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?

TFRC
ENST00000360110 (-) ENSG00000072274 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 1-127 196075341-196075360 / 196077064-196077122 / 196082043-196082090 127 0.9194 50 0.22
2
 CDS 128-224 196075244-196075340 97 0.8237 50 0.16
3
 CDS 225-341 196074094-196074125 / 196075159-196075243 117 0.8825 50 0.19
4
 CDS 347-445 196073990-196074088 99 0.8355 50 0.20
5
 CDS 448-532 196072126-196072152 / 196073930-196073987 85 0.8749 50 0.16
6
 CDS 534-639 196072019-196072124 106 0.9384 50 0.23
7
 CDS 642-751 196071403-196071498 / 196072003-196072016 110 0.7618 50 0.14
8
 CDS 752-859 196069468-196069568 / 196071396-196071402 108 0.8750 50 0.19
9
 CDS 860-959 196068044-196068130 / 196069455-196069467 100 0.8949 50 0.18
10
 CDS 962-1052 196067577-196067657 / 196068032-196068041 91 0.8812 50 0.23
11
 CDS 1055-1148 196065564-196065600 / 196067518-196067574 94 0.8408 50 0.17
12
 CDS 1150-1244 196065468-196065562 95 0.8747 50 0.20
13
 CDS 1248-1354 196064344-196064428 / 196065443-196065464 107 0.9094 50 0.19
14
 CDS 1355-1472 196062857-196062939 / 196064309-196064343 118 0.9000 50 0.20
15
 CDS 1474-1579 196060208-196060247 / 196062582-196062645 / 196062854-196062855 106 0.8444 50 0.21
16
 CDS 1581-1672 196058360-196058365 / 196058574-196058632 / 196060180-196060206 92 0.9149 50 0.18
17
 CDS 1673-1779 196055271-196055301 / 196058284-196058359 107 0.8442 50 0.20
18
 CDS 1783-1879 196055171-196055267 97 0.8553 50 0.19
19
 CDS 1882-1974 196053555-196053558 / 196055080-196055168 93 0.8417 50 0.16
20
 CDS 1979-2082 196053447-196053550 104 0.7741 50 0.16
21
 CDS 2085-2182 196052114-196052184 / 196053418-196053444 98 0.9103 50 0.22
22
 CDS 2183-2271 196052025-196052113 89 0.8597 50 0.20
23
 CDS,3'UTR 2272-2381 196051915-196052024 110 0.8448 50 0.19
24
 3'UTR 2382-2487 196051809-196051914 106 0.8637 50 0.28
25
 3'UTR 2491-2583 196051713-196051805 93 0.8572 50 0.31
26
 3'UTR 2584-2700 196051596-196051712 117 0.7991 50 0.31
27
 3'UTR 2703-2806 196051490-196051593 104 0.9398 50 0.47
28
 3'UTR 2807-2921 196051375-196051489 115 0.9206 50 0.37
29
 3'UTR 2923-3020 196051276-196051373 98 0.9270 50 0.26
30
 3'UTR 3022-3133 196051163-196051274 112 0.8123 50 0.25
31
 3'UTR 3135-3254 196051042-196051161 120 0.8911 50 0.32
32
 3'UTR 3258-3365 196050931-196051038 108 0.9639 50 0.54
33
 3'UTR 3366-3455 196050841-196050930 90 0.8710 50 0.25
34
 3'UTR 3456-3563 196050733-196050840 108 0.8599 50 0.26
35
 3'UTR 3564-3662 196050634-196050732 99 0.8224 50 0.29
36
 3'UTR 3663-3753 196050543-196050633 91 0.9408 50 0.45
37
 3'UTR 3758-3860 196050436-196050538 103 0.9649 50 0.56
38
 3'UTR 3864-3971 196050325-196050432 108 0.9142 50 0.27
39
 3'UTR 3972-4079 196050217-196050324 108 0.9169 50 0.34
40
 3'UTR 4086-4186 196050110-196050210 101 0.9205 50 0.28
41
 3'UTR 4188-4306 196049990-196050108 119 0.9264 50 0.31
42
 3'UTR 4308-4419 196049877-196049988 112 0.8795 50 0.28
43
 3'UTR 4420-4526 196049770-196049876 107 0.8537 50 0.26
44
 3'UTR 4528-4628 196049668-196049768 101 0.7697 50 0.23
45
 3'UTR 4629-4729 196049567-196049667 101 0.8849 50 0.33
46
 3'UTR 4731-4845 196049451-196049565 115 0.9141 50 0.40
47
 3'UTR 4846-5009 196049287-196049450 164 0.7624 74 0.23
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
40
TFRC

Aoi: Chr: Coords Strand:
TFRC 3 196050110 - 196050210 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: TFRC(-)
  • Length Length of region: 101 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 / 8daaec85cb / 2026-01-15 03:48