0.9059 50 0.37
33
 3'UTR 3410-3495 163572618-163572703 86 0.8836 50 0.48
34
 3'UTR 3496-3582 163572704-163572790 87 0.8429 50 0.42
35
 3'UTR 3584-3704 163572792-163572912 121 0.9501 50 0.28
36
 3'UTR 3708-3820 163572916-163573028 113 0.7718 50 0.19
37
 3'UTR 3825-3938 163573033-163573146 114 0.7782 50 0.23
38
 3'UTR 3941-4039 163573149-163573247 99 0.7501 50 0.24
39
 3'UTR 4043-4194 163573251-163573402 152 0.8907 50 0.37
40
 3'UTR 4195-4301 163573403-163573509 107 0.8139 50 0.25
41
 3'UTR 4303-4395 163573511-163573603 93 0.7868 50 0.27
42
 3'UTR 4396-4582 163573604-163573790 187 0.6504 68 0.30
Download CSV

Custom Gene Windows

QKI-285-434
Chr Coords Strand
6 163415002 - 163415151
150 bp
21s
completed
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
8
QKI

Aoi: Chr: Coords Strand:
QKI 6 163535075 - 163535125, 163561982 - 163562028 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: QKI(+)
  • Length Length of region: 98 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
1 2
production / 05e29e215d / 2026-04-04 11:44