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?

HTT
ENST00000355072 (+) ENSG00000197386 (+)

Custom Window:

Start

Size

100

150

300

500

Strand

+

-

Predict

	Region	Local Coords	Chrom Coords	Length	R	N	Gini	Action
1	CDS	446-550	3086976-3087022 / 3099274-3099331	105	0.3711	50	0.40
2	CDS	551-653	3099332-3099394 / 3103824-3103863	103	0.5206	50	0.32
3	CDS	655-767	3103865-3103883 / 3105357-3105436 / 3107285-3107298	113	0.7655	50	0.45
4	CDS	768-855	3107299-3107386	88	0.4004	50	0.30
5	CDS	858-952	3107389-3107423 / 3115304-3115363	95	0.3675	50	0.32
6	CDS	954-1056	3115365-3115445 / 3116085-3116106	103	0.4377	50	0.34
7	CDS	1059-1156	3116109-3116206	98	0.5816	50	0.43
8	CDS	1159-1249	3116209-3116263 / 3121228-3121263	91	0.3011	50	0.32
9	CDS	1251-1336	3121265-3121350	86	0.6237	50	0.38	View
10	CDS	1339-1458	3121353-3121432 / 3122889-3122928	120	0.6714	50	0.37
11	CDS	1459-1551	3122929-3122936 / 3125549-3125629 / 3127264-3127267	93	0.4787	50	0.38
12	CDS	1552-1650	3127268-3127366	99	0.4981	50	0.30
13	CDS	1652-1750	3127368-3127466	99	0.3612	50	0.33
14	CDS	1751-1835	3127467-3127551	85	0.5940	50	0.39
15	CDS	1836-1933	3127552-3127604 / 3129924-3129968	98	0.4264	50	0.31	View
16	CDS	1934-2025	3129969-3130047 / 3130305-3130317	92	0.6795	50	0.41
17	CDS	2026-2126	3130318-3130418	101	0.5702	50	0.33
18	CDS	2127-2230	3130419-3130423 / 3131286-3131384	104	0.4949	50	0.30
19	CDS	2236-2343	3131390-3131397 / 3131638-3131737	108	0.6142	50	0.46	View
20	CDS	2344-2429	3131738-3131775 / 3132562-3132609	86	0.4836	50	0.34	View
21	CDS	2430-2528	3132610-3132708	99	0.5163	50	0.39
22	CDS	2530-2639	3132710-3132720 / 3132814-3132911 / 3134401-3134401	110	0.2467	50	0.33
23	CDS	2640-2754	3134402-3134516	115	0.6125	50	0.40
24	CDS	2755-2852	3134517-3134540 / 3135904-3135967 / 3136226-3136235	98	0.4200	50	0.33
25	CDS	2855-2953	3136238-3136326 / 3140510-3140519	99	0.4364	50	0.37	View
26	CDS	2954-3051	3140520-3140617	98	0.3983	50	0.35
27	CDS	3053-3127	3140619-3140656 / 3142766-3142802	75	0.3250	50	0.30
28	CDS	3129-3209	3142804-3142884	81	0.3404	50	0.34
29	CDS	3210-3341	3142885-3142886 / 3145152-3145228 / 3146797-3146849	132	0.3533	50	0.40
30	CDS	3345-3605	3146853-3146948 / 3148005-3148169	261	0.4755	50	0.38	View
31	CDS	3606-3691	3148170-3148207 / 3154293-3154340	86	0.4738	50	0.47
32	CDS	3692-3780	3154341-3154419 / 3157072-3157081	89	0.2377	50	0.35
33	CDS	3781-3872	3157082-3157173	92	0.1595	50	0.34
34	CDS	3875-3971	3157176-3157199 / 3160282-3160354	97	0.4053	50	0.33
35	CDS	3972-4070	3160355-3160392 / 3172320-3172380	99	0.2878	50	0.28
36	CDS	4071-4168	3172381-3172397 / 3172908-3172988	98	0.5087	50	0.36
37	CDS	4170-4255	3172990-3173075	86	0.4760	50	0.42
38	CDS	4257-4354	3173077-3173131 / 3174721-3174763	98	0.4164	50	0.34	View
39	CDS	4355-4446	3174764-3174799 / 3174946-3175001	92	0.2925	50	0.26
40	CDS	4447-4570	3175002-3175107 / 3177332-3177349	124	0.4191	50	0.33	View
41	CDS	4574-4674	3177353-3177387 / 3178298-3178363	101	0.3661	50	0.29	View
42	CDS	4677-4769	3178366-3178446 / 3180515-3180526	93	0.4878	50	0.43	View
43	CDS	4772-4851	3180529-3180608	80	0.5125	50	0.36
44	CDS	4863-4961	3180620-3180651 / 3182354-3182420	99	0.4962	50	0.29
45	CDS	4965-5051	3182424-3182470 / 3186597-3186636	87	0.4340	50	0.27
46	CDS	5052-5166	3186637-3186719 / 3187651-3187682	115	0.4005	50	0.36	View
47	CDS	5170-5282	3187686-3187798	113	0.2386	50	0.35
48	CDS	5287-5369	3187803-3187885	83	0.3722	50	0.37
49	CDS	5375-5476	3188955-3189056	102	0.4726	50	0.33
50	CDS	5477-5583	3189057-3189093 / 3199732-3199801	107	0.4950	50	0.40	View
51	CDS	5584-5679	3199802-3199897	96	0.3879	50	0.39
52	CDS	5680-5760	3199898-3199939 / 3204007-3204045	81	0.4075	50	0.35	View
53	CDS	5762-5919	3204047-3204148 / 3206496-3206551	158	0.3955	50	0.41
54	CDS	5920-6761	3206552-3206675 / 3209827-3209949 / 3211929-3212130	842	0.4677	50	0.43	Error
55	CDS	6762-6866	3212131-3212142 / 3212564-3212656	105	0.3684	50	0.40
56	CDS	6869-7080	3212659-3212709 / 3213958-3214118	212	0.3520	50	0.43
57	CDS	7081-7167	3214119-3214135 / 3215110-3215179	87	0.4029	50	0.33
58	CDS	7170-7278	3215182-3215211 / 3217765-3217843	109	0.3371	50	0.33
59	CDS	7280-7368	3217845-3217933	89	0.4485	50	0.42	View
60	CDS	7369-7470	3217934-3217952 / 3220182-3220264	102	0.4268	50	0.39
61	CDS	7471-7559	3220265-3220308 / 3222387-3222431	89	0.3565	50	0.30	View
62	CDS	7567-7651	3222439-3222487 / 3223406-3223441	85	0.4917	50	0.49	View
63	CDS	7655-7746	3223445-3223536	92	0.4952	50	0.42	View
64	CDS	7748-7851	3223538-3223560 / 3223992-3224072	104	0.4556	50	0.37
65	CDS	7852-7943	3224073-3224131 / 3225661-3225693	92	0.3042	50	0.38
66	CDS	7944-8034	3225694-3225743 / 3228615-3228655	91	0.1771	50	0.36
67	CDS	8035-8123	3228656-3228744	89	0.5470	50	0.42	View
68	CDS	8131-8761	3228886-3229009 / 3235284-3235398 / 3235565-3235609	631	0.3992	50	0.40	Error
69	CDS	8762-8867	3235610-3235715	106	0.4140	50	0.41
70	CDS	8868-8961	3235716-3235778 / 3236149-3236179	94	0.5441	50	0.37
71	CDS	8962-9076	3236180-3236254 / 3238447-3238486	115	0.4957	50	0.37
72	CDS	9077-9156	3238487-3238566	80	0.2317	45	0.32
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

52
HTT

Aoi:	Chr:	Coords	Strand:
HTT	4	3199898 - 3199939, 3204007 - 3204045	+

Download Data & Images

Annotation Based on canonical annotations, the following gene is in your area of interest: HTT(+)
Length Length of region: 81 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

HTT ENST00000355072 (+) ENSG00000197386 (+)

Custom Gene Windows

completed 52 HTT

HTT
ENST00000355072 (+) ENSG00000197386 (+)

completed

52
HTT