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?

BIRC2
ENST00000227758 (+) ENSG00000110330 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 37-148 102347250-102347361 112 0.5901 50 0.42
2
 5'UTR 151-236 102347364-102347376 / 102348598-102348670 86 0.2377 50 0.31
3
 5'UTR 238-358 102348672-102348792 121 0.3220 50 0.32
4
 5'UTR 361-473 102348795-102348907 113 0.5132 50 0.30
5
 5'UTR 476-587 102348910-102349021 112 0.2454 50 0.28
6
 5'UTR 592-677 102349026-102349111 86 0.3338 50 0.30
7
 5'UTR 678-781 102349112-102349215 104 0.4538 50 0.38
8
 5'UTR 782-895 102349216-102349329 114 0.4564 50 0.33
9
 5'UTR 900-1022 102349334-102349456 123 0.5631 50 0.35
10
 5'UTR 1023-1124 102349457-102349558 102 0.2637 50 0.33
11
 5'UTR 1128-1215 102349562-102349649 88 0.4872 50 0.37
12
 5'UTR 1216-1312 102349650-102349746 97 0.1781 50 0.27
13
 5'UTR,CDS 1315-1421 102349749-102349855 107 0.6735 50 0.33
14
 CDS 1424-1506 102349858-102349940 83 0.1537 50 0.36
15
 CDS 1507-1589 102349941-102350023 83 0.3964 50 0.36
16
 CDS 1590-1712 102350024-102350146 123 0.2551 50 0.36
17
 CDS 1715-1808 102350149-102350242 94 0.5456 50 0.38
18
 CDS 1809-1901 102350243-102350335 93 0.3724 50 0.26
19
 CDS 1904-2076 102350338-102350510 173 0.3466 50 0.35
20
 CDS 2077-2182 102350511-102350616 106 0.5443 50 0.38
21
 CDS 2184-2280 102350618-102350714 97 0.4921 50 0.33
22
 CDS 2283-2431 102350717-102350749 / 102350844-102350943 / 102362896-102362911 149 0.3205 50 0.29
23
 CDS 2432-2529 102362912-102362974 / 102363668-102363702 98 0.3222 50 0.34
24
 CDS 2532-2636 102363705-102363716 / 102368306-102368398 105 0.3631 50 0.37
25
 CDS 2638-2723 102368400-102368485 86 0.3489 50 0.32
26
 CDS 2726-2813 102368488-102368548 / 102377496-102377522 88 0.3718 50 0.32
27
 CDS 2815-2911 102377524-102377620 97 0.2316 50 0.31
28
 CDS 2912-2995 102377621-102377704 84 0.5510 50 0.36
29
 CDS 2996-3096 102377705-102377750 / 102377857-102377898 / 102377990-102378002 101 0.3672 50 0.33
30
 CDS 3097-3213 102378003-102378119 117 0.3972 50 0.31
31
 CDS,3'UTR 3215-3310 102378121-102378216 96 0.4867 50 0.31
32
 3'UTR 3311-3417 102378217-102378323 107 0.5831 50 0.30
33
 3'UTR 3419-3549 102378325-102378455 131 0.2943 50 0.31
34
 3'UTR 3550-3714 102378456-102378620 165 0.4728 67 0.42
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
5
BIRC2

Aoi: Chr: Coords Strand:
BIRC2 11 102348910 - 102349021 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: BIRC2(+)
  • Length Length of region: 112 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 3 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 / 05e29e215d / 2026-03-18 15:46