Human RNA MaP

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

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How was this calculated?

LDLR
ENST00000558518 (+) ENSG00000130164 (+)

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	Region	Local Coords	Chrom Coords	Length	R	N	Gini	Action
1	5'UTR,CDS	38-158	11089500-11089615 / 11100223-11100227	121	0.5681	50	0.37
2	CDS	160-259	11100229-11100328	100	0.4836	50	0.29
3	CDS	262-373	11100331-11100345 / 11102664-11102760	112	0.2849	50	0.30
4	CDS	374-467	11102761-11102786 / 11105220-11105287	94	0.5733	50	0.35
5	CDS	472-562	11105292-11105382	91	0.4374	50	0.32
6	CDS	563-701	11105383-11105521	139	0.5209	50	0.29
7	CDS	702-799	11105522-11105600 / 11106565-11106583	98	0.5607	50	0.29
8	CDS	802-907	11106586-11106687 / 11107392-11107395	106	0.4761	50	0.25
9	CDS	908-993	11107396-11107481	86	0.5447	50	0.29
10	CDS	997-1084	11107485-11107514 / 11110652-11110709	88	0.5261	50	0.23
11	CDS	1086-1182	11110711-11110771 / 11111514-11111549	97	0.3629	50	0.33
12	CDS	1183-1296	11111550-11111639 / 11113278-11113301	114	0.3779	50	0.32
13	CDS	1297-1384	11113302-11113389	88	0.3723	50	0.31
14	CDS	1385-1474	11113390-11113449 / 11113535-11113564	90	0.4719	50	0.31
15	CDS	1477-1561	11113567-11113651	85	0.5008	50	0.32
16	CDS	1562-1669	11113652-11113759	108	0.4676	50	0.27
17	CDS	1673-1774	11116094-11116195	102	0.3373	50	0.24
18	CDS	1775-1859	11116196-11116212 / 11116859-11116926	85	0.3970	50	0.25
19	CDS	1865-1959	11116932-11116998 / 11120092-11120119	95	0.4611	50	0.28
20	CDS	1960-2053	11120120-11120213	94	0.5097	50	0.27
21	CDS	2054-2142	11120214-11120233 / 11120370-11120438	89	0.4762	50	0.29
22	CDS	2143-2230	11120439-11120522 / 11123174-11123177	88	0.5158	50	0.29
23	CDS	2233-2310	11123180-11123257	78	0.3682	50	0.26
24	CDS	2311-2395	11123258-11123342	85	0.4676	50	0.31
25	CDS	2396-2508	11123343-11123344 / 11128008-11128085 / 11129513-11129545	113	0.1968	50	0.26
26	CDS	2511-2594	11129548-11129631	84	0.4058	50	0.25
27	CDS,3'UTR	2595-2687	11129632-11129670 / 11131281-11131334	93	0.5132	50	0.27
28	3'UTR	2690-2780	11131337-11131427	91	0.7211	50	0.44
29	3'UTR	2782-2900	11131429-11131547	119	0.6976	50	0.38
30	3'UTR	2901-2998	11131548-11131645	98	0.4121	50	0.32
31	3'UTR	2999-3073	11131646-11131720	75	0.5270	50	0.37
32	3'UTR	3074-3296	11131721-11131943	223	0.4612	50	0.38
33	3'UTR	3297-3406	11131944-11132053	110	0.4141	50	0.44
34	3'UTR	3407-3498	11132054-11132145	92	0.5568	50	0.47
35	3'UTR	3499-3634	11132146-11132281	136	0.5291	50	0.36
36	3'UTR	3638-4204	11132285-11132851	567	0.5596	50	0.35	Error
37	3'UTR	4207-4292	11132854-11132939	86	0.5568	50	0.45
38	3'UTR	4294-4385	11132941-11133032	92	0.7101	50	0.43
39	3'UTR	4386-4495	11133033-11133142	110	0.7297	50	0.55
40	3'UTR	4497-4572	11133144-11133219	76	0.6911	50	0.49
41	3'UTR	4573-4679	11133220-11133326	107	0.4524	50	0.37
42	3'UTR	4680-4768	11133327-11133415	89	0.7824	50	0.52
43	3'UTR	4772-4915	11133419-11133562	144	0.5699	50	0.39
44	3'UTR	4916-5047	11133563-11133694	132	0.6340	50	0.38
45	3'UTR	5048-5133	11133695-11133780	86	0.3286	31	0.35
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Custom Gene Windows

Gene Window Instructions/Interpretation

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.
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.
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).
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.

Predict by Gene

LDLR ENST00000558518 (+) ENSG00000130164 (+)

Custom Gene Windows

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LDLR
ENST00000558518 (+) ENSG00000130164 (+)