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?

TARDBP
ENST00000240185 (+) ENSG00000120948 (+)

Visualize entire gene
100
150
300
500
+
-
Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 11-126 11012664-11012743 / 11013716-11013751 116 0.8010 50 0.28
2
 CDS 128-230 11013753-11013855 103 0.8154 50 0.21
3
 CDS 231-343 11013856-11013965 / 11016844-11016846 113 0.8608 50 0.24
4
 CDS 344-433 11016847-11016936 90 0.7397 50 0.17
5
 CDS 435-530 11016938-11017007 / 11018733-11018758 96 0.7860 50 0.17
6
 CDS 533-638 11018761-11018866 106 0.8651 50 0.19
7
 CDS 641-754 11018869-11018873 / 11020429-11020537 114 0.9104 50 0.22
8
 CDS 758-868 11020541-11020599 / 11022124-11022175 111 0.8532 50 0.22
9
 CDS 869-974 11022176-11022281 106 0.8787 50 0.18
10
 CDS 976-1092 11022283-11022399 117 0.8526 50 0.22
11
 CDS 1093-1180 11022400-11022487 88 0.8432 50 0.21
12
 CDS 1181-1295 11022488-11022602 115 0.8687 50 0.24
13
 CDS,3'UTR 1299-1431 11022606-11022738 133 0.8504 50 0.21
14
 3'UTR 1435-1556 11022742-11022863 122 0.8832 50 0.23
15
 3'UTR 1557-1663 11022864-11022970 107 0.9191 50 0.28
16
 3'UTR 1664-1764 11022971-11023071 101 0.9009 50 0.35
17
 3'UTR 1765-1875 11023072-11023182 111 0.9145 50 0.35
18
 3'UTR 1876-1979 11023183-11023286 104 0.9152 50 0.37
19
 3'UTR 1982-2085 11023289-11023392 104 0.8718 50 0.31
20
 3'UTR 2086-2203 11023393-11023510 118 0.8109 50 0.20
21
 3'UTR 2205-2330 11023512-11023637 126 0.9293 50 0.34
22
 3'UTR 2333-2434 11023640-11023741 102 0.9125 50 0.27
23
 3'UTR 2435-2575 11023742-11023882 141 0.8822 50 0.33
24
 3'UTR 2579-2708 11023886-11024015 130 0.8447 50 0.34
25
 3'UTR 2709-2815 11024016-11024122 107 0.3940 50 0.38
26
 3'UTR 2816-2919 11024123-11024226 104 0.3147 50 0.37
27
 3'UTR 2922-3038 11024229-11024345 117 0.4774 50 0.40
28
 3'UTR 3039-3167 11024346-11024474 129 0.4625 50 0.33
29
 3'UTR 3170-3283 11024477-11024590 114 0.4378 50 0.45
30
 3'UTR 3285-3543 11024592-11024850 259 0.3987 26 0.42
Download CSV

Custom Gene Windows

TARDBP-1054-1203
Chr Coords Strand
1 11022361 - 11022510
150 bp
10s
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
7
TARDBP

Aoi: Chr: Coords Strand:
TARDBP 1 11018869 - 11018873, 11020429 - 11020537 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TARDBP(+)
  • Length Length of region: 114 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 6 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 3 4 5
production / 05e29e215d / 2026-04-03 23:17