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?

STARD4
ENST00000296632 (-) ENSG00000164211 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 7-130 111512406-111512529 124 0.5435 50 0.28
2
 5'UTR,CDS 131-224 111507370-111507442 / 111512385-111512405 94 0.5039 50 0.23
3
 CDS 225-319 111502085-111502088 / 111506330-111506379 / 111507329-111507369 95 0.4236 50 0.19
4
 CDS 320-432 111501972-111502084 113 0.6494 50 0.25
5
 CDS 433-552 111501007-111501116 / 111501962-111501971 120 0.5468 50 0.21
6
 CDS 559-656 111500008-111500105 98 0.5390 50 0.24
7
 CDS 657-763 111499901-111500007 107 0.4868 50 0.22
8
 CDS,3'UTR 764-847 111499817-111499900 84 0.6872 50 0.22
9
 3'UTR 851-962 111499702-111499813 112 0.6531 50 0.25
10
 3'UTR 975-1080 111499584-111499689 106 0.8814 50 0.55
11
 3'UTR 1082-1199 111499465-111499582 118 0.8379 50 0.43
12
 3'UTR 1200-1296 111499368-111499464 97 0.7287 50 0.38
13
 3'UTR 1297-1387 111499277-111499367 91 0.6829 50 0.31
14
 3'UTR 1388-1509 111499155-111499276 122 0.6533 50 0.34
15
 3'UTR 1510-1631 111499033-111499154 122 0.7169 50 0.32
16
 3'UTR 1637-1755 111498909-111499027 119 0.5561 50 0.22
17
 3'UTR 1756-1889 111498775-111498908 134 0.5427 50 0.31
18
 3'UTR 1890-1978 111498686-111498774 89 0.5224 50 0.29
19
 3'UTR 1979-2096 111498568-111498685 118 0.6797 50 0.34
20
 3'UTR 2099-2235 111498429-111498565 137 0.6492 50 0.34
21
 3'UTR 2236-2330 111498334-111498428 95 0.5241 50 0.29
22
 3'UTR 2331-2416 111498248-111498333 86 0.3597 50 0.32
23
 3'UTR 2417-2517 111498147-111498247 101 0.4412 50 0.36
24
 3'UTR 2521-2641 111498023-111498143 121 0.2472 50 0.40
25
 3'UTR 2642-2737 111497927-111498022 96 0.2585 50 0.31
26
 3'UTR 2738-2852 111497812-111497926 115 0.4540 50 0.33
27
 3'UTR 2853-2959 111497705-111497811 107 0.2266 50 0.31
28
 3'UTR 2963-3065 111497599-111497701 103 0.2651 50 0.44
29
 3'UTR 3066-3178 111497486-111497598 113 0.3212 50 0.37
30
 3'UTR 3179-3285 111497379-111497485 107 0.3625 50 0.35
31
 3'UTR 3287-3382 111497282-111497377 96 0.3585 50 0.33
32
 3'UTR 3384-3482 111497182-111497280 99 0.3790 50 0.35
33
 3'UTR 3484-3614 111497050-111497180 131 0.4263 50 0.41
34
 3'UTR 3619-3715 111496949-111497045 97 0.2393 50 0.34
35
 3'UTR 3717-3830 111496834-111496947 114 0.5220 50 0.35
36
 3'UTR 3831-4039 111496625-111496833 209 0.4193 50 0.35
37
 3'UTR 4043-4145 111496519-111496621 103 0.5099 50 0.38
38
 3'UTR 4146-4250 111496414-111496518 105 0.4280 50 0.34
39
 3'UTR 4251-4410 111496254-111496413 160 0.3757 73 0.34
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
22
STARD4

Aoi: Chr: Coords Strand:
STARD4 5 111498248 - 111498333 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: STARD4(-)
  • 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 / 2026-03-20 05:58