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?

FLNB
ENST00000295956 (+) ENSG00000136068 (+)

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	Region	Local Coords	Chrom Coords	Length	R	N	Gini	Action
1	5'UTR	3-94	58008424-58008515	92	0.7516	50	0.32	View
2	5'UTR,CDS	95-186	58008516-58008607	92	0.6372	50	0.26	View
3	CDS	187-265	58008608-58008686	79	0.6733	50	0.29	View
4	CDS	267-355	58008688-58008776	89	0.6968	50	0.21	View
5	CDS	356-461	58008777-58008856 / 58077046-58077071	106	0.7931	50	0.24	View
6	CDS	462-566	58077072-58077176	105	0.6572	50	0.18	View
7	CDS	567-650	58077177-58077260	84	0.7743	50	0.18	View
8	CDS	652-750	58077262-58077294 / 58078717-58078782	99	0.8280	50	0.22	View
9	CDS	751-847	58078783-58078814 / 58081629-58081693	97	0.7282	50	0.19	View
10	CDS	848-919	58081694-58081765	72	0.8526	50	0.21	View
11	CDS	920-1007	58081766-58081776 / 58094836-58094912	88	0.7094	50	0.25	View
12	CDS	1011-1105	58094916-58094954 / 58096141-58096196	95	0.8256	50	0.25	View
13	CDS	1106-1193	58096197-58096218 / 58097815-58097880	88	0.8859	50	0.31	View
14	CDS	1194-1284	58097881-58097971	91	0.8315	50	0.24	View
15	CDS	1285-1401	58097972-58097977 / 58098711-58098821	117	0.7764	50	0.20	View
16	CDS	1402-1505	58098822-58098908 / 58102203-58102219	104	0.8083	50	0.25	View
17	CDS	1508-1593	58102222-58102307	86	0.8290	50	0.21	View
18	CDS	1600-1707	58102314-58102340 / 58103959-58104039	108	0.7800	50	0.19	View
19	CDS	1709-1800	58104041-58104085 / 58105080-58105126	92	0.7934	50	0.22	View
20	CDS	1804-1932	58105130-58105216 / 58106680-58106721	129	0.7359	50	0.19	View
21	CDS	1933-2029	58106722-58106818	97	0.6050	50	0.17	View
22	CDS	2030-2123	58106819-58106873 / 58108458-58108496	94	0.8011	50	0.22	View
23	CDS	2124-2222	58108497-58108571 / 58109179-58109202	99	0.7804	50	0.24	View
24	CDS	2223-2315	58109203-58109295	93	0.8455	50	0.30	View
25	CDS	2319-2415	58109299-58109322 / 58109576-58109648	97	0.8473	50	0.25	View
26	CDS	2416-2537	58109649-58109699 / 58110010-58110080	122	0.7688	50	0.22	View
27	CDS	2538-2631	58110081-58110170 / 58111791-58111794	94	0.7580	50	0.21	View
28	CDS	2633-2713	58111796-58111876	81	0.6451	50	0.18	View
29	CDS	2714-2801	58111877-58111881 / 58112149-58112231	88	0.8809	50	0.25	View
30	CDS	2802-2891	58112232-58112318 / 58118872-58118874	90	0.8121	50	0.23	View
31	CDS	2892-2991	58118875-58118974	100	0.7871	50	0.22	View
32	CDS	2992-3099	58118975-58118989 / 58121241-58121333	108	0.7573	50	0.23	View
33	CDS	3102-3203	58121336-58121437	102	0.6607	50	0.20	View
34	CDS	3205-3290	58121439-58121503 / 58123093-58123113	86	0.8364	50	0.25	View
35	CDS	3291-3398	58123114-58123221	108	0.7580	50	0.23	View
36	CDS	3400-3492	58123223-58123315	93	0.5948	50	0.20	View
37	CDS	3493-3593	58123316-58123416	101	0.6709	50	0.19	View
38	CDS	3595-3695	58123418-58123518	101	0.8051	50	0.25	View
39	CDS	3696-3787	58123519-58123610	92	0.8759	50	0.31	View
40	CDS	3788-3885	58123611-58123690 / 58124332-58124349	98	0.7374	50	0.21	View
41	CDS	3886-3973	58124350-58124437	88	0.7869	50	0.26	View
42	CDS	3974-4073	58124438-58124505 / 58125581-58125612	100	0.8463	50	0.28	View
43	CDS	4077-4166	58125616-58125705	90	0.8271	50	0.25	View
44	CDS	4170-4268	58125709-58125743 / 58126602-58126665	99	0.6779	50	0.16	View
45	CDS	4269-4363	58126666-58126760	95	0.6907	50	0.18	View
46	CDS	4364-4469	58126761-58126762 / 58130741-58130844	106	0.8349	50	0.28	View
47	CDS	4472-4581	58130847-58130908 / 58132808-58132855	110	0.8919	50	0.30	View
48	CDS	4582-4671	58132856-58132931 / 58134616-58134629	90	0.8598	50	0.29	View
49	CDS	4672-4775	58134630-58134733	104	0.7776	50	0.26	View
50	CDS	4776-4859	58134734-58134772 / 58135979-58136023	84	0.6293	50	0.19	View
51	CDS	4861-4956	58136025-58136120	96	0.8422	50	0.25	View
52	CDS	4958-5048	58136122-58136168 / 58138282-58138325	91	0.8057	50	0.26	View
53	CDS	5059-5156	58138336-58138433	98	0.8203	50	0.26	View
54	CDS	5158-5257	58138435-58138529 / 58141858-58141862	100	0.8067	50	0.26	View
55	CDS	5258-5361	58141863-58141929 / 58142650-58142686	104	0.5152	50	0.27	View
56	CDS	5362-5463	58142687-58142752 / 58143473-58143508	102	0.6791	50	0.18	View
57	CDS	5464-5558	58143509-58143603	95	0.7843	50	0.21	View
58	CDS	5559-5652	58143604-58143613 / 58145921-58146004	94	0.7503	50	0.25	View
59	CDS	5653-5741	58146005-58146049 / 58146820-58146863	89	0.7192	50	0.25	View
60	CDS	5742-5830	58146864-58146952	89	0.6004	50	0.18	View
61	CDS	5831-5917	58146953-58146993 / 58148206-58148251	87	0.8073	50	0.22	View
62	CDS	5918-6006	58148252-58148340	89	0.7545	50	0.25	View
63	CDS	6007-6090	58148341-58148364 / 58148649-58148708	84	0.6981	50	0.23	View
64	CDS	6091-6189	58148709-58148807	99	0.7385	50	0.24	View
65	CDS	6192-6297	58148810-58148852 / 58149850-58149912	106	0.7944	50	0.20	View
66	CDS	6301-6394	58149916-58150002 / 58150105-58150111	94	0.7950	50	0.20	View
67	CDS	6395-6495	58150112-58150212	101	0.7663	50	0.24	View
68	CDS	6496-6583	58150213-58150227 / 58153375-58153447	88	0.7811	50	0.27	View
69	CDS	6584-6681	58153448-58153545	98	0.5990	50	0.22	View
70	CDS	6682-6788	58153546-58153641 / 58154791-58154801	107	0.8601	50	0.28	View
71	CDS	6789-6895	58154802-58154908	107	0.8554	50	0.27	View
72	CDS	6898-6988	58154911-58154928 / 58155960-58156032	91	0.8664	50	0.25	View
73	CDS	6989-7074	58156033-58156075 / 58159554-58159596	86	0.7558	50	0.21	View
74	CDS	7080-7184	58159602-58159686 / 58163154-58163173	105	0.6276	50	0.21	View
75	CDS	7185-7285	58163174-58163274	101	0.8359	50	0.23	View
76	CDS	7290-7379	58163279-58163330 / 58168440-58168477	90	0.7074	50	0.23	View
77	CDS	7383-7468	58168481-58168566	86	0.6790	50	0.25	View
78	CDS	7469-7552	58168567-58168650	84	0.6453	50	0.25	View
79	CDS	7557-7648	58168655-58168658 / 58169590-58169677	92	0.7767	50	0.28	View
80	CDS	7650-7750	58169679-58169779	101	0.6972	50	0.31	View
81	CDS	7751-7841	58169780-58169793 / 58170575-58170651	91	0.7947	50	0.25	View
82	CDS	7842-7943	58170652-58170753	102	0.7208	50	0.22	View
83	CDS,3'UTR	7947-8062	58170757-58170872	116	0.6280	50	0.31	View
84	3'UTR	8063-8168	58170873-58170978	106	0.6310	50	0.33	View
85	3'UTR	8170-8248	58170980-58171058	79	0.6489	50	0.38	View
86	3'UTR	8249-8342	58171059-58171152	94	0.7561	50	0.35	View
87	3'UTR	8343-8452	58171153-58171262	110	0.7677	50	0.30	View
88	3'UTR	8454-8541	58171264-58171351	88	0.5922	50	0.35	View
89	3'UTR	8543-8634	58171353-58171444	92	0.7715	50	0.41	View
90	3'UTR	8635-8742	58171445-58171552	108	0.7774	50	0.35	View
91	3'UTR	8743-8823	58171553-58171633	81	0.5602	50	0.32	View
92	3'UTR	8824-8906	58171634-58171716	83	0.6221	50	0.30	View
93	3'UTR	8907-9015	58171717-58171825	109	0.5266	50	0.33	View
94	3'UTR	9017-9130	58171827-58171940	114	0.6140	50	0.32	View
95	3'UTR	9131-9268	58171941-58172078	138	0.8161	50	0.37	View
96	3'UTR	9270-9413	58172080-58172223	144	0.5321	74	0.30	View
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

26
FLNB

Aoi:	Chr:	Coords	Strand:
FLNB	3	58109649 - 58109699, 58110010 - 58110080	+

Download Data & Images

Annotation Based on canonical annotations, the following gene is in your area of interest: FLNB(+)
Length Length of region: 122 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 3 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

FLNB ENST00000295956 (+) ENSG00000136068 (+)

Custom Gene Windows

completed 26 FLNB

FLNB
ENST00000295956 (+) ENSG00000136068 (+)

completed

26
FLNB