Parameters
input_file: 20090715_LUh6_2_hg19_ensembl59_S_iCLIP_hnRNPC_HeLa_bedGraph-cDNA.bed.gz
input_res_type: single hits (=G+T), cDNA counts
mapped_to: hg19
annot_ver: ensembl59
maxU_within: -300
maxD_within: 300
maxU_flanking: -1000
maxD_flanking: 1000
smoothing: 0

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 241506
[x-link sites] used in any map: 36606 (15.16%)
[single hits (=G+T), cDNA counts] total: 241506
[single hits (=G+T), cDNA counts] used in any map: 40092 (15.60%)

map	span (upstream; downstream)	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map
exon-intron	-300; 300	10057	4.16%	27.47%	10565	4.11%	26.35%
intron-exon	-300; 300	9392	3.89%	25.66%	9859	3.84%	24.59%
5-ncRNA	-1000; 300	3350	1.39%	9.15%	4205	1.64%	10.49%
ncRNA-3	-300; 1000	3534	1.46%	9.65%	4349	1.69%	10.85%
ORF-3UTR	-300; 300	1662	0.69%	4.54%	1785	0.69%	4.45%
5UTR-ORF	-300; 300	254	0.11%	0.69%	280	0.11%	0.70%
inter-5UTR	-1000; 300	928	0.38%	2.54%	1025	0.40%	2.56%
3UTR-inter	-300; 1000	2392	0.99%	6.53%	2578	1.00%	6.43%
inter-5	-1000; 300	2938	1.22%	8.03%	3413	1.33%	8.51%
3-inter	-300; 1000	4356	1.80%	11.90%	5044	1.96%	12.58%
BP best in intron	-300; 100	9595	3.97%	26.21%	10078	3.92%	25.14%

Download statistics in tab-delimited format.
Download graphs in tab-delimited format.

RNAmap exon-intron

junction is at position zero.
upstream is regions of type: ORF, 3UTR, 5UTR
downstream is regions of type: intron

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	9662	4.00%	26.39%	96.07%	7556	1.22428
anti	395	0.16%	1.08%	3.93%	356	0.0500507
both	10057	4.16%	27.47%	100.00%	7892	1.27433
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	10150	3.95%	25.32%	96.07%	7556	1.28611
anti	415	0.16%	1.04%	3.93%	356	0.0525849
both	10565	4.11%	26.35%	100.00%	7892	1.3387

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr5:179049848@-	-158; 300	HNRNPH1	20; 0	33; 0
chr9:134363483@+	-121; 300	BAT2L	9; 0	10; 0
chr7:95045186@-	-211; 300	PON2	9; 0	9; 0
chr5:78909906@+	-75; 300	PAPD4	9; 0	10; 0
chr9:21818201@+	-84; 300	MTAP	8; 0	12; 0
chr1:11077064@+	-82; 300	TARDBP	8; 0	8; 0
chr8:98827629@+	-37; 300	LAPTM4B	7; 0	8; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 7	0; 10
chr4:39928393@-	-44; 300	PDS5A	7; 0	7; 0
chr3:186506209@+	-300; 300	EIF4A2	7; 0	7; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr5:179049848@-	-158; 300	HNRNPH1	20; 0	33; 0
chr9:21818201@+	-84; 300	MTAP	8; 0	12; 0
chr9:134363483@+	-121; 300	BAT2L	9; 0	10; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 7	0; 10
chr5:78909906@+	-75; 300	PAPD4	9; 0	10; 0
chr19:17450408@+	-83; 300	GTPBP3	7; 0	10; 0
chr12:20523178@+	-300; 300	PDE3A	7; 0	10; 0
chr7:95045186@-	-211; 300	PON2	9; 0	9; 0
chr4:24541330@-	-296; 279	DHX15	6; 0	9; 0
chr16:586142@+	-57; 300	SOLH	6; 0	9; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap intron-exon

junction is at position zero.
upstream is regions of type: intron
downstream is regions of type: ORF, 3UTR, 5UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	8882	3.68%	24.26%	94.57%	7002	1.19462
anti	510	0.21%	1.39%	5.43%	446	0.0685945
both	9392	3.89%	25.66%	100.00%	7435	1.26321
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	9330	3.63%	23.27%	94.63%	7002	1.25488
anti	529	0.21%	1.32%	5.37%	446	0.07115
both	9859	3.84%	24.59%	100.00%	7435	1.32603

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr1:1413405@+	-300; 300	ATAD3B	18; 0	25; 0
chr17:57915655@+	-300; 51	TMEM49	15; 0	19; 0
chr9:131456919@+	-292; 300	SET	13; 0	14; 0
chr5:179041959@-	-293; 300	HNRNPH1	13; 0	13; 0
chr12:54678332@+	-116; 300	HNRNPA1	13; 0	24; 0
chr5:138651035@+	-300; 196	MATR3	12; 0	17; 0
chr5:58882324@-	-300; 62	PDE4D	11; 0	12; 0
chr1:21102497@-	-296; 278	HP1BP3	10; 0	11; 0
chr1:76259066@+	-300; 300	RABGGTB	10; 0	14; 0
chr1:70697230@+	-137; 155	SFRS11	10; 0	10; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr1:1413405@+	-300; 300	ATAD3B	18; 0	25; 0
chr12:54678332@+	-116; 300	HNRNPA1	13; 0	24; 0
chr17:57915655@+	-300; 51	TMEM49	15; 0	19; 0
chr5:138651035@+	-300; 196	MATR3	12; 0	17; 0
chr9:131456919@+	-292; 300	SET	13; 0	14; 0
chr5:58571944@-	-300; 300	PDE4D	9; 0	14; 0
chr3:47702944@-	-300; 81	SMARCC1	8; 0	14; 0
chr1:21101497@-	-222; 300	HP1BP3	9; 0	14; 0
chr1:76259066@+	-300; 300	RABGGTB	10; 0	14; 0
chr5:179041959@-	-293; 300	HNRNPH1	13; 0	13; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 5-ncRNA

junction is at position zero.
upstream is regions of type: intron, inter, telo
downstream is regions of type: ncRNA

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	1644	0.68%	4.49%	49.07%	822	0.875866
anti	1706	0.71%	4.66%	50.93%	1082	0.908897
both	3350	1.39%	9.15%	100.00%	1877	1.78476
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	2420	0.94%	6.04%	57.55%	822	1.28929
anti	1785	0.69%	4.45%	42.45%	1082	0.950986
both	4205	1.64%	10.49%	100.00%	1877	2.24028

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	151; 0	340; 0
chr8:128231332@-	-1000; 139	AC020688.1	64; 1	100; 1
chr17:57918626@+	-338; 36	hsa-mir-21	48; 0	222; 0
chrUn_gl000220:109077@+	-758; 300	18S	23; 0	39; 0
chr17:41445449@-	-1000; 87	AC087650.5	23; 0	44; 0
chr7:1609708@+	-1000; 230	AC093734.11	0; 18	0; 20
chr20:47896855@+	-555; 45	C20orf199, SNORD12-ENSG00000222365	16; 0	87; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	14; 0	29; 0
chrUn_gl000220:113347@+	-585; 300	28S	13; 0	16; 0
chr20:47895476@+	-101; 44	C20orf199, SNORD12-ENSG00000209042	13; 0	47; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	151; 0	340; 0
chr17:57918626@+	-338; 36	hsa-mir-21	48; 0	222; 0
chr8:128231332@-	-1000; 139	AC020688.1	64; 1	100; 1
chr20:47896855@+	-555; 45	C20orf199, SNORD12-ENSG00000222365	16; 0	87; 0
chr20:47895476@+	-101; 44	C20orf199, SNORD12-ENSG00000209042	13; 0	47; 0
chr17:41445449@-	-1000; 87	AC087650.5	23; 0	44; 0
chrUn_gl000220:109077@+	-758; 300	18S	23; 0	39; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	11; 0	32; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	8; 0	32; 0
chr1:11968208@+	-1000; 60	U5-ENSG00000199347	10; 0	31; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap ncRNA-3

junction is at position zero.
upstream is regions of type: ncRNA
downstream is regions of type: intron, inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	1874	0.78%	5.12%	53.03%	887	0.974012
anti	1660	0.69%	4.53%	46.97%	1052	0.862786
both	3534	1.46%	9.65%	100.00%	1924	1.8368
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	2599	1.01%	6.48%	59.76%	887	1.35083
anti	1750	0.68%	4.36%	40.24%	1052	0.909563
both	4349	1.69%	10.85%	100.00%	1924	2.2604

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	196; 0	449; 0
chrUn_gl000220:118417@+	-300; 1000	28S	46; 0	73; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 38	0; 58
chr11:62609089@-	-96; 978	U2-ENSG00000222328	29; 0	50; 0
chr1:11969863@-	-60; 1000	U5-ENSG00000201801	26; 0	132; 0
chrUn_gl000220:110946@+	-300; 539	18S	23; 0	36; 0
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	22; 0	50; 0
chr1:45187456@-	-59; 1000	U5-ENSG00000199377	22; 0	24; 0
chr1:11968328@+	-60; 1000	U5-ENSG00000199347	21; 0	35; 0
chr17:56709001@-	-98; 543	TEX14, U3-ENSG00000212195	16; 0	19; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	196; 0	449; 0
chr1:11969863@-	-60; 1000	U5-ENSG00000201801	26; 0	132; 0
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	10; 3	91; 5
chrUn_gl000220:118417@+	-300; 1000	28S	46; 0	73; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 38	0; 58
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	22; 0	50; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	29; 0	50; 0
chr11:10823012@-	-71; 189	EIF4G2, snoU97	15; 0	48; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	9; 0	39; 0
chrUn_gl000220:110946@+	-300; 539	18S	23; 0	36; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap ORF-3UTR

junction is at position zero.
upstream is regions of type: ORF
downstream is regions of type: 3UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	1576	0.65%	4.31%	94.83%	970	1.52418
anti	86	0.04%	0.23%	5.17%	72	0.0831721
both	1662	0.69%	4.54%	100.00%	1034	1.60735
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	1695	0.66%	4.23%	94.96%	970	1.63926
anti	90	0.04%	0.22%	5.04%	72	0.0870406
both	1785	0.69%	4.45%	100.00%	1034	1.72631

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr17:57917272@+	-72; 300	TMEM49	29; 0	36; 0
chr12:46754890@-	-51; 300	SLC38A2	17; 0	28; 0
chr1:35650053@-	-70; 300	SFPQ	14; 0	16; 0
chr17:4849191@-	-50; 123	PFN1	11; 0	26; 0
chr19:1037899@+	-138; 300	CNN2	10; 0	10; 0
chrX:70794505@+	-300; 300	OGT	9; 0	9; 0
chr3:55503877@-	-300; 116	WNT5A	9; 0	10; 0
chr19:19105798@-	-145; 252	SFRS14	9; 0	10; 0
chr5:179155786@+	-98; 287	CANX	8; 0	8; 0
chr22:38881684@-	-300; 300	DDX17	8; 0	9; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr17:57917272@+	-72; 300	TMEM49	29; 0	36; 0
chr12:46754890@-	-51; 300	SLC38A2	17; 0	28; 0
chr17:4849191@-	-50; 123	PFN1	11; 0	26; 0
chr1:35650053@-	-70; 300	SFPQ	14; 0	16; 0
chr17:15531925@-	-207; 300	TRIM16	7; 0	13; 0
chr3:55503877@-	-300; 116	WNT5A	9; 0	10; 0
chr19:19105798@-	-145; 252	SFRS14	9; 0	10; 0
chr19:1037899@+	-138; 300	CNN2	10; 0	10; 0
chrX:70794505@+	-300; 300	OGT	9; 0	9; 0
chr22:38881684@-	-300; 300	DDX17	8; 0	9; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 5UTR-ORF

junction is at position zero.
upstream is regions of type: 5UTR
downstream is regions of type: ORF

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	231	0.10%	0.63%	90.94%	160	1.3125
anti	23	0.01%	0.06%	9.06%	16	0.130682
both	254	0.11%	0.69%	100.00%	176	1.44318
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	255	0.10%	0.64%	91.07%	160	1.44886
anti	25	0.01%	0.06%	8.93%	16	0.142045
both	280	0.11%	0.70%	100.00%	176	1.59091

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr7:1608974@-	-300; 108	PSMG3	11; 0	11; 0
chr6:31508971@-	-66; 265	BAT1	5; 0	6; 0
chr2:118854132@+	-65; 122	INSIG2	5; 0	5; 0
chr17:43226557@+	-300; 300	HEXIM1	5; 0	5; 0
chr1:23885933@-	-176; 158	ID3	5; 0	6; 0
chr5:138643104@+	-89; 300	MATR3	4; 0	6; 0
chr5:32789507@+	-282; 183	C5orf23	4; 0	5; 0
chr2:27884262@-	-300; 300	SUPT7L	4; 0	4; 0
chr19:49468764@+	-100; 51	FTL	4; 0	7; 0
chr2:113404405@+	-133; 167	SLC20A1	3; 0	5; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr7:1608974@-	-300; 108	PSMG3	11; 0	11; 0
chr19:49468764@+	-100; 51	FTL	4; 0	7; 0
chr6:31508971@-	-66; 265	BAT1	5; 0	6; 0
chr5:138643104@+	-89; 300	MATR3	4; 0	6; 0
chr1:23885933@-	-176; 158	ID3	5; 0	6; 0
chr5:32789507@+	-282; 183	C5orf23	4; 0	5; 0
chr2:118854132@+	-65; 122	INSIG2	5; 0	5; 0
chr2:113404405@+	-133; 167	SLC20A1	3; 0	5; 0
chr17:43226557@+	-300; 300	HEXIM1	5; 0	5; 0
chr13:45010763@-	-109; 62	TSC22D1	3; 0	5; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap inter-5UTR

junction is at position zero.
upstream is regions of type: inter, telo
downstream is regions of type: 5UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	263	0.11%	0.72%	28.34%	178	0.445008
anti	665	0.28%	1.82%	71.66%	426	1.12521
both	928	0.38%	2.54%	100.00%	591	1.57022
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	274	0.11%	0.68%	26.73%	178	0.463621
anti	751	0.29%	1.87%	73.27%	426	1.27073
both	1025	0.40%	2.56%	100.00%	591	1.73435

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr6:166401114@+	-1000; 249	AL132661.1	0; 19	0; 26
chr20:47894962@-	-1000; 248	ZNFX1	0; 16	0; 50
chr1:173837219@+	-1000; 87	ZBTB37	0; 14	0; 16
chr8:33370702@-	-1000; 286	C8orf41	1; 12	1; 17
chr16:88785022@+	-1000; 84	AC138028.2	0; 10	0; 12
chr2:190648810@+	-1000; 254	PMS1	0; 8	0; 8
chr5:147647742@+	-1000; 164	SPINK5L3	7; 0	8; 0
chr11:62623517@+	-1000; 112	SLC3A2	0; 7	0; 9
chr9:140095756@-	-1000; 297	C9orf75	5; 1	5; 1
chr16:4524718@+	-1000; 65	HMOX2	0; 6	0; 6

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr20:47894962@-	-1000; 248	ZNFX1	0; 16	0; 50
chr6:166401114@+	-1000; 249	AL132661.1	0; 19	0; 26
chr8:33370702@-	-1000; 286	C8orf41	1; 12	1; 17
chr1:173837219@+	-1000; 87	ZBTB37	0; 14	0; 16
chr16:88785022@+	-1000; 84	AC138028.2	0; 10	0; 12
chr11:62623517@+	-1000; 112	SLC3A2	0; 7	0; 9
chr5:147647742@+	-1000; 164	SPINK5L3	7; 0	8; 0
chr22:45559721@+	-1000; 78	NUP50	0; 5	0; 8
chr2:190648810@+	-1000; 254	PMS1	0; 8	0; 8
chr15:99192199@+	-1000; 300	IGF1R	6; 0	7; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 3UTR-inter

junction is at position zero.
upstream is regions of type: 3UTR
downstream is regions of type: inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	1829	0.76%	5.00%	76.46%	1175	1.19621
anti	563	0.23%	1.54%	23.54%	383	0.368215
both	2392	0.99%	6.53%	100.00%	1529	1.56442
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	1975	0.77%	4.93%	76.61%	1175	1.29169
anti	603	0.23%	1.50%	23.39%	383	0.394375
both	2578	1.00%	6.43%	100.00%	1529	1.68607

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr17:57917950@+	-300; 338	TMEM49	21; 0	57; 0
chr5:10435491@+	-300; 1000	MARCH6	15; 0	19; 0
chr19:54972979@-	-144; 1000	LENG9	0; 15	0; 16
chr17:4848518@+	-104; 1000	RNF167	0; 11	0; 26
chr22:38879452@+	-263; 1000	KDELR3	0; 10	0; 12
chr17:79476997@-	-300; 1000	ACTG1	10; 0	17; 0
chr19:34891236@+	-148; 1000	GPI	9; 0	12; 0
chrX:102930422@-	-300; 1000	MORF4L2	8; 0	9; 0
chr5:172195091@-	-300; 1000	DUSP1	8; 0	9; 0
chr5:17276943@+	-300; 1000	BASP1	8; 0	9; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr17:57917950@+	-300; 338	TMEM49	21; 0	57; 0
chr17:4848518@+	-104; 1000	RNF167	0; 11	0; 26
chr5:10435491@+	-300; 1000	MARCH6	15; 0	19; 0
chr17:79476997@-	-300; 1000	ACTG1	10; 0	17; 0
chr19:54972979@-	-144; 1000	LENG9	0; 15	0; 16
chr22:38879452@+	-263; 1000	KDELR3	0; 10	0; 12
chr19:34891236@+	-148; 1000	GPI	9; 0	12; 0
chr5:32604185@+	-300; 1000	SUB1	7; 0	10; 0
chrX:102930422@-	-300; 1000	MORF4L2	8; 0	9; 0
chr5:172195091@-	-300; 1000	DUSP1	8; 0	9; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap inter-5

junction is at position zero.
upstream is regions of type: inter, telo
downstream is regions of type: ORF, intron, 3UTR, 5UTR, ncRNA

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	800	0.33%	2.19%	27.23%	448	0.460035
anti	2138	0.89%	5.84%	72.77%	1327	1.22944
both	2938	1.22%	8.03%	100.00%	1739	1.68948
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	1005	0.39%	2.51%	29.45%	448	0.577918
anti	2408	0.94%	6.01%	70.55%	1327	1.3847
both	3413	1.33%	8.51%	100.00%	1739	1.96262

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 69	0; 191
chr8:128231332@-	-1000; 139	AC020688.1	64; 1	100; 1
chrUn_gl000220:109077@+	-758; 300	18S	23; 0	39; 0
chr17:41445449@-	-1000; 87	AC087650.5	23; 0	44; 0
chr7:1609708@+	-1000; 230	AC093734.11	0; 18	0; 20
chr6:166401114@+	-1000; 249	AL132661.1	0; 18	0; 25
chr20:47894962@-	-1000; 248	ZNFX1	0; 16	0; 50
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	14; 0	29; 0
chr1:173837219@+	-1000; 87	ZBTB37	0; 14	0; 16
chrUn_gl000220:113347@+	-585; 300	28S	13; 0	16; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 69	0; 191
chr8:128231332@-	-1000; 139	AC020688.1	64; 1	100; 1
chr20:47894962@-	-1000; 248	ZNFX1	0; 16	0; 50
chr17:41445449@-	-1000; 87	AC087650.5	23; 0	44; 0
chrUn_gl000220:109077@+	-758; 300	18S	23; 0	39; 0
chr1:11968208@+	-1000; 60	U5-ENSG00000199347	10; 0	31; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	14; 0	29; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 18	0; 25
chr1:11969983@-	-628; 60	U5-ENSG00000201801	7; 0	24; 0
chr7:1609708@+	-1000; 230	AC093734.11	0; 18	0; 20

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 3-inter

junction is at position zero.
upstream is regions of type: ORF, intron, 3UTR, 5UTR, ncRNA
downstream is regions of type: inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	2631	1.09%	7.19%	60.40%	1525	1.03176
anti	1725	0.71%	4.71%	39.60%	1066	0.676471
both	4356	1.80%	11.90%	100.00%	2550	1.70824
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	3185	1.24%	7.94%	63.14%	1525	1.24902
anti	1859	0.72%	4.64%	36.86%	1066	0.72902
both	5044	1.96%	12.58%	100.00%	2550	1.97804

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	196; 0	449; 0
chrUn_gl000220:118417@+	-300; 1000	28S	46; 0	73; 0
chr7:5566780@-	-300; 1000	ACTB	40; 0	109; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 38	0; 58
chr17:16344889@-	-300; 1000	C17orf76	0; 24	0; 49
chrUn_gl000220:110946@+	-300; 539	18S	23; 0	36; 0
chr17:57917950@+	-300; 338	TMEM49	21; 0	57; 0
chr5:10435491@+	-300; 1000	MARCH6	15; 0	19; 0
chr19:54972979@-	-144; 1000	LENG9	0; 15	0; 16
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	14; 0	21; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	196; 0	449; 0
chr7:5566780@-	-300; 1000	ACTB	40; 0	109; 0
chrUn_gl000220:118417@+	-300; 1000	28S	46; 0	73; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 38	0; 58
chr17:57917950@+	-300; 338	TMEM49	21; 0	57; 0
chr17:16344889@-	-300; 1000	C17orf76	0; 24	0; 49
chrUn_gl000220:110946@+	-300; 539	18S	23; 0	36; 0
chr17:4848518@+	-104; 1000	RNF167	0; 11	0; 26
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	14; 0	21; 0
chr5:10435491@+	-300; 1000	MARCH6	15; 0	19; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap "BP best in intron"

BP is at position zero.
upstream is usptream of branch point
downstream is downstream of branch point

[eps]

x-links and BPs distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [BPs] in map	[x-link sites] per unique [BP]
same	9175	3.80%	25.06%	95.62%	7168	1.21797
anti	420	0.17%	1.15%	4.38%	381	0.0557547
both	9595	3.97%	26.21%	100.00%	7533	1.27373
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [BPs] in map	[single hits (=G+T), cDNA counts] per unique [BP]
same	9640	3.75%	24.04%	95.65%	7168	1.2797
anti	438	0.17%	1.09%	4.35%	381	0.0581442
both	10078	3.92%	25.14%	100.00%	7533	1.33785

Top 10 BPs with largest x-link sites sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr17:57915352@+	-300; 100	TMEM49	15; 0	32; 0
chr9:33259146@-	-300; 100	AL161445.1	12; 0	17; 0
chr21:44842114@-	-300; 100	SIK1	12; 0	17; 0
chr17:62496969@-	-300; 79	DDX5	9; 0	11; 0
chr5:43504200@-	-300; 100	C5orf34	8; 0	8; 0
chr20:62890905@+	-300; 100	PCMTD2	8; 0	9; 0
chr11:47829005@-	-300; 100	NUP160	8; 0	8; 0
chr8:144672927@-	-300; 20	EEF1D	7; 0	10; 0
chr8:23425382@+	-300; 100	SLC25A37	7; 0	7; 0
chr5:147649349@+	-300; 100	SPINK5L3	7; 0	8; 0

Top 10 BPs with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr17:57915352@+	-300; 100	TMEM49	15; 0	32; 0
chr9:33259146@-	-300; 100	AL161445.1	12; 0	17; 0
chr21:44842114@-	-300; 100	SIK1	12; 0	17; 0
chr17:62496969@-	-300; 79	DDX5	9; 0	11; 0
chr12:49666009@+	-300; 24	TUBA1C	7; 0	11; 0
chr8:144672927@-	-300; 20	EEF1D	7; 0	10; 0
chr20:62890905@+	-300; 100	PCMTD2	8; 0	9; 0
chr16:70571951@+	-300; 100	SNORD111-ENSG00000221066	4; 0	9; 0
chr1:1413786@+	-300; 100	ATAD3B	6; 0	9; 0
chr5:43504200@-	-300; 100	C5orf34	8; 0	8; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.