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?

NEAT1
ENST00000646243 (+) ENSG00000245532 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 lncRNA 1-113 65423096-65423113 / 65423295-65423383 / 65423627-65423632 113 0.9609 50 0.33
2
 lncRNA 117-214 65423636-65423733 98 0.8787 50 0.24
3
 lncRNA 217-363 65423736-65423882 147 0.8390 50 0.23
4
 lncRNA 364-470 65423883-65423989 107 0.9242 50 0.23
5
 lncRNA 474-578 65423993-65424097 105 0.9404 50 0.25
6
 lncRNA 581-692 65424100-65424211 112 0.9134 50 0.21
7
 lncRNA 693-781 65424212-65424300 89 0.9161 50 0.27
8
 lncRNA 782-891 65424301-65424410 110 0.9152 50 0.23
9
 lncRNA 896-996 65424415-65424515 101 0.8493 50 0.19
10
 lncRNA 1001-1127 65424520-65424646 127 0.8736 50 0.18
11
 lncRNA 1129-1256 65424648-65424775 128 0.8781 50 0.19
12
 lncRNA 1264-1393 65424783-65424912 130 0.9203 50 0.24
13
 lncRNA 1394-1572 65424913-65425091 179 0.8525 50 0.19
14
 lncRNA 1573-1684 65425092-65425203 112 0.9022 50 0.17
15
 lncRNA 1685-1773 65425204-65425292 89 0.9846 50 0.34
16
 lncRNA 1774-1906 65425293-65425425 133 0.9458 50 0.28
17
 lncRNA 1907-2010 65425426-65425529 104 0.9378 50 0.30
18
 lncRNA 2011-2136 65425530-65425655 126 0.9526 50 0.22
19
 lncRNA 2137-2261 65425656-65425780 125 0.8727 50 0.21
20
 lncRNA 2263-2366 65425782-65425885 104 0.9207 50 0.25
21
 lncRNA 2367-2476 65425886-65425995 110 0.8910 50 0.23
22
 lncRNA 2477-2596 65425996-65426115 120 0.8122 50 0.17
23
 lncRNA 2600-2726 65426119-65426245 127 0.9358 50 0.31
24
 lncRNA 2727-2848 65426246-65426367 122 0.8518 50 0.19
25
 lncRNA 2853-2989 65426372-65426508 137 0.7762 65 0.21
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
22
NEAT1

Aoi: Chr: Coords Strand:
NEAT1 11 65425996 - 65426115 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: NEAT1(+)
  • Length Length of region: 120 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 2 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 / 2026-03-22 06:32