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?

CHD2
ENST00000394196 (+) ENSG00000173575 (+)

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	Region	Local Coords	Chrom Coords	Length	R	N	Gini	Action
1	5'UTR	14-117	92900337-92900440	104	0.5715	50	0.34
2	5'UTR	118-233	92900441-92900556	116	0.9170	50	0.37	View
3	5'UTR	236-368	92900559-92900691	133	0.6417	50	0.29	View
4	5'UTR	369-508	92900692-92900824 / 92901167-92901173	140	0.4939	50	0.31
5	5'UTR,CDS	509-608	92901174-92901273	100	0.2682	50	0.32
6	CDS	609-705	92901274-92901299 / 92924321-92924391	97	0.2863	50	0.31
7	CDS	706-799	92924392-92924485	94	0.3972	50	0.31
8	CDS	801-892	92924487-92924552 / 92927244-92927269	92	0.3678	50	0.28
9	CDS	899-987	92927276-92927330 / 92929030-92929063	89	0.2719	50	0.30
10	CDS	989-1062	92929065-92929091 / 92937518-92937564	74	0.4241	50	0.37
11	CDS	1063-1135	92937565-92937625 / 92939578-92939589	73	0.3650	50	0.40
12	CDS	1136-1226	92939590-92939680	91	0.3874	50	0.31
13	CDS	1227-1318	92939681-92939718 / 92941822-92941875	92	0.2159	50	0.27
14	CDS	1341-1435	92941898-92941955 / 92942843-92942879	95	0.4491	50	0.36
15	CDS	1437-1532	92942881-92942976	96	0.4492	50	0.30
16	CDS	1537-1613	92942981-92943057	77	0.5712	50	0.38
17	CDS	1614-1712	92943058-92943068 / 92944415-92944502	99	0.2759	50	0.30
18	CDS	1714-1801	92944504-92944515 / 92945821-92945865 / 92946038-92946068	88	0.3929	50	0.32
19	CDS	1803-1899	92946070-92946166	97	0.2040	50	0.31
20	CDS	1901-1970	92946168-92946216 / 92948952-92948972	70	0.3592	50	0.33
21	CDS	1976-2074	92948978-92949076	99	0.1794	50	0.30
22	CDS	2075-2159	92953357-92953441	85	0.4701	50	0.34
23	CDS	2160-2319	92953442-92953573 / 92955423-92955450	160	0.3545	50	0.36
24	CDS	2320-3114	92955451-92955512 / 92971765-92971927 / 92972265-92972417 / 92974879-92974915	795	0.4390	50	0.36	Error
25	CDS	3151-3265	92978235-92978349	115	0.4283	50	0.41
26	CDS	3266-3361	92978350-92978383 / 92979135-92979196	96	0.5148	50	0.41
27	CDS	3362-3451	92979197-92979283 / 92980815-92980817	90	0.2838	50	0.38
28	CDS	3452-3547	92980818-92980911 / 92981365-92981366	96	0.3360	50	0.34
29	CDS	3548-3647	92981367-92981457 / 92984330-92984338	100	0.2962	50	0.31
30	CDS	3652-3745	92984343-92984436	94	0.5027	50	0.42
31	CDS	3746-3836	92984437-92984500 / 92985498-92985524	91	0.4332	50	0.34
32	CDS	3837-3930	92985525-92985618	94	0.4915	50	0.39
33	CDS	3931-4044	92985619-92985673 / 92991476-92991517 / 92992859-92992875	114	0.3569	50	0.34
34	CDS	4048-4150	92992879-92992981	103	0.3765	50	0.32
35	CDS	4151-4239	92992982-92992998 / 92996957-92997028	89	0.2799	50	0.35
36	CDS	4241-4329	92997030-92997095 / 92997253-92997275	89	0.3073	50	0.44
37	CDS	4330-4445	92997276-92997391	116	0.3112	50	0.33
38	CDS	4448-4652	92997394-92997403 / 93000512-93000583	205	0.4234	50	0.36
39	CDS	4653-4840	93000584-93000640 / 93002177-93002307	188	0.2220	50	0.34
40	CDS	4842-4930	93002309-93002317 / 93004617-93004696	89	0.2718	50	0.38
41	CDS	4934-5030	93004700-93004751 / 93009145-93009189	97	0.2479	50	0.33
42	CDS	5032-5111	93009191-93009270	80	0.3524	50	0.36
43	CDS	5113-5211	93009272-93009323 / 93012345-93012391	99	0.4913	50	0.42
44	CDS	5212-5299	93012392-93012444 / 93014696-93014730	88	0.3101	50	0.28
45	CDS	5301-5379	93014732-93014810	79	0.4324	50	0.40
46	CDS	5380-5536	93014811-93014909 / 93020012-93020069	157	0.4282	50	0.40
47	CDS	5537-5624	93020070-93020157	88	0.3280	50	0.31
48	CDS	5625-5706	93020158-93020239	82	0.0654	50	0.30
49	CDS	5707-5791	93020240-93020258 / 93024372-93024437	85	0.5402	50	0.36
50	CDS	5795-5878	93024441-93024524	84	0.4604	50	0.37
51	CDS,3'UTR	5880-6221	93024526-93024867	342	0.2745	50	0.35
52	3'UTR	6222-6313	93024868-93024959	92	0.4334	50	0.41
53	3'UTR	6318-6942	93024964-93025588	625	0.6128	50	0.39	Error
54	3'UTR	6946-7049	93025592-93025695	104	0.5184	50	0.38
55	3'UTR	7059-7173	93025705-93025819	115	0.2602	50	0.34
56	3'UTR	7174-7335	93025820-93025981	162	0.0603	50	0.34
57	3'UTR	7336-7423	93025982-93026069	88	0.3228	50	0.37
58	3'UTR	7424-7543	93026070-93026189	120	0.3600	50	0.34
59	3'UTR	7545-7648	93026191-93026294	104	0.4061	50	0.38
60	3'UTR	7649-8235	93026295-93026881	587	0.4014	50	0.43	Error
61	3'UTR	8237-8347	93026883-93026993	111	0.4637	50	0.42
62	3'UTR	8350-8448	93026996-93027094	99	0.3889	50	0.37
63	3'UTR	8449-8571	93027095-93027217	123	0.3278	50	0.35
64	3'UTR	8572-9162	93027218-93027808	591	0.5204	31	0.52	Error
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

2
CHD2

Aoi:	Chr:	Coords	Strand:
CHD2	15	92900441 - 92900556	+

Download Data & Images

Annotation Based on canonical annotations, the following gene is in your area of interest: CHD2(+)
Length Length of region: 116 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 13 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

CHD2 ENST00000394196 (+) ENSG00000173575 (+)

Custom Gene Windows

completed 2 CHD2

CHD2
ENST00000394196 (+) ENSG00000173575 (+)

completed

2
CHD2