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?

BRCA1
ENST00000357654 (-) ENSG00000012048 (-)

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	Region	Local Coords	Chrom Coords	Length	R	N	Gini
1	5'UTR,CDS	53-159	43124051-43124115 / 43125271-43125312	107	0.4261	50	0.39
2	CDS	160-262	43106519-43106533 / 43115726-43115779 / 43124017-43124050	103	0.3739	50	0.37
3	CDS	263-345	43104937-43104956 / 43106456-43106518	83	0.3082	50	0.34
4	CDS	347-450	43104226-43104261 / 43104868-43104935	104	0.4357	50	0.38
5	CDS	451-535	43104141-43104225	85	0.3835	50	0.31
6	CDS	536-624	43099811-43099880 / 43104122-43104140	89	0.4425	50	0.32
7	CDS	626-728	43095901-43095922 / 43097244-43097289 / 43099775-43099809	103	0.2772	50	0.30
8	CDS	729-820	43094824-43094860 / 43095846-43095900	92	0.4590	50	0.43
9	CDS	823-913	43094731-43094821	91	0.1523	50	0.31
10	CDS	914-999	43094645-43094730	86	0.4437	50	0.32
11	CDS	1001-1090	43094554-43094643	90	0.3989	50	0.33
12	CDS	1091-1179	43094465-43094553	89	0.4775	50	0.34
13	CDS	1180-1274	43094370-43094464	95	0.1171	50	0.26
14	CDS	1275-1391	43094253-43094369	117	0.5155	50	0.32
15	CDS	1393-1486	43094158-43094251	94	0.2988	50	0.30
16	CDS	1487-1568	43094076-43094157	82	0.2899	50	0.32
17	CDS	1575-1650	43093994-43094069	76	0.6249	50	0.39
18	CDS	1651-1737	43093907-43093993	87	0.3435	50	0.34
19	CDS	1738-1826	43093818-43093906	89	0.4385	50	0.35
20	CDS	1828-1907	43093737-43093816	80	0.6096	50	0.37
21	CDS	1908-1994	43093650-43093736	87	0.3118	50	0.29
22	CDS	1995-2082	43093562-43093649	88	0.3829	50	0.36
23	CDS	2083-2159	43093485-43093561	77	0.2661	50	0.33
24	CDS	2160-2242	43093402-43093484	83	0.4254	50	0.34
25	CDS	2244-2323	43093321-43093400	80	0.1374	50	0.35
26	CDS	2324-2429	43093215-43093320	106	0.1938	50	0.29
27	CDS	2430-2524	43093120-43093214	95	0.1198	50	0.27
28	CDS	2530-2620	43093024-43093114	91	0.3855	50	0.30
29	CDS	2621-2711	43092933-43093023	91	0.1854	50	0.29
30	CDS	2712-2802	43092842-43092932	91	0.5058	50	0.39
31	CDS	2803-2886	43092758-43092841	84	0.2519	50	0.28
32	CDS	2888-2995	43092649-43092756	108	0.3139	50	0.32
33	CDS	2996-3072	43092572-43092648	77	0.3452	50	0.33
34	CDS	3073-3163	43092481-43092571	91	0.3420	50	0.35
35	CDS	3165-3247	43092397-43092479	83	0.4429	50	0.30
36	CDS	3250-3345	43092299-43092394	96	0.2571	50	0.27
37	CDS	3346-3442	43092202-43092298	97	0.3439	50	0.32
38	CDS	3444-3539	43092105-43092200	96	0.3182	50	0.33
39	CDS	3541-3651	43091993-43092103	111	0.4029	50	0.33
40	CDS	3653-3745	43091899-43091991	93	0.4508	50	0.37
41	CDS	3746-3840	43091804-43091898	95	0.3988	50	0.30
42	CDS	3843-3936	43091708-43091801	94	0.2244	50	0.24
43	CDS	3938-4038	43091606-43091706	101	0.3494	50	0.30
44	CDS	4039-4184	43091460-43091605	146	0.4642	50	0.41
45	CDS	4186-4284	43090958-43091032 / 43091435-43091458	99	0.4688	50	0.33
46	CDS	4289-4371	43082503-43082575 / 43090944-43090953	83	0.3257	50	0.34
47	CDS	4372-4455	43082419-43082502	84	0.2997	50	0.35
48	CDS	4457-4579	43076506-43076614 / 43082404-43082417	123	0.3271	50	0.32
49	CDS	4580-4676	43074443-43074521 / 43076488-43076505	97	0.3015	50	0.33
50	CDS	4678-4802	43071225-43071238 / 43074331-43074441	125	0.2537	50	0.38
51	CDS	4803-4915	43071112-43071224	113	0.2604	50	0.40
52	CDS	4916-5013	43071014-43071111	98	0.4864	50	0.35
53	CDS	5017-5110	43067685-43067695 / 43070928-43071010	94	0.2971	50	0.25
54	CDS	5111-5206	43063933-43063951 / 43067608-43067684	96	0.3913	50	0.26
55	CDS	5207-5311	43057131-43057135 / 43063333-43063373 / 43063874-43063932	105	0.3280	50	0.35
56	CDS	5317-5403	43051105-43051117 / 43057052-43057125	87	0.2900	50	0.28
57	CDS	5405-5568	43047655-43047703 / 43049121-43049194 / 43051063-43051103	164	0.3872	50	0.43
58	CDS	5569-5679	43045704-43045802 / 43047643-43047654	111	0.6014	50	0.45
59	3'UTR	5822-5923	43045460-43045561	102	0.2066	50	0.41
60	3'UTR	5925-6046	43045337-43045458	122	0.3427	50	0.41
61	3'UTR	6050-6142	43045241-43045333	93	0.3982	50	0.38
62	3'UTR	6145-6265	43045118-43045238	121	0.4143	50	0.37
63	3'UTR	6266-6365	43045018-43045117	100	0.5501	50	0.44
64	3'UTR	6366-6451	43044932-43045017	86	0.4620	50	0.49
65	3'UTR	6452-6551	43044832-43044931	100	0.7789	50	0.58
66	3'UTR	6557-6671	43044712-43044826	115	0.3235	50	0.34
67	3'UTR	6672-6811	43044572-43044711	140	0.2628	70	0.32
Download CSV

Custom Gene Windows

Chr	Coords	Strand
17	43044630 - 43045129 500 bp

63s

completed

Chr	Coords	Strand
17	43045142 - 43045641 500 bp

65s

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

BRCA1

Aoi:	Chr:	Coords	Strand:
BRCA1	17	43045142 - 43045641	-

Download Data & Images

Annotation Based on canonical annotations, the following gene is in your area of interest: BRCA1(-)
Length Length of region: 500 nt.
Coverage 79.5% 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

BRCA1 ENST00000357654 (-) ENSG00000012048 (-)

Custom Gene Windows

completed BRCA1

BRCA1
ENST00000357654 (-) ENSG00000012048 (-)

completed

BRCA1