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?

ITCH
ENST00000374864 (+) ENSG00000078747 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 36-133 34363308-34363349 / 34369394-34369449 98 0.5588 50 0.34
2
 5'UTR,CDS 134-233 34369450-34369470 / 34393791-34393869 100 0.4816 50 0.28
3
 CDS 236-327 34393872-34393881 / 34408651-34408732 92 0.5661 50 0.26
4
 CDS 328-398 34408733-34408792 / 34412515-34412525 71 0.4439 50 0.24
5
 CDS 399-506 34412526-34412633 108 0.4202 50 0.27
6
 CDS 509-616 34412636-34412639 / 34413742-34413845 108 0.4507 50 0.25
7
 CDS 623-712 34413852-34413879 / 34424480-34424525 / 34438474-34438489 90 0.4248 50 0.25
8
 CDS 714-812 34438491-34438589 99 0.6745 50 0.28
9
 CDS 813-882 34438590-34438631 / 34440155-34440182 70 0.6478 50 0.30
10
 CDS 885-971 34440185-34440271 87 0.4451 50 0.27
11
 CDS 974-1068 34440274-34440344 / 34442208-34442231 95 0.6682 50 0.35
12
 CDS 1069-1168 34442232-34442303 / 34445287-34445314 100 0.6315 50 0.27
13
 CDS 1169-1256 34445315-34445402 88 0.6591 50 0.23
14
 CDS 1258-1350 34445404-34445461 / 34449411-34449445 93 0.4412 50 0.19
15
 CDS 1351-1439 34449446-34449480 / 34457390-34457443 89 0.5647 50 0.23
16
 CDS 1442-1532 34457446-34457474 / 34462093-34462154 91 0.6338 50 0.30
17
 CDS 1533-1611 34462155-34462221 / 34470048-34470059 79 0.5382 50 0.26
18
 CDS 1613-1709 34470061-34470120 / 34471444-34471480 97 0.5263 50 0.23
19
 CDS 1710-1815 34471481-34471515 / 34477772-34477842 106 0.3831 50 0.23
20
 CDS 1818-1929 34477845-34477860 / 34479630-34479725 112 0.5426 50 0.24
21
 CDS 1930-2038 34479726-34479789 / 34480599-34480643 109 0.6647 50 0.28
22
 CDS 2041-2135 34480646-34480732 / 34481066-34481073 95 0.5464 50 0.28
23
 CDS 2136-2242 34481074-34481180 107 0.4029 50 0.22
24
 CDS 2244-2348 34481182-34481206 / 34489266-34489345 105 0.7020 50 0.30
25
 CDS 2349-2449 34489346-34489386 / 34489822-34489881 101 0.5822 50 0.30
26
 CDS 2450-2554 34489882-34489926 / 34492501-34492560 105 0.6178 50 0.23
27
 CDS 2557-2654 34492563-34492597 / 34504331-34504393 98 0.5014 50 0.24
28
 CDS 2657-2745 34504396-34504403 / 34507695-34507775 89 0.6050 50 0.32
29
 CDS,3'UTR 2746-2852 34507776-34507882 107 0.8042 50 0.42
30
 3'UTR 2853-2962 34507883-34507992 110 0.5788 50 0.29
31
 3'UTR 2965-3063 34507995-34508093 99 0.4262 50 0.29
32
 3'UTR 3064-3178 34508094-34508208 115 0.5243 50 0.38
33
 3'UTR 3179-3301 34508209-34508331 123 0.5752 50 0.39
34
 3'UTR 3302-3401 34508332-34508431 100 0.4497 50 0.32
35
 3'UTR 3407-3507 34508437-34508537 101 0.5661 50 0.33
36
 3'UTR 3514-3606 34508544-34508636 93 0.8833 50 0.70
37
 3'UTR 3607-3711 34508637-34508741 105 0.6048 50 0.41
38
 3'UTR 3717-3828 34508747-34508858 112 0.6548 50 0.40
39
 3'UTR 3832-3930 34508862-34508960 99 0.5111 50 0.40
40
 3'UTR 3931-4034 34508961-34509064 104 0.3419 50 0.36
41
 3'UTR 4038-4213 34509068-34509243 176 0.5285 50 0.38
42
 3'UTR 4215-4311 34509245-34509341 97 0.4300 50 0.44
43
 3'UTR 4317-4395 34509347-34509425 79 0.2366 50 0.34
44
 3'UTR 4397-4489 34509427-34509519 93 0.2895 50 0.40
45
 3'UTR 4490-4593 34509520-34509623 104 0.6949 50 0.46
46
 3'UTR 4597-4710 34509627-34509740 114 0.4933 50 0.37
47
 3'UTR 4713-4810 34509743-34509840 98 0.4573 50 0.36
48
 3'UTR 4811-4915 34509841-34509945 105 0.4147 50 0.33
49
 3'UTR 4916-5011 34509946-34510041 96 0.2837 50 0.35
50
 3'UTR 5014-5138 34510044-34510168 125 0.6530 50 0.50
51
 3'UTR 5139-5242 34510169-34510272 104 0.5673 50 0.40
52
 3'UTR 5243-5403 34510273-34510433 161 0.2672 73 0.38
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
35
ITCH

Aoi: Chr: Coords Strand:
ITCH 20 34508437 - 34508537 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: ITCH(+)
  • 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
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production / b252b9f76a / 2025-07-17 08:16