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

Advanced Options

How was this calculated?

SELENOT
ENST00000471696 (+) ENSG00000198843 (+)

Custom Window:

Strand

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Size

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	Region	Local Coords	Chrom Coords	Length	R	N	Gini	Action
1	5'UTR,CDS	6-127	150603326-150603447	122	0.7786	50	0.33
2	CDS	128-245	150603448-150603499 / 150622385-150622450	118	0.7722	50	0.33
3	CDS	246-330	150622451-150622495 / 150623043-150623082	85	0.7466	50	0.31
4	CDS	331-452	150623083-150623169 / 150624812-150624846	122	0.5952	50	0.28
5	CDS	453-556	150624847-150624899 / 150627010-150627060	104	0.8243	50	0.43
6	CDS,3'UTR	557-639	150627061-150627143	83	0.5776	50	0.23
7	3'UTR	641-736	150627145-150627163 / 150627659-150627735	96	0.9640	50	0.64	View
8	3'UTR	738-847	150627737-150627846	110	0.9331	50	0.58	View
9	3'UTR	849-959	150627848-150627958	111	0.7259	50	0.33
10	3'UTR	960-1087	150627959-150628086	128	0.7914	50	0.41
11	3'UTR	1088-1185	150628087-150628184	98	0.7815	50	0.34
12	3'UTR	1187-1338	150628186-150628337	152	0.5738	70	0.29
Download CSV

Custom Gene Windows

Chr	Coords	Strand
3	150603363 - 150603496 150622385 - 150622495 150623043 - 150623169 150624812 - 150624899 150627092 - 150627131 500 bp

66s

completed

Chr	Coords	Strand
3	150627132 - 150627160 150629966 - 150630436 500 bp

10s

completed

Chr	Coords	Strand
3	600 - 750 151 bp

2s

completed

Chr	Coords	Strand
3	650 - 900 251 bp

2s

completed

Chr	Coords	Strand
3	150627132 - 150627143 150630149 - 150630436 300 bp

6s

completed

Chr	Coords	Strand
3	150627132 - 150627149 150629955 - 150630436 500 bp

10s

completed

Chr	Coords	Strand
3	150627132 - 150627151 150630307 - 150630436 150 bp

4s

completed

Chr	Coords	Strand
3	150627132 - 150627151 150630307 - 150630436 150 bp

4s

completed

Chr	Coords	Strand
3	150630277 - 150630426 150 bp

3s

completed

Chr	Coords	Strand
3	150623043 - 150623101 150624812 - 150624899 150627010 - 150627131 150627133 - 150627163 300 bp

43s

completed

Chr	Coords	Strand
3	150629942 - 150630241 300 bp

5s

completed

Chr	Coords	Strand
3	150627010 - 150627078 150627132 - 150627163 150630238 - 150630436 300 bp

43s

completed

Chr	Coords	Strand
3	150629942 - 150630241 300 bp

5s

completed

Chr	Coords	Strand
3	150627010 - 150627060 150627132 - 150627163 150630220 - 150630436 300 bp

44s

completed

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

SELENOT

Aoi:	Chr:	Coords	Strand:
SELENOT	3	150603363 - 150603496, 150622385 - 150622495, 150623043 - 150623169, 150624812 - 150624899, 150627092 - 150627131	-

Download Data & Images

Annotation Based on canonical annotations, the following gene is in your area of interest: SELENOT(+)
Length Length of region: 500 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 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.

Predict by Gene

SELENOT ENST00000471696 (+) ENSG00000198843 (+)

Custom Gene Windows

completed SELENOT

SELENOT
ENST00000471696 (+) ENSG00000198843 (+)

completed

SELENOT