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?

DNAJC13
ENST00000260818 (+) ENSG00000138246 (+)

Visualize entire gene
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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 89-195 132417590-132417696 107 0.8235 50 0.53
2
 5'UTR,CDS 196-292 132417697-132417760 / 132434538-132434570 97 0.7682 50 0.37
3
 CDS 294-392 132434572-132434618 / 132446475-132446526 99 0.5146 50 0.27
4
 CDS 393-482 132446527-132446550 / 132447321-132447386 90 0.3295 50 0.29
5
 CDS 483-567 132447387-132447470 / 132447898-132447898 85 0.5121 50 0.32
6
 CDS 569-657 132447900-132447939 / 132450647-132450695 89 0.6238 50 0.35
7
 CDS 664-756 132450702-132450794 93 0.5167 50 0.30
8
 CDS 758-870 132450796-132450847 / 132453298-132453358 113 0.3783 50 0.26
9
 CDS 871-968 132453359-132453456 98 0.3921 50 0.24
10
 CDS 969-1061 132453457-132453504 / 132453599-132453643 93 0.5290 50 0.27
11
 CDS 1063-1158 132453645-132453694 / 132454066-132454111 96 0.6032 50 0.25
12
 CDS 1162-1270 132454115-132454157 / 132456235-132456300 109 0.5278 50 0.29
13
 CDS 1271-1366 132456301-132456396 96 0.4912 50 0.39
14
 CDS 1368-1465 132456398-132456401 / 132456501-132456580 / 132456663-132456676 98 0.3170 50 0.30
15
 CDS 1466-1551 132456677-132456762 86 0.5516 50 0.38
16
 CDS 1554-1663 132456765-132456832 / 132457269-132457310 110 0.6070 50 0.31
17
 CDS 1664-1755 132457311-132457368 / 132460250-132460283 92 0.2045 50 0.25
18
 CDS 1756-1863 132460284-132460357 / 132461050-132461083 108 0.5516 50 0.33
19
 CDS 1865-1968 132461085-132461188 104 0.4532 50 0.36
20
 CDS 1974-2069 132461194-132461205 / 132462467-132462523 / 132463696-132463722 96 0.4173 50 0.33
21
 CDS 2070-2163 132463723-132463816 94 0.4161 50 0.28
22
 CDS 2165-2261 132465995-132466070 / 132466299-132466319 97 0.5803 50 0.30
23
 CDS 2266-2364 132466324-132466394 / 132467170-132467197 99 0.5327 50 0.31
24
 CDS 2365-2466 132467198-132467299 102 0.6289 50 0.29
25
 CDS 2470-2550 132467303-132467313 / 132473145-132473214 81 0.7636 50 0.30
26
 CDS 2552-2645 132473216-132473227 / 132474932-132475013 94 0.5375 50 0.31
27
 CDS 2646-2749 132475014-132475085 / 132477789-132477820 104 0.3958 50 0.29
28
 CDS 2750-2855 132477821-132477892 / 132477981-132478014 106 0.4068 50 0.27
29
 CDS 2859-2953 132478018-132478112 95 0.6497 50 0.31
30
 CDS 2954-3054 132478113-132478140 / 132479227-132479289 / 132480369-132480378 101 0.6368 50 0.33
31
 CDS 3055-3146 132480379-132480470 92 0.6426 50 0.33
32
 CDS 3147-3246 132482226-132482325 100 0.2656 50 0.23
33
 CDS 3247-3341 132482326-132482330 / 132483375-132483464 95 0.2376 50 0.27
34
 CDS 3342-3448 132483465-132483571 107 0.7027 50 0.31
35
 CDS 3449-3531 132483572-132483577 / 132484588-132484664 83 0.6396 50 0.31
36
 CDS 3534-3631 132484667-132484672 / 132488298-132488389 98 0.7354 50 0.33
37
 CDS 3633-3737 132488391-132488452 / 132488976-132489018 105 0.4293 50 0.33
38
 CDS 3739-3832 132489020-132489021 / 132490897-132490988 94 0.2710 50 0.27
39
 CDS 3838-3941 132490994-132491051 / 132492414-132492459 104 0.5753 50 0.33
40
 CDS 3942-4021 132492460-132492539 80 0.4286 50 0.26
41
 CDS 4022-4116 132492540-132492615 / 132494144-132494162 95 0.2809 50 0.25
42
 CDS 4117-4211 132494163-132494257 95 0.3606 50 0.28
43
 CDS 4212-4296 132494258-132494259 / 132495088-132495166 / 132496528-132496531 85 0.4358 50 0.28
44
 CDS 4303-4391 132496538-132496626 89 0.3413 50 0.30
45
 CDS 4392-4473 132496627-132496663 / 132499126-132499170 82 0.2074 50 0.33
46
 CDS 4474-4563 132499171-132499260 90 0.4347 50 0.34
47
 CDS 4564-4670 132499261-132499310 / 132499734-132499790 107 0.3846 50 0.30
48
 CDS 4671-4775 132499791-132499808 / 132500794-132500880 105 0.3608 50 0.26
49
 CDS 4776-4899 132500881-132500913 / 132502289-132502379 124 0.4450 50 0.28
50
 CDS 4909-5000 132502389-132502468 / 132503214-132503225 92 0.3009 50 0.32
51
 CDS 5001-5091 132503226-132503316 91 0.4816 50 0.34
52
 CDS 5092-5191 132503317-132503381 / 132505302-132505336 100 0.3577 50 0.29
53
 CDS 5192-5282 132505337-132505415 / 132507237-132507248 91 0.4970 50 0.31
54
 CDS 5283-5394 132507249-132507353 / 132511067-132511073 112 0.4544 50 0.28
55
 CDS 5395-5485 132511074-132511164 91 0.3675 50 0.32
56
 CDS 5488-5589 132511167-132511244 / 132513008-132513031 102 0.4181 50 0.29
57
 CDS 5590-5704 132513032-132513099 / 132514571-132514617 115 0.3551 50 0.27
58
 CDS 5707-5813 132514620-132514670 / 132516422-132516477 107 0.2838 50 0.31
59
 CDS 5814-5903 132516478-132516496 / 132516704-132516774 90 0.5784 50 0.35
60
 CDS 5904-6002 132516775-132516816 / 132522828-132522884 99 0.2583 50 0.29
61
 CDS 6003-6099 132522885-132522981 97 0.4872 50 0.32
62
 CDS 6103-6208 132522985-132522997 / 132523157-132523199 / 132523540-132523589 106 0.3972 50 0.31
63
 CDS 6215-6316 132523596-132523697 102 0.5132 50 0.38
64
 CDS 6318-6402 132523699-132523713 / 132525610-132525679 85 0.2145 50 0.36
65
 CDS 6403-6493 132525680-132525770 91 0.5251 50 0.37
66
 CDS 6496-6604 132525773-132525789 / 132526141-132526232 109 0.3152 50 0.35
67
 CDS 6605-6697 132526233-132526281 / 132528189-132528232 93 0.3830 50 0.34
68
 CDS 6698-6791 132528233-132528326 94 0.4856 50 0.37
69
 CDS 6793-6890 132528328-132528332 / 132530998-132531090 98 0.3898 50 0.34
70
 CDS 6891-6980 132531091-132531097 / 132538176-132538258 90 0.5571 50 0.30
71
 CDS,3'UTR 6983-7066 132538261-132538344 84 0.3991 50 0.34
72
 3'UTR 7068-7174 132538346-132538452 107 0.3573 50 0.37
73
 3'UTR 7175-7285 132538453-132538563 111 0.4723 50 0.34
74
 3'UTR 7287-7391 132538565-132538669 105 0.6970 50 0.45
75
 3'UTR 7392-7444 132538670-132538722 53 0.4729 31 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.

completed
42
DNAJC13

Aoi: Chr: Coords Strand:
DNAJC13 3 132494163 - 132494257 +
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: DNAJC13(+)
  • Length Length of region: 95 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 2 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 / 6840c0a13a / 2026-05-28 16:14