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?

SRSF1
ENST00000258962 (-) ENSG00000136450 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 2-138 58007109-58007245 137 0.8646 50 0.22
2
 CDS 139-225 58007022-58007108 87 0.9490 50 0.17
3
 CDS 226-318 58006513-58006527 / 58006944-58007021 93 0.8063 50 0.16
4
 CDS 324-450 58006381-58006507 127 0.8359 50 0.28
5
 CDS 451-567 58005895-58005973 / 58006343-58006380 117 0.9213 50 0.27
6
 CDS 568-672 58005590-58005600 / 58005801-58005894 105 0.8819 50 0.19
7
 CDS 673-768 58005494-58005589 96 0.7480 50 0.14
8
 CDS 769-853 58005409-58005493 85 0.9093 50 0.20
9
 3'UTR 855-977 58005285-58005407 123 0.8783 50 0.18
10
 3'UTR 980-1087 58005175-58005282 108 0.9391 50 0.27
11
 3'UTR 1088-1243 58005019-58005174 156 0.9385 50 0.24
12
 3'UTR 1245-1357 58004905-58005017 113 0.9119 50 0.19
13
 3'UTR 1362-1454 58004808-58004900 93 0.8751 50 0.22
14
 3'UTR 1457-1572 58004690-58004805 116 0.9595 50 0.37
15
 3'UTR 1576-1695 58004567-58004686 120 0.9356 50 0.31
16
 3'UTR 1696-1794 58004468-58004566 99 0.9282 50 0.28
17
 3'UTR 1798-1903 58004359-58004464 106 0.8935 50 0.23
18
 3'UTR 1904-2002 58004260-58004358 99 0.9055 50 0.26
19
 3'UTR 2004-2106 58004156-58004258 103 0.8462 50 0.30
20
 3'UTR 2107-2208 58004054-58004155 102 0.9841 50 0.52
21
 3'UTR 2211-2334 58003928-58004051 124 0.9085 50 0.28
22
 3'UTR 2337-2440 58003822-58003925 104 0.9439 50 0.27
23
 3'UTR 2443-2565 58003697-58003819 123 0.9331 50 0.28
24
 3'UTR 2567-2671 58003591-58003695 105 0.8605 50 0.24
25
 3'UTR 2673-2767 58003495-58003589 95 0.8536 50 0.41
26
 3'UTR 2769-2891 58003371-58003493 123 0.5776 50 0.32
27
 3'UTR 2894-3002 58003260-58003368 109 0.4668 50 0.31
28
 3'UTR 3011-3121 58003141-58003251 111 0.7215 50 0.36
29
 3'UTR 3122-3221 58003041-58003140 100 0.5562 50 0.35
30
 3'UTR 3222-3341 58002921-58003040 120 0.9216 50 0.64
31
 3'UTR 3345-3454 58002808-58002917 110 0.6319 50 0.32
32
 3'UTR 3455-3550 58002712-58002807 96 0.5983 50 0.40
33
 3'UTR 3551-3662 58002600-58002711 112 0.3672 50 0.32
34
 3'UTR 3663-3760 58002502-58002599 98 0.5993 50 0.42
35
 3'UTR 3761-3880 58002382-58002501 120 0.5398 50 0.34
36
 3'UTR 3881-3991 58002271-58002381 111 0.5474 50 0.30
37
 3'UTR 3994-4099 58002163-58002268 106 0.7163 50 0.33
38
 3'UTR 4100-4204 58002058-58002162 105 0.4607 50 0.34
39
 3'UTR 4205-4321 58001941-58002057 117 0.5187 50 0.41
40
 3'UTR 4323-4427 58001835-58001939 105 0.3636 50 0.28
41
 3'UTR 4428-4540 58001722-58001834 113 0.7076 50 0.37
42
 3'UTR 4542-4728 58001534-58001720 187 0.2814 50 0.30
43
 3'UTR 4729-4830 58001432-58001533 102 0.5870 50 0.36
44
 3'UTR 4832-4947 58001315-58001430 116 0.4564 50 0.27
45
 3'UTR 4949-5113 58001149-58001313 165 0.3938 50 0.27
46
 3'UTR 5117-5215 58001047-58001145 99 0.3330 50 0.32
47
 3'UTR 5216-5294 58000968-58001046 79 0.4055 50 0.35
48
 3'UTR 5295-5343 58000919-58000967 49 0.2974 25 0.33
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
15
SRSF1

Aoi: Chr: Coords Strand:
SRSF1 17 58004567 - 58004686 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: SRSF1(-)
  • 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 11 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 / 19ff247cc9 / 2026-03-16 19:51