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?

MLXIP
ENST00000319080 (+) ENSG00000175727 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 29-127 122078784-122078882 99 0.3942 50 0.46
2
 CDS 129-261 122078884-122079016 133 0.5407 50 0.43
3
 CDS 263-344 122079018-122079099 82 0.4752 50 0.41
4
 CDS 345-427 122079100-122079182 83 0.6268 50 0.38
5
 CDS 428-526 122079183-122079266 / 122127256-122127270 99 0.5309 50 0.39
6
 CDS 528-625 122127272-122127362 / 122127883-122127889 98 0.4368 50 0.31
7
 CDS 627-718 122127891-122127968 / 122129137-122129150 92 0.5840 50 0.38
8
 CDS 719-808 122129151-122129226 / 122129588-122129601 90 0.3702 50 0.28
9
 CDS 811-907 122129604-122129629 / 122129941-122130011 97 0.7114 50 0.43
10
 CDS 908-993 122130012-122130097 86 0.6511 50 0.38
11
 CDS 994-1082 122130098-122130112 / 122130844-122130917 89 0.4753 50 0.31
12
 CDS 1087-1175 122130922-122130933 / 122132292-122132368 89 0.6076 50 0.25
13
 CDS 1176-1251 122132369-122132383 / 122133348-122133408 76 0.6437 50 0.32
14
 CDS 1252-1334 122133409-122133491 83 0.6139 50 0.39
15
 CDS 1335-1420 122133492-122133577 86 0.6074 50 0.37
16
 CDS 1421-1495 122133578-122133652 75 0.7000 50 0.41
17
 CDS 1496-1574 122133653-122133731 79 0.5473 50 0.36
18
 CDS 1575-1649 122133732-122133806 75 0.5559 50 0.38
19
 CDS 1651-1753 122133808-122133910 103 0.3460 50 0.37
20
 CDS 1755-1983 122133912-122133987 / 122135224-122135345 / 122135489-122135519 229 0.4254 50 0.37
21
 CDS 1985-2146 122135521-122135666 / 122137469-122137484 162 0.2572 50 0.38
22
 CDS 2147-2229 122137485-122137567 83 0.5428 50 0.44
23
 CDS 2230-2315 122137568-122137590 / 122138194-122138256 86 0.3775 50 0.45
24
 CDS 2317-2393 122138258-122138295 / 122138424-122138462 77 0.3599 50 0.34
25
 CDS 2394-2486 122138463-122138551 / 122138815-122138818 93 0.5161 50 0.43
26
 CDS 2489-2576 122138821-122138908 88 0.4534 50 0.41
27
 CDS,3'UTR 2577-3162 122138909-122138938 / 122140954-122141083 / 122141691-122142116 586 0.4416 50 0.42
Error
28
 3'UTR 3163-3275 122142117-122142229 113 0.4251 50 0.43
29
 3'UTR 3276-3597 122142230-122142551 322 0.4965 50 0.44
30
 3'UTR 3598-3735 122142552-122142689 138 0.4482 50 0.47
31
 3'UTR 3739-3838 122142693-122142792 100 0.6317 50 0.46
32
 3'UTR 3839-3955 122142793-122142909 117 0.4441 50 0.44
33
 3'UTR 3957-4385 122142911-122143339 429 0.7312 50 0.47
34
 3'UTR 4388-4477 122143342-122143431 90 0.2862 50 0.43
35
 3'UTR 4481-4586 122143435-122143540 106 0.2895 50 0.38
36
 3'UTR 4587-4676 122143541-122143630 90 0.4497 50 0.40
37
 3'UTR 4680-4786 122143634-122143740 107 0.4353 50 0.40
38
 3'UTR 4963-5076 122143917-122144030 114 0.3801 50 0.40
39
 3'UTR 5077-5196 122144031-122144150 120 0.3857 50 0.42
40
 3'UTR 5197-5854 122144151-122144808 658 0.5524 50 0.44
Error
41
 3'UTR 5855-7161 122144809-122146115 1307 0.6887 50 0.46
Error
42
 3'UTR 7162-7283 122146116-122146237 122 0.5197 50 0.40
43
 3'UTR 7284-7416 122146238-122146370 133 0.4194 50 0.35
44
 3'UTR 7417-7512 122146371-122146466 96 0.4042 50 0.44
45
 3'UTR 7514-7619 122146468-122146573 106 0.2722 50 0.42
46
 3'UTR 7621-7820 122146575-122146774 200 0.2913 50 0.37
47
 3'UTR 7823-7942 122146777-122146896 120 0.3243 50 0.40
48
 3'UTR 7946-8032 122146900-122146986 87 0.6410 50 0.40
49
 3'UTR 8033-8241 122146987-122147195 209 0.5317 50 0.47
50
 3'UTR 8242-8313 122147196-122147267 72 0.5126 43 0.44
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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MLXIP

Aoi: Chr: Coords Strand:
MLXIP 12 122146987 - 122147195 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: MLXIP(+)
  • Length Length of region: 209 nt.
  • Structures This region has 8 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.
  • Coverage 60.199999999999996% of the region's A/C bases included in the filtered DMS dataset. This is lower than the recommended 70%. While structure prediction is still possible even without any coverage, the structures will be based on the sequence alone, rather than based on experimental constraints.
Structures
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production / 6840c0a13a / 2026-06-08 03:10