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?

BCOR
ENST00000672922 (-) ENSG00000183337 (-)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 CDS 307-403 40076463-40076532 / 40077844-40077870 97 0.3525 50 0.35
2
 CDS 404-506 40075087-40075180 / 40076454-40076462 103 0.5473 50 0.38
3
 CDS 507-619 40074974-40075086 113 0.4671 50 0.35
4
 CDS 620-700 40074893-40074973 81 0.3612 50 0.36
5
 CDS 723-815 40074778-40074870 93 0.5121 50 0.41
6
 CDS 816-902 40074691-40074777 87 0.4248 50 0.35
7
 CDS 903-995 40074598-40074690 93 0.3890 50 0.31
8
 CDS 996-1075 40074518-40074597 80 0.3916 50 0.39
9
 CDS 1425-1523 40074070-40074168 99 0.4730 50 0.41
10
 CDS 1530-1618 40073975-40074063 89 0.6554 50 0.37
11
 CDS 1619-1715 40073878-40073974 97 0.4229 50 0.35
12
 CDS 1716-1809 40073784-40073877 94 0.3627 50 0.35
13
 CDS 1813-1902 40073691-40073780 90 0.2082 50 0.35
14
 CDS 1906-1989 40073604-40073687 84 0.4472 50 0.39
15
 CDS 1990-2066 40073527-40073603 77 0.4775 50 0.36
16
 CDS 2067-2208 40073385-40073526 142 0.5095 50 0.37
17
 CDS 2209-2346 40073247-40073384 138 0.4252 50 0.39
18
 CDS 2351-2448 40073145-40073242 98 0.6679 50 0.38
19
 CDS 2449-2531 40073062-40073144 83 0.5417 50 0.31
20
 CDS 2532-2612 40072981-40073061 81 0.3667 50 0.33
21
 CDS 2613-2697 40072896-40072980 85 0.2376 50 0.29
22
 CDS 2700-2783 40072810-40072893 84 0.5070 50 0.42
23
 CDS 2786-2882 40072711-40072807 97 0.2952 50 0.35
24
 CDS 2884-2983 40072610-40072709 100 0.2078 50 0.37
25
 CDS 2984-3070 40072523-40072609 87 0.5160 50 0.45
26
 CDS 3072-3163 40072430-40072521 92 0.5499 50 0.37
27
 CDS 3171-3264 40071671-40071690 / 40072349-40072422 94 0.2709 50 0.32
28
 CDS 3265-3363 40071095-40071159 / 40071637-40071670 99 0.4251 50 0.32
29
 CDS 3364-3446 40071012-40071094 83 0.3982 50 0.35
30
 CDS 3450-3540 40064545-40064599 / 40070973-40071008 91 0.4076 50 0.32
31
 CDS 3541-3635 40064450-40064544 95 0.6539 50 0.47
32
 CDS 3637-3726 40064359-40064448 90 0.6202 50 0.46
33
 CDS 3727-3908 40063794-40063952 / 40064336-40064358 182 0.3426 50 0.44
34
 CDS 3909-3999 40063703-40063793 91 0.6374 50 0.44
35
 CDS 4000-4084 40063618-40063702 85 0.3996 50 0.32
36
 CDS 4085-4174 40062992-40063071 / 40063608-40063617 90 0.5357 50 0.41
37
 CDS 4175-4254 40062912-40062991 80 0.4135 50 0.33
38
 CDS 4255-4338 40062828-40062911 84 0.5282 50 0.32
39
 CDS 4339-4435 40062379-40062393 / 40062746-40062827 97 0.5050 50 0.36
40
 CDS 4438-4649 40062165-40062376 212 0.4768 50 0.38
41
 CDS 4650-4756 40057241-40057321 / 40062139-40062164 107 0.3181 50 0.29
42
 CDS 4758-4866 40055490-40055513 / 40057155-40057239 109 0.4318 50 0.40
43
 CDS 4867-4958 40055398-40055489 92 0.5056 50 0.37
44
 CDS 4959-5067 40054042-40054042 / 40054256-40054333 / 40055368-40055397 109 0.4721 50 0.31
45
 CDS 5068-5167 40053942-40054041 100 0.3900 50 0.26
46
 CDS 5172-5267 40052357-40052400 / 40053886-40053937 96 0.4904 50 0.37
47
 CDS 5268-5485 40052139-40052356 218 0.2863 50 0.37
48
 CDS,3'UTR 5486-5589 40052035-40052138 104 0.2920 50 0.34
49
 3'UTR 5593-5683 40051941-40052031 91 0.5186 50 0.33
50
 3'UTR 5688-5832 40051792-40051936 145 0.4157 50 0.33
51
 3'UTR 5833-5960 40051664-40051791 128 0.5536 50 0.34
52
 3'UTR 5961-6047 40051577-40051663 87 0.7132 50 0.49
53
 3'UTR 6048-6155 40051469-40051576 108 0.6675 50 0.36
54
 3'UTR 6156-6222 40051402-40051468 67 0.3176 28 0.32
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.

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BCOR

Aoi: Chr: Coords Strand:
BCOR X 40072430 - 40072521 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: BCOR(-)
  • Length Length of region: 92 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 4 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 / 2026-02-11 19:46