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?

ZNF609
ENST00000326648 (+) ENSG00000180357 (+)

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	Region	Local Coords	Chrom Coords	Length	R	N	Gini
40	CDS	3700-3795	64676166-64676256 / 64678116-64678120	96	0.6627	50	0.38
1	5'UTR	138-263	64460715-64460838 / 64499293-64499294	126	0.5579	50	0.41
2	5'UTR	264-375	64499295-64499406	112	0.6017	50	0.25
3	5'UTR,CDS	376-488	64499407-64499519	113	0.6210	50	0.27
4	CDS	490-585	64499521-64499616	96	0.4713	50	0.30
5	CDS	586-661	64499617-64499692	76	0.6441	50	0.34
6	CDS	662-747	64499693-64499778	86	0.6354	50	0.34
7	CDS	752-859	64499783-64499890	108	0.6726	50	0.34
8	CDS	860-956	64499891-64499987	97	0.7380	50	0.28
9	CDS	957-1080	64499988-64500111	124	0.6723	50	0.26
10	CDS	1082-1174	64500113-64500166 / 64622827-64622865	93	0.4646	50	0.30
11	CDS	1175-1280	64622866-64622971	106	0.6253	50	0.35
12	CDS	1281-1392	64622972-64623052 / 64670346-64670376	112	0.5549	50	0.31
13	CDS	1393-1480	64670377-64670433 / 64673916-64673946	88	0.5019	50	0.38
14	CDS	1481-1564	64673947-64674030	84	0.5895	50	0.40
15	CDS	1565-1645	64674031-64674111	81	0.3702	50	0.31
16	CDS	1646-1721	64674112-64674187	76	0.5164	50	0.36
17	CDS	1725-1815	64674191-64674281	91	0.7002	50	0.35
18	CDS	1820-1895	64674286-64674361	76	0.4949	50	0.35
19	CDS	1896-1971	64674362-64674437	76	0.4209	50	0.33
20	CDS	1972-2074	64674438-64674540	103	0.4467	50	0.36
21	CDS	2075-2152	64674541-64674618	78	0.3964	50	0.32
22	CDS	2156-2257	64674622-64674723	102	0.4145	50	0.30
23	CDS	2262-2345	64674728-64674811	84	0.3998	50	0.27
24	CDS	2347-2416	64674813-64674882	70	0.5546	50	0.31
25	CDS	2417-2492	64674883-64674958	76	0.6549	50	0.37
26	CDS	2493-2571	64674959-64675037	79	0.5691	50	0.34
27	CDS	2572-2657	64675038-64675123	86	0.5875	50	0.35
28	CDS	2658-2745	64675124-64675211	88	0.4927	50	0.29
29	CDS	2747-2831	64675213-64675297	85	0.6784	50	0.38
30	CDS	2832-2909	64675298-64675375	78	0.6203	50	0.40
31	CDS	2910-3012	64675376-64675478	103	0.5071	50	0.31
32	CDS	3014-3099	64675480-64675565	86	0.4884	50	0.33
33	CDS	3100-3186	64675566-64675652	87	0.6345	50	0.39
34	CDS	3188-3275	64675654-64675741	88	0.5402	50	0.26
35	CDS	3276-3359	64675742-64675825	84	0.4326	50	0.26
36	CDS	3360-3435	64675826-64675901	76	0.4429	50	0.32
37	CDS	3437-3530	64675903-64675996	94	0.3323	50	0.27
38	CDS	3531-3610	64675997-64676076	80	0.6768	50	0.38
39	CDS	3612-3699	64676078-64676165	88	0.6295	50	0.38
41	CDS	3796-3897	64678121-64678222	102	0.6379	50	0.34
42	CDS	3898-3995	64678223-64678320	98	0.6555	50	0.32
43	CDS	3997-4075	64678322-64678400	79	0.4862	50	0.36
44	CDS	4078-4156	64678403-64678481	79	0.3890	50	0.29
45	CDS	4161-4254	64680188-64680281	94	0.3168	50	0.39
46	CDS	4259-4450	64680286-64680360 / 64680646-64680762	192	0.4568	50	0.41
47	CDS	4451-4525	64680763-64680837	75	0.5927	50	0.38
48	CDS	4526-4607	64680838-64680862 / 64681309-64681365	82	0.5622	50	0.33
49	CDS,3'UTR	4608-4699	64681366-64681387 / 64681692-64681761	92	0.3617	50	0.36
50	3'UTR	4700-4795	64681762-64681857	96	0.5669	50	0.48
51	3'UTR	4796-4916	64681858-64681978	121	0.3559	50	0.42
52	3'UTR	4917-5239	64681979-64682301	323	0.3411	50	0.43
53	3'UTR	5241-5345	64682303-64682407	105	0.6889	50	0.46
54	3'UTR	5346-5438	64682408-64682500	93	0.6677	50	0.48
55	3'UTR	5441-5678	64682503-64682740	238	0.5400	50	0.41
56	3'UTR	5682-5772	64682744-64682834	91	0.6754	50	0.37
57	3'UTR	5775-5886	64682837-64682948	112	0.5690	50	0.39
58	3'UTR	5888-5985	64682950-64683047	98	0.7613	50	0.41
59	3'UTR	5986-6118	64683048-64683180	133	0.4942	50	0.40
60	3'UTR	6120-6218	64683182-64683280	99	0.4830	50	0.36
61	3'UTR	6219-6317	64683281-64683379	99	0.8216	50	0.40
62	3'UTR	6318-6428	64683380-64683490	111	0.6672	50	0.43
63	3'UTR	6431-6507	64683493-64683569	77	0.4762	50	0.38
64	3'UTR	6508-6598	64683570-64683660	91	0.6383	50	0.42
65	3'UTR	6601-6725	64683663-64683787	125	0.6094	50	0.44
66	3'UTR	6727-6835	64683789-64683897	109	0.6966	50	0.50
67	3'UTR	6836-6954	64683898-64684016	119	0.5830	50	0.35
68	3'UTR	6956-7048	64684018-64684110	93	0.5188	50	0.40
69	3'UTR	7049-7143	64684111-64684205	95	0.2942	50	0.31
70	3'UTR	7150-7231	64684212-64684293	82	0.6987	50	0.42
71	3'UTR	7234-7310	64684296-64684372	77	0.6581	50	0.45
72	3'UTR	7312-7412	64684374-64684474	101	0.6838	50	0.34
73	3'UTR	7413-7510	64684475-64684572	98	0.6089	50	0.34
74	3'UTR	7511-7598	64684573-64684660	88	0.3615	50	0.30
75	3'UTR	7600-7709	64684662-64684771	110	0.4656	50	0.35
76	3'UTR	7710-7811	64684772-64684873	102	0.5162	50	0.38
77	3'UTR	7814-7898	64684876-64684960	85	0.5074	50	0.37
78	3'UTR	7900-8009	64684962-64685071	110	0.9401	50	0.61
79	3'UTR	8017-8180	64685079-64685242	164	0.4488	34	0.40
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Custom Gene Windows

Chr	Coords	Strand
15	64676166 - 64676256 91 bp

6s

completed

Chr	Coords	Strand
15	64684704 - 64685203 500 bp

64s

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

ZNF609

Aoi:	Chr:	Coords	Strand:
ZNF609-7642-8141	15	64684704 - 64685203	+

Download Data & Images

Predict by Gene

ZNF609 ENST00000326648 (+) ENSG00000180357 (+)

Custom Gene Windows

completed ZNF609

ZNF609
ENST00000326648 (+) ENSG00000180357 (+)

completed

ZNF609