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?

PAN3
ENST00000380958 (+) ENSG00000152520 (+)

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	Region	Local Coords	Chrom Coords	Length	R	N	Gini	Action
1	CDS	311-494	28138855-28139038	184	0.3865	50	0.47
2	CDS	496-604	28139040-28139087 / 28174272-28174332	109	0.5253	50	0.33
3	CDS	605-695	28174333-28174393 / 28176493-28176522	91	0.3964	50	0.33
4	CDS	696-1314	28176523-28176559 / 28177865-28177935 / 28256292-28256492	619	0.3229	50	0.37	Error
5	CDS	1317-1450	28256495-28256539 / 28260447-28260535	134	0.3646	50	0.35
6	CDS	1453-1552	28260538-28260551 / 28261401-28261458 / 28266715-28266742	100	0.3324	50	0.32
7	CDS	1554-1970	28266744-28266876 / 28267095-28267211 / 28270701-28270765	417	0.6307	50	0.44	View
8	CDS	1972-2068	28270767-28270863	97	0.3888	50	0.42
9	CDS	2069-2175	28270864-28270866 / 28271981-28272071 / 28277237-28277249	107	0.2931	50	0.34
10	CDS	2177-2281	28277251-28277355	105	0.2000	50	0.32
11	CDS	2284-2392	28277358-28277376 / 28280412-28280501	109	0.2815	50	0.33
12	CDS	2394-2485	28280503-28280541 / 28281315-28281367	92	0.3223	50	0.34
13	CDS	2488-2596	28281370-28281379 / 28287984-28288082	109	0.4470	50	0.39
14	CDS	2597-2704	28288083-28288122 / 28292382-28292449	108	0.4840	50	0.36
15	CDS,3'UTR	2705-2813	28292450-28292558	109	0.4637	50	0.47
16	3'UTR	2814-2897	28292559-28292642	84	0.6153	50	0.49
17	3'UTR	2900-3013	28292645-28292758	114	0.5107	50	0.34
18	3'UTR	3015-3136	28292760-28292881	122	0.6326	50	0.47
19	3'UTR	3137-3259	28292882-28293004	123	0.5541	50	0.35
20	3'UTR	3261-3401	28293006-28293146	141	0.2546	50	0.39
21	3'UTR	3406-3530	28293151-28293275	125	0.5257	50	0.43
22	3'UTR	3533-3777	28293278-28293522	245	0.3751	50	0.43
23	3'UTR	3779-4400	28293524-28294145	622	0.3794	50	0.42	Error
24	3'UTR	4401-4511	28294146-28294256	111	0.2470	50	0.38
25	3'UTR	4514-4613	28294259-28294358	100	0.5370	50	0.44
26	3'UTR	4615-4726	28294360-28294471	112	0.4965	50	0.32
27	3'UTR	4728-4860	28294473-28294605	133	0.4948	50	0.31
28	3'UTR	4864-4953	28294609-28294698	90	0.4974	50	0.38
29	3'UTR	4955-5062	28294700-28294807	108	0.4537	50	0.32
30	3'UTR	5066-5212	28294811-28294957	147	0.4827	50	0.35
31	3'UTR	5213-5461	28294958-28295206	249	0.3879	74	0.44
Download CSV

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

7
PAN3

Aoi:	Chr:	Coords	Strand:
PAN3	13	28266744 - 28266876, 28267095 - 28267211, 28270701 - 28270765	+

Download Data & Images

Annotation Based on canonical annotations, the following gene is in your area of interest: PAN3(+)
Length Length of region: 315 nt.
Structures This region has 20 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 30.5% 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.

Predict by Gene

PAN3 ENST00000380958 (+) ENSG00000152520 (+)

Custom Gene Windows

completed 7 PAN3

PAN3
ENST00000380958 (+) ENSG00000152520 (+)

completed

7
PAN3