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?

LMNA
ENST00000675939 (+) ENSG00000160789 (+)

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	Region	Local Coords	Chrom Coords	Length	R	N	Gini	Action
1	5'UTR	18-90	156114717-156114789	73	0.6317	50	0.19	View
2	5'UTR	91-173	156114790-156114872	83	0.7765	50	0.18
3	5'UTR,CDS	177-260	156114876-156114959	84	0.8157	50	0.22	View
4	CDS	262-351	156114961-156115050	90	0.8067	50	0.21	View
5	CDS	353-452	156115052-156115151	100	0.8538	50	0.21
6	CDS	455-543	156115154-156115242	89	0.8530	50	0.21	View
7	CDS	547-649	156115246-156115274 / 156130617-156130690	103	0.8787	50	0.18
8	CDS	650-756	156130691-156130773 / 156134403-156134426	107	0.9623	50	0.25	View
9	CDS	757-852	156134427-156134522	96	0.8599	50	0.13
10	CDS	853-964	156134523-156134528 / 156134805-156134910	112	0.9067	50	0.17
11	CDS	968-1063	156134914-156134975 / 156135187-156135220	96	0.8546	50	0.21
12	CDS	1065-1151	156135222-156135308	87	0.9256	50	0.20
13	CDS	1153-1252	156135310-156135312 / 156135901-156135997	100	0.9069	50	0.21
14	CDS	1256-1348	156136001-156136093	93	0.8434	50	0.19
15	CDS	1350-1441	156136095-156136121 / 156136214-156136278	92	0.9368	50	0.27
16	CDS	1442-1524	156136279-156136361	83	0.9220	50	0.23
17	CDS	1525-1633	156136362-156136436 / 156136921-156136954	109	0.9067	50	0.21	View
18	CDS	1634-1736	156136955-156137028 / 156137113-156137141	103	0.8453	50	0.21
19	CDS	1737-1826	156137142-156137231	90	0.8818	50	0.22	View
20	CDS	1827-1926	156137232-156137232 / 156137654-156137743 / 156138488-156138496	100	0.7314	50	0.20
21	CDS	1929-2022	156138499-156138592	94	0.8166	50	0.26	View
22	CDS	2025-2137	156138595-156138707	113	0.8140	50	0.30	View
23	CDS,3'UTR	2138-2213	156138708-156138757 / 156139080-156139105	76	0.5889	50	0.23	View
24	3'UTR	2214-2317	156139106-156139209	104	0.9052	50	0.56
25	3'UTR	2318-2401	156139210-156139293	84	0.8520	32	0.33
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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.

completed

17
LMNA

Aoi:	Chr:	Coords	Strand:
LMNA	1	156136362 - 156136436, 156136921 - 156136954	+

Download Data & Images

Annotation Based on canonical annotations, the following gene is in your area of interest: LMNA(+)
Length Length of region: 109 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 10 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.

Predict by Gene

LMNA ENST00000675939 (+) ENSG00000160789 (+)

Custom Gene Windows

completed 17 LMNA

LMNA
ENST00000675939 (+) ENSG00000160789 (+)

completed

17
LMNA