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?

ZBTB20
ENST00000675478 (-) ENSG00000181722 (-)

Visualize entire gene
100
150
300
500
+
-
Predict
  Region Local Coords Chrom Coords Length R N Gini Action
1
 5'UTR,CDS 479-795 114380393-114380404 / 114389005-114389105 / 114500352-114500391 317 0.2159 50 0.32
2
 CDS 797-888 114380300-114380391 92 0.5822 50 0.35
3
 CDS,3'UTR 889-3460 114338543-114339426 / 114380217-114380299 2572 0.2649 50 0.40
Error
4
 3'UTR 3461-3551 114338452-114338542 91 0.2268 50 0.46
5
 3'UTR 3552-3672 114338331-114338451 121 0.5948 50 0.48
6
 3'UTR 3673-3832 114338171-114338330 160 0.4049 50 0.43
7
 3'UTR 3834-3946 114338057-114338169 113 0.1967 50 0.40
8
 3'UTR 3947-4332 114337671-114338056 386 0.1698 50 0.43
9
 3'UTR 4333-4522 114337481-114337670 190 0.5898 50 0.49
10
 3'UTR 4524-4636 114337367-114337479 113 0.2966 50 0.37
11
 3'UTR 4641-4724 114337279-114337362 84 0.4164 50 0.38
12
 3'UTR 4726-5123 114336880-114337277 398 0.4440 50 0.39
13
 3'UTR 5124-5503 114336500-114336879 380 0.2726 50 0.32
14
 3'UTR 5504-5606 114336397-114336499 103 0.2919 50 0.31
15
 3'UTR 5608-5711 114336292-114336395 104 0.4220 50 0.30
16
 3'UTR 5712-6158 114335845-114336291 447 0.1779 50 0.36
17
 3'UTR 6164-6292 114335711-114335839 129 0.2871 50 0.47
18
 3'UTR 6293-6398 114335605-114335710 106 0.3759 50 0.37
19
 3'UTR 6399-6494 114335509-114335604 96 0.5705 50 0.41
20
 3'UTR 6496-6591 114335412-114335507 96 0.2904 50 0.33
21
 3'UTR 6596-6718 114335285-114335407 123 0.3201 50 0.39
22
 3'UTR 6720-6808 114335195-114335283 89 0.2510 50 0.33
23
 3'UTR 6811-7161 114334842-114335192 351 0.2905 50 0.35
24
 3'UTR 7165-7493 114334510-114334838 329 0.2253 50 0.33
25
 3'UTR 7494-7858 114334145-114334509 365 0.3397 50 0.42
26
 3'UTR 7859-7951 114334052-114334144 93 0.4227 50 0.41
27
 3'UTR 7953-8050 114333953-114334050 98 0.2596 50 0.42
28
 3'UTR 8057-8142 114333861-114333946 86 0.3234 50 0.35
29
 3'UTR 8143-8239 114333764-114333860 97 0.2194 50 0.33
30
 3'UTR 8240-8341 114333662-114333763 102 0.4203 50 0.38
31
 3'UTR 8343-8431 114333572-114333660 89 0.2318 50 0.32
32
 3'UTR 8432-9999 114332004-114333571 1568 0.4046 50 0.41
Error
33
 3'UTR 10001-10741 114331262-114332002 741 0.0754 50 0.40
Error
34
 3'UTR 10742-10834 114331169-114331261 93 0.5954 50 0.40
35
 3'UTR 10837-10963 114331040-114331166 127 0.1901 50 0.34
36
 3'UTR 10967-11101 114330902-114331036 135 0.3918 50 0.34
37
 3'UTR 11103-11208 114330795-114330900 106 0.3653 50 0.33
38
 3'UTR 11217-11497 114330506-114330786 281 0.6812 50 0.41
39
 3'UTR 11498-11593 114330410-114330505 96 0.5018 50 0.34
40
 3'UTR 11595-11800 114330203-114330408 206 0.3699 50 0.33
41
 3'UTR 11805-11919 114330084-114330198 115 0.4093 50 0.35
42
 3'UTR 11922-12037 114329966-114330081 116 0.2817 50 0.39
43
 3'UTR 12041-12134 114329869-114329962 94 0.3822 50 0.43
44
 3'UTR 12137-13108 114328895-114329866 972 0.3350 50 0.35
Error
45
 3'UTR 13113-13431 114328572-114328890 319 0.3677 50 0.39
46
 3'UTR 13435-13700 114328303-114328568 266 0.4955 50 0.44
47
 3'UTR 13701-13822 114328181-114328302 122 0.5790 50 0.45
48
 3'UTR 13823-13910 114328093-114328180 88 0.3410 50 0.34
49
 3'UTR 13911-13996 114328007-114328092 86 0.2946 50 0.38
50
 3'UTR 13998-14096 114327907-114328005 99 0.2573 50 0.45
51
 3'UTR 14097-14258 114327745-114327906 162 0.3849 50 0.37
52
 3'UTR 14259-14907 114327096-114327744 649 0.3388 50 0.36
Error
53
 3'UTR 14908-14999 114327004-114327095 92 0.4821 50 0.39
54
 3'UTR 15004-15419 114326584-114326999 416 0.4352 50 0.43
55
 3'UTR 15426-16930 114325073-114326577 1505 0.4679 50 0.40
Error
56
 3'UTR 16933-17034 114324969-114325070 102 0.4499 50 0.38
57
 3'UTR 17037-17136 114324867-114324966 100 0.4198 50 0.35
58
 3'UTR 17142-17259 114324744-114324861 118 0.1554 50 0.30
59
 3'UTR 17265-17372 114324631-114324738 108 0.2171 50 0.36
60
 3'UTR 17374-17519 114324484-114324629 146 0.2491 50 0.36
61
 3'UTR 17522-17643 114324360-114324481 122 0.2732 50 0.39
62
 3'UTR 17644-18491 114323512-114324359 848 0.3736 50 0.49
Error
63
 3'UTR 18492-18586 114323417-114323511 95 0.6174 50 0.60
64
 3'UTR 18588-18682 114323321-114323415 95 0.3347 50 0.36
65
 3'UTR 18685-18774 114323229-114323318 90 0.3178 50 0.31
66
 3'UTR 18775-18904 114323099-114323228 130 0.4203 50 0.41
67
 3'UTR 18905-19009 114322994-114323098 105 0.1713 50 0.38
68
 3'UTR 19012-19104 114322899-114322991 93 0.5116 50 0.40
69
 3'UTR 19105-19364 114322639-114322898 260 0.3557 50 0.37
70
 3'UTR 19365-19453 114322550-114322638 89 0.4433 50 0.33
71
 3'UTR 19456-19602 114322401-114322547 147 0.2548 50 0.39
72
 3'UTR 19604-19728 114322275-114322399 125 0.2317 50 0.35
73
 3'UTR 19729-19828 114322175-114322274 100 0.2958 50 0.36
74
 3'UTR 19829-19926 114322077-114322174 98 0.3332 50 0.37
75
 3'UTR 19927-20034 114321969-114322076 108 0.4098 50 0.42
76
 3'UTR 20037-20161 114321842-114321966 125 0.3262 50 0.39
77
 3'UTR 20164-20263 114321740-114321839 100 0.5208 50 0.37
78
 3'UTR 20264-20484 114321519-114321739 221 0.3509 50 0.41
79
 3'UTR 20485-21077 114320926-114321518 593 0.5030 50 0.40
Error
80
 3'UTR 21080-21202 114320801-114320923 123 0.3695 50 0.35
81
 3'UTR 21205-21417 114320586-114320798 213 0.2779 50 0.32
82
 3'UTR 21418-21528 114320475-114320585 111 0.6121 50 0.32
83
 3'UTR 21530-21674 114320329-114320473 145 0.4502 50 0.30
84
 3'UTR 21678-21756 114320247-114320325 79 0.5245 50 0.50
85
 3'UTR 21757-21949 114320054-114320246 193 0.2619 50 0.39
86
 3'UTR 21951-22302 114319701-114320052 352 0.5705 50 0.48
87
 3'UTR 22305-22413 114319590-114319698 109 0.2966 50 0.36
88
 3'UTR 22414-22660 114319343-114319589 247 0.1549 50 0.35
89
 3'UTR 22662-22932 114319071-114319341 271 0.4437 50 0.42
90
 3'UTR 22933-23073 114318930-114319070 141 0.3060 50 0.41
91
 3'UTR 23074-25561 114316442-114318929 2488 0.3723 50 0.42
Error
92
 3'UTR 25563-25640 114316363-114316440 78 0.4303 50 0.41
93
 3'UTR 25644-25731 114316272-114316359 88 0.5831 50 0.42
94
 3'UTR 25732-25828 114316175-114316271 97 0.4264 50 0.37
95
 3'UTR 25833-25959 114316044-114316170 127 0.3588 50 0.41
96
 3'UTR 25960-26107 114315896-114316043 148 0.5713 50 0.53
97
 3'UTR 26112-26235 114315768-114315891 124 0.4145 50 0.41
98
 3'UTR 26236-26341 114315662-114315767 106 0.5624 50 0.43
99
 3'UTR 26342-26484 114315519-114315661 143 0.6543 50 0.49
100
 3'UTR 26489-26624 114315379-114315514 136 0.5076 50 0.44
101
 3'UTR 26626-26728 114315275-114315377 103 0.3145 50 0.37
102
 3'UTR 26729-26831 114315172-114315274 103 0.7386 50 0.44
103
 3'UTR 26833-26934 114315069-114315170 102 0.4368 50 0.38
104
 3'UTR 26937-27025 114314978-114315066 89 0.4013 50 0.38
105
 3'UTR 27027-27356 114314647-114314976 330 0.2910 66 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
1
ZBTB20

Aoi: Chr: Coords Strand:
ZBTB20 3 114380393 - 114380404, 114389005 - 114389105, 114500352 - 114500391 -
Download Data & Images


  • Annotation Based on canonical annotations, the following genes are in your area of interest: ZBTB20(-), ZBTB20-AS1(+), ZBTB20-AS5(+)
  • Length Length of region: 153 nt.
  • Structures This region has 5 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.
  • Coverage 58.099999999999994% of the region's A/C bases included in the filtered DMS dataset. This is lower than the recommended 70%. While structure prediction is still possible even without any coverage, the structures will be based on the sequence alone, rather than based on experimental constraints.
Structures
1 2 3 4
production / 8daaec85cb / 2026-01-15 03:47