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
Coords (max 500bp)
Coords 1  
Additional Coordinates
Coords 2 Optional
Coords 3 Optional
Coords 4 Optional


How was this calculated?

NFKB1
ENST00000226574 (+) ENSG00000109320 (+)

Visualize entire gene
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  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 374-634 102501732-102501788 / 102525512-102525557 / 102537858-102537895 261 0.3025 50 0.33
2
 CDS 635-726 102537896-102537956 / 102566987-102567017 92 0.2494 50 0.39
3
 CDS 732-825 102567023-102567116 94 0.3886 50 0.39
4
 CDS 826-916 102567117-102567135 / 102576876-102576947 91 0.5071 50 0.29
5
 CDS 919-1026 102576950-102577039 / 102578881-102578898 108 0.5761 50 0.30
6
 CDS 1028-1124 102578900-102578996 97 0.3365 50 0.27
7
 CDS 1125-1209 102578997-102579039 / 102580535-102580576 85 0.6386 50 0.39
8
 CDS 1212-1328 102580579-102580639 / 102582866-102582921 117 0.3286 50 0.32
9
 CDS 1334-1542 102582927-102582957 / 102584682-102584820 / 102593425-102593463 209 0.2858 50 0.35
10
 CDS 1543-1681 102593464-102593568 / 102594892-102594925 139 0.5133 50 0.38
11
 CDS 1689-1781 102594933-102594981 / 102596138-102596181 93 0.4569 50 0.31
12
 CDS 1782-1863 102596182-102596263 82 0.4733 50 0.29
13
 CDS 1864-1966 102596264-102596332 / 102597520-102597553 103 0.4843 50 0.27
14
 CDS 1967-2065 102597554-102597652 99 0.4478 50 0.34
15
 CDS 2071-2168 102597658-102597661 / 102600895-102600988 98 0.2730 50 0.36
16
 CDS 2169-2279 102600989-102601009 / 102606496-102606585 111 0.4540 50 0.33
17
 CDS 2286-2370 102606592-102606676 85 0.5080 50 0.34
18
 CDS 2374-2476 102606680-102606697 / 102607150-102607234 103 0.4048 50 0.36
19
 CDS 2478-2578 102607236-102607319 / 102607649-102607665 101 0.4709 50 0.40
20
 CDS 2579-2663 102607666-102607750 85 0.7294 50 0.46
21
 CDS 2666-2770 102610576-102610680 105 0.4166 50 0.34
22
 CDS 2772-2866 102610682-102610699 / 102612044-102612110 / 102612434-102612443 95 0.4792 50 0.30
23
 CDS 2867-2967 102612444-102612544 101 0.3566 50 0.32
24
 CDS 2969-3071 102612546-102612606 / 102613425-102613466 103 0.2079 50 0.33
25
 CDS 3072-3150 102613467-102613545 79 0.3790 50 0.40
26
 CDS 3153-3240 102613548-102613581 / 102616434-102616487 88 0.6282 50 0.46
27
 CDS 3242-3328 102616489-102616575 87 0.3758 50 0.29
28
 CDS,3'UTR 3330-3409 102616577-102616656 80 0.3326 50 0.39
29
 3'UTR 3410-3502 102616657-102616749 93 0.6429 50 0.39
30
 3'UTR 3506-3618 102616753-102616865 113 0.3962 50 0.38
31
 3'UTR 3621-3724 102616868-102616971 104 0.4758 46 0.36
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.

Recently Visualized

NFKB1
Chr Coords Strand
4 102616986 - 102617285
300 bp
5s
completed
production / 362c1546a7 / 2025-05-20 14:27