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?

TEAD1
ENST00000334310 (+) ENSG00000187079 (+)

Visualize entire gene
100
150
300
500
+
-
Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 2-97 12675504-12675561 / 12764179-12764216 96 0.7585 50 0.33
2
 5'UTR,CDS 98-182 12764217-12764301 85 0.8005 50 0.24
3
 CDS 184-279 12764303-12764398 96 0.8389 50 0.24
4
 CDS 282-366 12764401-12764434 / 12862250-12862300 85 0.7749 50 0.22
5
 CDS 369-460 12862303-12862314 / 12864838-12864900 / 12878889-12878900 / 12879708-12879712 92 0.6156 50 0.25
6
 CDS 462-549 12879714-12879801 88 0.7813 50 0.29
7
 CDS 552-643 12879804-12879842 / 12881005-12881051 / 12881896-12881901 92 0.5828 50 0.25
8
 CDS 645-730 12881903-12881957 / 12883001-12883031 86 0.7015 50 0.31
9
 CDS 731-826 12883032-12883125 / 12924912-12924913 96 0.5618 50 0.22
10
 CDS 829-932 12924916-12925019 104 0.7168 50 0.21
11
 CDS 934-1033 12925021-12925052 / 12930174-12930241 100 0.6622 50 0.22
12
 CDS 1035-1125 12930243-12930326 / 12937109-12937115 91 0.5499 50 0.21
13
 CDS 1126-1214 12937116-12937204 89 0.6961 50 0.20
14
 CDS,3'UTR 1215-1303 12937205-12937293 89 0.6248 50 0.21
15
 3'UTR 1304-1398 12937294-12937388 95 0.7001 50 0.30
16
 3'UTR 1405-1520 12937395-12937510 116 0.6062 50 0.28
17
 3'UTR 1521-1614 12937511-12937604 94 0.7235 50 0.30
18
 3'UTR 1618-1713 12937608-12937703 96 0.6146 50 0.24
19
 3'UTR 1714-1824 12937704-12937814 111 0.5470 50 0.26
20
 3'UTR 1825-1918 12937815-12937908 94 0.6205 50 0.25
21
 3'UTR 1920-2000 12937910-12937990 81 0.6664 50 0.30
22
 3'UTR 2001-2098 12937991-12938088 98 0.7498 50 0.31
23
 3'UTR 2099-2205 12938089-12938195 107 0.7905 50 0.31
24
 3'UTR 2210-2301 12938200-12938291 92 0.7733 50 0.29
25
 3'UTR 2302-2396 12938292-12938386 95 0.5656 50 0.26
26
 3'UTR 2397-2499 12938387-12938489 103 0.9007 50 0.53
27
 3'UTR 2500-2607 12938490-12938597 108 0.7284 50 0.22
28
 3'UTR 2610-2716 12938600-12938706 107 0.7436 50 0.25
29
 3'UTR 2719-2833 12938709-12938823 115 0.7553 50 0.24
30
 3'UTR 2834-2932 12938824-12938922 99 0.7753 50 0.26
31
 3'UTR 2933-3006 12938923-12938996 74 0.8424 50 0.34
32
 3'UTR 3007-3070 12938997-12939060 64 0.6103 27 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
31
TEAD1

Aoi: Chr: Coords Strand:
TEAD1 11 12938923 - 12938996 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TEAD1(+)
  • Length Length of region: 74 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 1 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
production / 05e29e215d / 2026-03-22 06:29