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?

ZMIZ1
ENST00000334512 (+) ENSG00000108175 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 300-404 79069265-79069270 / 79118915-79119013 105 0.4370 50 0.29
2
 5'UTR 407-513 79119016-79119024 / 79139682-79139777 / 79162053-79162054 107 0.3597 50 0.26
3
 5'UTR 516-634 79162057-79162133 / 79201584-79201625 119 0.6277 50 0.28
4
 5'UTR,CDS 637-715 79201628-79201692 / 79208336-79208349 79 0.3961 50 0.28
5
 CDS 718-814 79208352-79208448 97 0.5264 50 0.38
6
 CDS 821-919 79216174-79216272 99 0.2817 50 0.35
7
 CDS 920-1012 79216273-79216274 / 79277181-79277271 93 0.4226 50 0.35
8
 CDS 1013-1102 79277272-79277325 / 79289775-79289810 90 0.4913 50 0.39
9
 CDS 1104-1184 79289812-79289889 / 79290959-79290961 81 0.5783 50 0.38
10
 CDS 1185-1263 79290962-79291040 79 0.4506 50 0.32
11
 CDS 1264-1404 79291041-79291176 / 79292158-79292162 141 0.4284 50 0.38
12
 CDS 1405-1489 79292163-79292247 85 0.5766 50 0.41
13
 CDS 1492-1570 79292250-79292328 79 0.7473 50 0.40
14
 CDS 1572-1656 79292330-79292356 / 79293381-79293438 85 0.5350 50 0.35
15
 CDS 1657-1751 79293439-79293533 95 0.7534 50 0.48
16
 CDS 1752-1831 79293534-79293613 80 0.6598 50 0.38
17
 CDS 1832-1907 79293614-79293653 / 79296471-79296506 76 0.5558 50 0.24
18
 CDS 1908-1971 79296507-79296570 64 0.4719 50 0.35
19
 CDS 1972-2052 79296571-79296651 81 0.5646 50 0.41
20
 CDS 2053-2134 79296652-79296653 / 79297613-79297690 / 79298406-79298407 82 0.4763 50 0.32
21
 CDS 2136-2213 79298409-79298486 78 0.6501 50 0.37
22
 CDS 2214-2288 79298487-79298561 75 0.3723 50 0.35
23
 CDS 2290-2488 79298563-79298580 / 79299050-79299191 / 79300732-79300770 199 0.3998 50 0.35
24
 CDS 2491-2572 79300773-79300854 82 0.5517 50 0.38
25
 CDS 2573-2645 79300855-79300927 73 0.4401 50 0.33
26
 CDS 2646-2738 79300928-79300942 / 79302107-79302184 93 0.3383 50 0.38
27
 CDS 2739-2838 79302185-79302212 / 79304015-79304086 100 0.3747 50 0.37
28
 CDS 2839-2935 79304087-79304175 / 79305164-79305171 97 0.5577 50 0.38
29
 CDS 2937-3052 79305173-79305231 / 79305533-79305589 116 0.5365 50 0.27
30
 CDS 3055-3140 79305592-79305601 / 79306100-79306175 86 0.5144 50 0.35
31
 CDS 3141-3227 79306176-79306262 87 0.4517 50 0.35
32
 CDS 3229-3302 79306264-79306337 74 0.5896 50 0.36
33
 CDS 3303-3383 79306338-79306344 / 79307405-79307478 81 0.5407 50 0.39
34
 CDS 3384-3452 79307479-79307547 69 0.6239 50 0.45
35
 CDS 3453-3638 79307548-79307571 / 79310924-79311085 186 0.5763 50 0.35
36
 CDS 3639-3730 79311086-79311177 92 0.6254 50 0.46
37
 CDS 3732-3814 79311179-79311184 / 79312642-79312718 83 0.6654 50 0.36
38
 CDS,3'UTR 3817-3897 79312721-79312801 81 0.5926 50 0.35
39
 3'UTR 3898-3982 79312802-79312886 85 0.5799 50 0.45
40
 3'UTR 3984-4087 79312888-79312991 104 0.5610 50 0.39
41
 3'UTR 4088-4171 79312992-79313075 84 0.5421 50 0.44
42
 3'UTR 4172-4266 79313076-79313170 95 0.3279 50 0.39
43
 3'UTR 4268-4366 79313172-79313270 99 0.7151 50 0.51
44
 3'UTR 4367-4448 79313271-79313352 82 0.5084 50 0.43
45
 3'UTR 4449-4525 79313353-79313429 77 0.6190 50 0.42
46
 3'UTR 4532-4629 79313436-79313533 98 0.5406 50 0.33
47
 3'UTR 4632-4732 79313536-79313636 101 0.4975 50 0.35
48
 3'UTR 4733-4823 79313637-79313727 91 0.4093 50 0.36
49
 3'UTR 4824-4911 79313728-79313815 88 0.3422 50 0.33
50
 3'UTR 4914-5018 79313818-79313922 105 0.4488 50 0.36
51
 3'UTR 5019-5128 79313923-79314032 110 0.6566 50 0.45
52
 3'UTR 5129-5200 79314033-79314104 72 0.7376 50 0.45
53
 3'UTR 5201-5357 79314105-79314261 157 0.4934 50 0.46
54
 3'UTR 5358-5468 79314262-79314372 111 0.4961 50 0.38
55
 3'UTR 5470-5575 79314374-79314479 106 0.6513 50 0.38
56
 3'UTR 5578-5702 79314482-79314606 125 0.3866 50 0.32
57
 3'UTR 5703-5801 79314607-79314705 99 0.6199 50 0.49
58
 3'UTR 5802-5911 79314706-79314815 110 0.5164 50 0.38
59
 3'UTR 5912-6008 79314816-79314912 97 0.5122 50 0.38
60
 3'UTR 6010-6120 79314914-79315024 111 0.4179 50 0.43
61
 3'UTR 6122-6215 79315026-79315119 94 0.6793 50 0.51
62
 3'UTR 6217-6351 79315121-79315255 135 0.4666 50 0.44
63
 3'UTR 6354-6459 79315258-79315363 106 0.6379 50 0.34
64
 3'UTR 6461-6551 79315365-79315455 91 0.5712 50 0.31
65
 3'UTR 6552-6633 79315456-79315537 82 0.5035 50 0.38
66
 3'UTR 6636-6741 79315540-79315645 106 0.4280 50 0.28
67
 3'UTR 6742-6826 79315646-79315730 85 0.4996 50 0.36
68
 3'UTR 6830-6942 79315734-79315846 113 0.5423 50 0.32
69
 3'UTR 6943-7026 79315847-79315930 84 0.5764 50 0.35
70
 3'UTR 7027-7143 79315931-79316047 117 0.8050 50 0.37
71
 3'UTR 7149-7253 79316053-79316157 105 0.5825 50 0.32
72
 3'UTR 7256-7320 79316160-79316224 65 0.4532 50 0.30
73
 3'UTR 7323-7393 79316227-79316297 71 0.8079 30 0.40
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
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ZMIZ1

Aoi: Chr: Coords Strand:
ZMIZ1 10 79305592 - 79305601, 79306100 - 79306175 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: ZMIZ1(+)
  • Length Length of region: 86 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 / 05e29e215d / 2026-04-04 03:14