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?

SGMS1
ENST00000361781 (-) ENSG00000198964 (-)

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	Region	Local Coords	Chrom Coords	Length	R	N	Gini	Action
1	5'UTR	97-208	50623749-50623860	112	0.5142	50	0.49
2	5'UTR	210-315	50590183-50590247 / 50623707-50623747	106	0.2626	50	0.33	View
3	5'UTR	316-411	50519856-50519921 / 50590153-50590182	96	0.1927	50	0.27
4	5'UTR	413-575	50460719-50460814 / 50519831-50519854	163	0.4968	50	0.41
5	5'UTR	576-714	50344334-50344345 / 50433476-50433556 / 50460673-50460718	139	0.3568	50	0.35
6	5'UTR	717-807	50344241-50344331	91	0.4636	50	0.30
7	5'UTR	808-899	50344149-50344240	92	0.4477	50	0.34
8	5'UTR,CDS	901-1012	50344036-50344147	112	0.7029	50	0.36
9	CDS	1013-1097	50343951-50344035	85	0.6062	50	0.35
10	CDS	1098-1183	50343865-50343950	86	0.5303	50	0.34
11	CDS	1184-1258	50343790-50343864	75	0.5401	50	0.34
12	CDS	1259-1360	50343688-50343789	102	0.6029	50	0.36
13	CDS	1364-1458	50343590-50343684	95	0.7093	50	0.36
14	CDS	1459-1575	50327304-50327322 / 50343492-50343589	117	0.4745	50	0.30
15	CDS	1581-1686	50311404-50311415 / 50327205-50327298	106	0.7446	50	0.42
16	CDS	1691-1789	50311301-50311399	99	0.6582	50	0.31
17	CDS	1790-1902	50308075-50308148 / 50311262-50311300	113	0.6514	50	0.33
18	CDS	1905-2001	50307316-50307321 / 50307982-50308072	97	0.5360	50	0.31
19	CDS	2002-2101	50307216-50307315	100	0.4430	50	0.25
20	CDS,3'UTR	2102-2195	50307122-50307215	94	0.6527	50	0.28
21	3'UTR	2196-2276	50307041-50307121	81	0.4425	50	0.27
22	3'UTR	2277-2376	50306941-50307040	100	0.5835	50	0.35
23	3'UTR	2377-2470	50306847-50306940	94	0.5298	50	0.37
24	3'UTR	2471-2573	50306744-50306846	103	0.5987	50	0.39
25	3'UTR	2574-2684	50306633-50306743	111	0.5923	50	0.36
26	3'UTR	2685-2783	50306534-50306632	99	0.4508	50	0.35
27	3'UTR	2788-2883	50306434-50306529	96	0.4188	50	0.32
28	3'UTR	2884-3005	50306312-50306433	122	0.2249	50	0.32
29	3'UTR	3009-3112	50306205-50306308	104	0.3486	50	0.34
30	3'UTR	3114-3213	50306104-50306203	100	0.6158	50	0.45	View
31	3'UTR	3214-3316	50306001-50306103	103	0.4877	50	0.36
32	3'UTR	3317-3412	50305905-50306000	96	0.7003	50	0.44
33	3'UTR	3415-3519	50305798-50305902	105	0.4666	50	0.34
34	3'UTR	3531-3583	50305734-50305786	53	0.2667	28	0.29
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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.

Recently Visualized

Chr	Coords	Strand
10	50306104 - 50306203 100 bp

5s

completed

Chr	Coords	Strand
10	50590183 - 50590247 50623707 - 50623747 106 bp

12s

completed

Predict by Gene

SGMS1 ENST00000361781 (-) ENSG00000198964 (-)

Custom Gene Windows

Recently Visualized

SGMS1
ENST00000361781 (-) ENSG00000198964 (-)