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?

GPX4
ENST00000354171 (+) ENSG00000167468 (+)

Custom Window:

Strand

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Size

100

150

300

500

	Region	Local Coords	Chrom Coords	Length	R	N	Gini	Action
1	CDS	65-175	1104058-1104127 / 1105186-1105226	111	0.7373	50	0.28
2	CDS	176-273	1105227-1105280 / 1105366-1105409	98	0.8894	50	0.32
3	CDS	274-370	1105410-1105506	97	0.9626	50	0.53
4	CDS	372-466	1105508-1105510 / 1105658-1105749	95	0.8959	50	0.24
5	CDS	467-554	1105750-1105809 / 1106242-1106266 / 1106400-1106402	88	0.8953	50	0.35
6	CDS,3'UTR	555-648	1106403-1106459 / 1106540-1106576	94	0.9247	50	0.33
7	3'UTR	649-732	1106577-1106660	84	0.9816	50	0.70	View
8	3'UTR	741-847	1106669-1106775	107	0.8128	62	0.47
Download CSV

Custom Gene Windows

Chr	Coords	Strand
19	1106625 - 1106774 150 bp

18s

completed

Chr	Coords	Strand
19	1104044 - 1104044 1105186 - 1105280 1105366 - 1105510 1105658 - 1105809 1106242 - 1106266 1106400 - 1106459 1106548 - 1106569 500 bp

69s

completed

Chr	Coords	Strand
19	1105186 - 1105243 1105366 - 1105510 1105713 - 1105809 300 bp

46s

completed

Chr	Coords	Strand
19	1106242 - 1106242 1106400 - 1106459 1106540 - 1106569 1106571 - 1106779 300 bp

47s

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

GPX4

Aoi:	Chr:	Coords	Strand:
GPX4	19	1106242 - 1106242, 1106400 - 1106459, 1106540 - 1106569, 1106571 - 1106779	-

Download Data & Images

Annotation Based on canonical annotations, the following gene is in your area of interest: GPX4(+)
Length Length of region: 300 nt.
Coverage 99.3% 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

GPX4 ENST00000354171 (+) ENSG00000167468 (+)

Custom Gene Windows

completed GPX4

GPX4
ENST00000354171 (+) ENSG00000167468 (+)

completed

GPX4