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?

AAGAB
ENST00000261880 (-) ENSG00000103591 (-)

Visualize entire gene
100
150
300
500
+
-
Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 6-103 67254559-67254656 98 0.5950 50 0.35
2
 CDS 104-204 67236720-67236820 101 0.3507 50 0.24
3
 CDS 205-308 67236491-67236504 / 67236630-67236719 104 0.6366 50 0.33
4
 CDS 310-413 67236047-67236068 / 67236408-67236489 104 0.7444 50 0.33
5
 CDS 414-519 67231860-67231897 / 67235979-67236046 106 0.5784 50 0.21
6
 CDS 520-612 67209498-67209544 / 67231814-67231859 93 0.5929 50 0.22
7
 CDS 613-697 67208610-67208658 / 67209462-67209497 85 0.5700 50 0.21
8
 CDS 707-803 67204091-67204148 / 67208562-67208600 97 0.7605 50 0.26
9
 CDS 809-897 67203551-67203597 / 67204044-67204085 89 0.5328 50 0.19
10
 CDS,3'UTR 898-1002 67202797-67202898 / 67203548-67203550 105 0.6613 50 0.22
11
 3'UTR 1003-1105 67202694-67202796 103 0.6971 50 0.26
12
 3'UTR 1106-1240 67202559-67202693 135 0.6878 50 0.29
13
 3'UTR 1245-1340 67202459-67202554 96 0.5787 50 0.25
14
 3'UTR 1341-1467 67202332-67202458 127 0.8355 50 0.38
15
 3'UTR 1472-1574 67202225-67202327 103 0.8436 50 0.32
16
 3'UTR 1575-1689 67202110-67202224 115 0.6878 50 0.26
17
 3'UTR 1690-1799 67202000-67202109 110 0.6286 50 0.38
18
 3'UTR 1801-1888 67201911-67201998 88 0.5198 50 0.36
19
 3'UTR 1890-2004 67201795-67201909 115 0.6651 50 0.32
20
 3'UTR 2012-2115 67201684-67201787 104 0.4040 50 0.29
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
19
AAGAB

Aoi: Chr: Coords Strand:
AAGAB 15 67201795 - 67201909 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: AAGAB(-)
  • Length Length of region: 115 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 5 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 / 2026-04-04 03:38