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?

ZHX1
ENST00000297857 (-) ENSG00000165156 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 221-371 123267382-123267386 / 123274122-123274267 151 0.2836 50 0.40
2
 5'UTR 373-466 123267287-123267380 94 0.6169 50 0.27
3
 5'UTR 469-570 123256082-123256171 / 123267273-123267284 102 0.4476 50 0.28
4
 5'UTR 572-660 123255992-123256080 89 0.5506 50 0.32
5
 5'UTR,CDS 662-749 123255903-123255990 88 0.6501 50 0.32
6
 CDS 750-843 123255809-123255902 94 0.8209 50 0.32
7
 CDS 845-943 123255709-123255807 99 0.7487 50 0.30
8
 CDS 944-1052 123255600-123255708 109 0.4386 50 0.27
9
 CDS 1053-1142 123255510-123255599 90 0.4357 50 0.21
10
 CDS 1143-1245 123255407-123255509 103 0.4583 50 0.25
11
 CDS 1246-1334 123255318-123255406 89 0.6319 50 0.27
12
 CDS 1335-1417 123255235-123255317 83 0.6238 50 0.25
13
 CDS 1422-1513 123255139-123255230 92 0.7954 50 0.32
14
 CDS 1514-1602 123255050-123255138 89 0.6828 50 0.26
15
 CDS 1603-1679 123254973-123255049 77 0.4616 50 0.28
16
 CDS 1682-1775 123254877-123254970 94 0.4824 50 0.27
17
 CDS 1779-1866 123254786-123254873 88 0.7235 50 0.40
18
 CDS 1869-1966 123254686-123254783 98 0.6812 50 0.34
19
 CDS 1967-2040 123254612-123254685 74 0.7474 50 0.27
20
 CDS 2042-2126 123254526-123254610 85 0.6882 50 0.24
21
 CDS 2128-2211 123254441-123254524 84 0.5008 50 0.22
22
 CDS 2212-2297 123254355-123254440 86 0.5951 50 0.30
23
 CDS 2298-2380 123254272-123254354 83 0.5103 50 0.32
24
 CDS 2381-2472 123254180-123254271 92 0.5416 50 0.34
25
 CDS 2473-2561 123254091-123254179 89 0.5197 50 0.27
26
 CDS 2563-2648 123254004-123254089 86 0.5289 50 0.23
27
 CDS 2650-2739 123253913-123254002 90 0.7080 50 0.31
28
 CDS 2745-2839 123253813-123253907 95 0.7507 50 0.28
29
 CDS 2843-2946 123253706-123253809 104 0.8506 50 0.41
30
 CDS 2947-3033 123253619-123253705 87 0.7296 50 0.26
31
 CDS 3034-3123 123253529-123253618 90 0.6877 50 0.24
32
 CDS 3125-3233 123253419-123253527 109 0.5080 50 0.19
33
 CDS 3236-3323 123253329-123253416 88 0.6327 50 0.26
34
 CDS,3'UTR 3324-3419 123250232-123250320 / 123253322-123253328 96 0.7637 50 0.35
35
 3'UTR 3429-3504 123250147-123250222 76 0.4246 50 0.24
36
 3'UTR 3513-3599 123250052-123250138 87 0.5414 50 0.34
37
 3'UTR 3601-3717 123249934-123250050 117 0.4255 50 0.29
38
 3'UTR 3718-3847 123249804-123249933 130 0.6749 50 0.42
39
 3'UTR 3848-3949 123249702-123249803 102 0.3870 50 0.40
40
 3'UTR 3950-4051 123249600-123249701 102 0.2902 50 0.31
41
 3'UTR 4052-4142 123249509-123249599 91 0.3034 50 0.31
42
 3'UTR 4143-4254 123249397-123249508 112 0.7564 50 0.43
43
 3'UTR 4255-4360 123249291-123249396 106 0.8082 50 0.50
44
 3'UTR 4361-4465 123249186-123249290 105 0.5563 50 0.24
45
 3'UTR 4466-4585 123249066-123249185 120 0.6644 50 0.31
46
 3'UTR 4587-4704 123248947-123249064 118 0.5042 50 0.31
47
 3'UTR 4707-4811 123248840-123248944 105 0.4436 50 0.31
48
 3'UTR 4812-4888 123248763-123248839 77 0.3661 37 0.35
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
5
ZHX1

Aoi: Chr: Coords Strand:
ZHX1 8 123255903 - 123255990 -
Download Data & Images


  • Annotation Based on canonical annotations, the following genes are in your area of interest: ZHX1-C8orf76(-), ZHX1(-)
  • Length Length of region: 88 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 3 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 / 2026-03-20 19:32