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?

HCFC1
ENST00000310441 (-) ENSG00000172534 (-)

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Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR 1-102 153971717-153971818 102 0.5749 50 0.28
2
 5'UTR 104-223 153971596-153971715 120 0.7122 50 0.26
3
 5'UTR 225-319 153971500-153971594 95 0.6655 50 0.28
4
 5'UTR 320-421 153971398-153971499 102 0.7703 50 0.31
5
 5'UTR 424-533 153971286-153971395 110 0.7010 50 0.31
6
 5'UTR 534-657 153971162-153971285 124 0.8128 50 0.26
7
 5'UTR 658-756 153971063-153971161 99 0.8817 50 0.36
8
 5'UTR 757-871 153970948-153971062 115 0.5931 50 0.21
9
 5'UTR 872-975 153970844-153970947 104 0.7628 50 0.29
10
 5'UTR,CDS 976-1083 153970736-153970843 108 0.8216 50 0.40
11
 CDS 1084-1178 153964720-153964726 / 153970648-153970735 95 0.8318 50 0.28
12
 CDS 1179-1305 153964593-153964719 127 0.8442 50 0.31
13
 CDS 1306-1389 153964216-153964284 / 153964578-153964592 84 0.6974 50 0.27
14
 CDS 1390-1484 153963431-153963433 / 153964124-153964215 95 0.7054 50 0.26
15
 CDS 1485-1580 153963335-153963430 96 0.7175 50 0.33
16
 CDS 1583-1681 153963234-153963332 99 0.7045 50 0.33
17
 CDS 1683-1771 153962226-153962306 / 153963225-153963232 89 0.6034 50 0.32
18
 CDS 1772-1878 153961546-153961648 / 153962222-153962225 107 0.6222 50 0.24
19
 CDS 1879-1970 153960327-153960414 / 153961542-153961545 92 0.9193 50 0.34
20
 CDS 1971-2064 153960160-153960161 / 153960235-153960326 94 0.7809 50 0.33
21
 CDS 2065-2145 153960079-153960159 81 0.6861 50 0.23
22
 CDS 2147-2221 153960003-153960077 75 0.6613 50 0.25
23
 CDS 2222-2301 153959923-153960002 80 0.6541 50 0.28
24
 CDS 2302-2373 153959851-153959922 72 0.7704 50 0.29
25
 CDS 2374-2466 153959448-153959491 / 153959802-153959850 93 0.6113 50 0.35
26
 CDS 2469-2562 153959352-153959445 94 0.5985 50 0.31
27
 CDS 2563-2656 153958694-153958766 / 153959331-153959351 94 0.7428 50 0.39
28
 CDS 2657-2742 153958608-153958693 86 0.4896 50 0.29
29
 CDS 2743-2834 153958197-153958249 / 153958569-153958607 92 0.8202 50 0.29
30
 CDS 2835-2915 153958116-153958196 81 0.7319 50 0.39
31
 CDS 2916-3013 153957880-153957886 / 153958025-153958115 98 0.7917 50 0.32
32
 CDS 3014-3108 153957785-153957879 95 0.6466 50 0.27
33
 CDS 3109-3186 153957459-153957533 / 153957782-153957784 78 0.8112 50 0.30
34
 CDS 3187-3265 153957380-153957458 79 0.8290 50 0.32
35
 CDS 3266-3342 153957050-153957060 / 153957314-153957379 77 0.6059 50 0.27
36
 CDS 3343-3421 153956971-153957049 79 0.9242 50 0.35
37
 CDS 3423-3514 153956724-153956763 / 153956918-153956969 92 0.7028 50 0.36
38
 CDS 3516-3610 153956628-153956722 95 0.6350 50 0.27
39
 CDS 3611-3701 153956324-153956411 / 153956625-153956627 91 0.8078 50 0.31
40
 CDS 3703-3780 153956245-153956322 78 0.8574 50 0.38
41
 CDS 3781-3852 153955525-153955542 / 153956191-153956244 72 0.7102 50 0.25
42
 CDS 3853-3946 153955431-153955524 94 0.6763 50 0.24
43
 CDS 3947-4036 153955341-153955430 90 0.5781 50 0.25
44
 CDS 4037-4111 153955266-153955340 75 0.7304 50 0.31
45
 CDS 4112-4222 153955155-153955265 111 0.7952 50 0.29
46
 CDS 4223-4293 153955084-153955154 71 0.7198 50 0.28
47
 CDS 4294-4366 153955011-153955083 73 0.6011 50 0.27
48
 CDS 4367-4466 153954911-153955010 100 0.7885 50 0.30
49
 CDS 4469-4548 153954829-153954908 80 0.6621 50 0.38
50
 CDS 4549-4647 153954730-153954828 99 0.8035 50 0.32
51
 CDS 4648-4744 153954633-153954729 97 0.7376 50 0.27
52
 CDS 4745-4838 153954539-153954632 94 0.8484 50 0.36
53
 CDS 4839-4908 153954469-153954538 70 0.6820 50 0.25
54
 CDS 4911-4983 153954394-153954466 73 0.7470 50 0.29
55
 CDS 4985-5071 153954306-153954392 87 0.8013 50 0.32
56
 CDS 5072-5170 153954207-153954305 99 0.6444 50 0.30
57
 CDS 5172-5253 153954124-153954205 82 0.7621 50 0.34
58
 CDS 5255-5331 153953751-153953770 / 153954066-153954122 77 0.6414 50 0.27
59
 CDS 5333-5415 153953667-153953749 83 0.4217 50 0.25
60
 CDS 5416-5506 153952928-153952958 / 153953607-153953666 91 0.5088 50 0.30
61
 CDS 5507-5598 153952836-153952927 92 0.6349 50 0.42
62
 CDS 5599-5704 153952730-153952835 106 0.5204 50 0.33
63
 CDS 5705-5779 153952655-153952729 75 0.4570 50 0.32
64
 CDS 5780-5869 153952565-153952654 90 0.6895 50 0.44
65
 CDS 5870-5958 153952121-153952158 / 153952514-153952564 89 0.6489 50 0.36
66
 CDS 5959-6056 153952023-153952120 98 0.5963 50 0.29
67
 CDS 6057-6137 153951942-153952022 81 0.5678 50 0.34
68
 CDS 6138-6225 153951854-153951941 88 0.8554 50 0.42
69
 CDS 6226-6316 153951630-153951707 / 153951841-153951853 91 0.7188 50 0.35
70
 CDS 6317-6397 153951448-153951487 / 153951589-153951629 81 0.6271 50 0.30
71
 CDS 6398-6495 153951350-153951447 98 0.5268 50 0.27
72
 CDS 6497-6591 153950903-153950997 95 0.4991 50 0.24
73
 CDS 6597-6695 153950530-153950543 / 153950813-153950897 99 0.6854 50 0.33
74
 CDS 6697-6788 153950437-153950528 92 0.8763 50 0.38
75
 CDS 6790-6880 153950345-153950435 91 0.8762 50 0.41
76
 CDS 6881-6955 153950270-153950344 75 0.7452 50 0.30
77
 CDS 6956-7035 153949564-153949616 / 153950243-153950269 80 0.8519 50 0.30
78
 CDS,3'UTR 7037-7124 153949309-153949386 / 153949553-153949562 88 0.5871 50 0.25
79
 3'UTR 7125-7196 153949237-153949308 72 0.7243 50 0.27
80
 3'UTR 7198-7301 153949132-153949235 104 0.7567 50 0.38
81
 3'UTR 7302-7401 153949032-153949131 100 0.8159 50 0.45
82
 3'UTR 7403-7510 153948923-153949030 108 0.7655 50 0.37
83
 3'UTR 7518-7613 153948820-153948915 96 0.7399 50 0.36
84
 3'UTR 7614-7700 153948733-153948819 87 0.5564 50 0.29
85
 3'UTR 7701-7786 153948647-153948732 86 0.8584 50 0.41
86
 3'UTR 7802-7998 153948435-153948631 197 0.7950 50 0.31
87
 3'UTR 7999-8099 153948334-153948434 101 0.7597 50 0.41
88
 3'UTR 8100-8205 153948228-153948333 106 0.6541 50 0.29
89
 3'UTR 8211-8295 153948138-153948222 85 0.8530 50 0.49
90
 3'UTR 8296-8401 153948032-153948137 106 0.8177 50 0.45
91
 3'UTR 8402-8506 153947927-153948031 105 0.8999 50 0.37
92
 3'UTR 8507-8588 153947845-153947926 82 0.7851 50 0.32
93
 3'UTR 8590-8700 153947733-153947843 111 0.8513 50 0.36
94
 3'UTR 8702-8802 153947631-153947731 101 0.6595 50 0.28
95
 3'UTR 8807-8861 153947572-153947626 55 0.4339 26 0.33
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
57
HCFC1

Aoi: Chr: Coords Strand:
HCFC1 X 153954124 - 153954205 -
Download Data & Images


  • Annotation Based on canonical annotations, the following gene is in your area of interest: HCFC1(-)
  • Length Length of region: 82 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 / 8daaec85cb / 2026-01-15 02:23