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?

ATP13A3
ENST00000645538 (-) ENSG00000133657 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 28-141 194486862-194486975 114 0.2544 50 0.41
2
 5'UTR 142-233 194486770-194486861 92 0.4081 50 0.33
3
 5'UTR 234-336 194486667-194486769 103 0.4688 50 0.33
4
 5'UTR 339-447 194485826-194485835 / 194486566-194486664 109 0.8527 50 0.37
5
 5'UTR,CDS 448-553 194462163-194462236 / 194485794-194485825 106 0.8300 50 0.26
6
 CDS 554-680 194460728-194460831 / 194462140-194462162 127 0.8028 50 0.26
7
 CDS 685-801 194459921-194459971 / 194460658-194460723 117 0.8198 50 0.28
8
 CDS 802-892 194459830-194459920 91 0.6848 50 0.23
9
 CDS 895-980 194459495-194459541 / 194459789-194459827 86 0.7454 50 0.24
10
 CDS 981-1087 194455961-194455962 / 194457094-194457174 / 194459471-194459494 107 0.7252 50 0.21
11
 CDS 1088-1198 194454350-194454392 / 194455893-194455960 111 0.6594 50 0.20
12
 CDS 1204-1307 194453762-194453778 / 194454258-194454344 104 0.8409 50 0.29
13
 CDS 1310-1413 194450227-194450276 / 194453706-194453759 104 0.5451 50 0.20
14
 CDS 1414-1516 194448616-194448636 / 194450145-194450226 103 0.4878 50 0.21
15
 CDS 1517-1613 194448519-194448615 97 0.7342 50 0.23
16
 CDS 1614-1713 194447972-194448009 / 194448457-194448518 100 0.4924 50 0.17
17
 CDS 1718-1822 194447863-194447967 105 0.7167 50 0.23
18
 CDS 1827-1936 194447013-194447115 / 194447852-194447858 110 0.6437 50 0.24
19
 CDS 1938-2035 194444774-194444786 / 194446927-194447011 98 0.7889 50 0.33
20
 CDS 2036-2155 194441391-194441461 / 194444725-194444773 120 0.7648 50 0.26
21
 CDS 2156-2262 194438946-194438972 / 194441311-194441390 107 0.7969 50 0.26
22
 CDS 2263-2343 194438865-194438945 81 0.7548 50 0.28
23
 CDS 2344-2464 194437371-194437464 / 194437556-194437573 / 194438856-194438864 121 0.8131 50 0.34
24
 CDS 2468-2561 194437179-194437215 / 194437311-194437367 94 0.8251 50 0.28
25
 CDS 2563-2653 194433889-194433896 / 194437095-194437177 91 0.7347 50 0.22
26
 CDS 2657-2744 194433798-194433885 88 0.5142 50 0.20
27
 CDS 2745-2853 194431810-194431892 / 194433772-194433797 109 0.8258 50 0.41
28
 CDS 2856-2940 194431723-194431807 85 0.7099 50 0.29
29
 CDS 2941-3046 194431127-194431226 / 194431717-194431722 106 0.7436 50 0.29
30
 CDS 3047-3163 194430302-194430315 / 194430943-194431022 / 194431104-194431126 117 0.6888 50 0.26
31
 CDS 3173-3281 194430093-194430181 / 194430273-194430292 109 0.7261 50 0.23
32
 CDS 3282-3395 194429682-194429774 / 194430072-194430092 114 0.6387 50 0.23
33
 CDS 3398-3508 194427217-194427252 / 194428845-194428917 / 194429678-194429679 111 0.6954 50 0.27
34
 CDS 3509-3629 194427096-194427216 121 0.7444 50 0.24
35
 CDS 3630-3722 194425458-194425529 / 194427075-194427095 93 0.8834 50 0.30
36
 CDS 3724-3816 194425364-194425456 93 0.8477 50 0.36
37
 CDS 3817-3947 194413820-194413839 / 194419879-194419967 / 194425342-194425363 131 0.7979 50 0.39
38
 CDS 3952-4070 194406055-194406116 / 194413759-194413815 119 0.6639 50 0.23
39
 CDS 4071-4151 194405974-194406054 81 0.5501 50 0.20
40
 CDS,3'UTR 4152-4250 194405875-194405973 99 0.4988 50 0.23
41
 3'UTR 4251-4367 194405758-194405874 117 0.6522 50 0.26
42
 3'UTR 4368-4444 194405681-194405757 77 0.6222 50 0.24
43
 3'UTR 4445-4578 194405547-194405680 134 0.7794 50 0.31
44
 3'UTR 4579-4682 194405443-194405546 104 0.8430 50 0.38
45
 3'UTR 4684-4798 194405327-194405441 115 0.6923 50 0.20
46
 3'UTR 4799-4911 194405214-194405326 113 0.7952 50 0.27
47
 3'UTR 4912-5043 194405082-194405213 132 0.8989 50 0.29
48
 3'UTR 5044-5174 194404951-194405081 131 0.8451 50 0.35
49
 3'UTR 5181-5303 194404822-194404944 123 0.7098 50 0.24
50
 3'UTR 5304-5403 194404722-194404821 100 0.8208 50 0.32
51
 3'UTR 5404-5503 194404622-194404721 100 0.9147 50 0.43
52
 3'UTR 5504-5586 194404539-194404621 83 0.8272 50 0.31
53
 3'UTR 5588-5688 194404437-194404537 101 0.7642 50 0.25
54
 3'UTR 5690-5789 194404336-194404435 100 0.8824 50 0.39
55
 3'UTR 5790-5879 194404246-194404335 90 0.7031 50 0.29
56
 3'UTR 5881-5987 194404138-194404244 107 0.7856 50 0.29
57
 3'UTR 5988-6107 194404018-194404137 120 0.8235 50 0.28
58
 3'UTR 6108-6201 194403924-194404017 94 0.8158 50 0.29
59
 3'UTR 6202-6340 194403785-194403923 139 0.4110 50 0.26
60
 3'UTR 6343-6460 194403665-194403782 118 0.7363 50 0.28
61
 3'UTR 6461-6571 194403554-194403664 111 0.7282 50 0.28
62
 3'UTR 6573-6675 194403450-194403552 103 0.6427 50 0.28
63
 3'UTR 6685-6786 194403339-194403440 102 0.5983 50 0.27
64
 3'UTR 6787-6876 194403249-194403338 90 0.5513 50 0.22
65
 3'UTR 6877-6988 194403137-194403248 112 0.8399 50 0.34
66
 3'UTR 6989-7074 194403051-194403136 86 0.7262 50 0.29
67
 3'UTR 7075-7214 194402911-194403050 140 0.7133 50 0.31
68
 3'UTR 7215-7329 194402796-194402910 115 0.7017 50 0.37
69
 3'UTR 7331-7381 194402744-194402794 51 0.3492 29 0.35
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
51
ATP13A3

Aoi: Chr: Coords Strand:
ATP13A3 3 194404622 - 194404721 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: ATP13A3(-)
  • Length Length of region: 100 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 / 05e29e215d / 2026-03-24 16:46