Parameters
input_file: 20090715_LUh6_2_hg19_ensembl59_G_iCLIP_hnRNPC_HeLa_bedGraph-cDNA-hits-in-genome.bed.gz
input_res_type: single hits in whole-genome, cDNA counts
mapped_to: hg19
annot_ver: ensembl59
maxU_within: -300
maxD_within: 300
maxU_flanking: -1000
maxD_flanking: 1000
smoothing: 5

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 233593
[x-link sites] used in any map: 35758 (15.31%)
[single hits in whole-genome, cDNA counts] total: 233593
[single hits in whole-genome, cDNA counts] used in any map: 39160 (15.77%)

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 in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map
exon-intron	-300; 300	9829	4.21%	27.49%	10324	4.16%	26.36%
intron-exon	-300; 300	9234	3.95%	25.82%	9690	3.90%	24.74%
5-ncRNA	-1000; 300	3231	1.38%	9.04%	4060	1.63%	10.37%
ncRNA-3	-300; 1000	3414	1.46%	9.55%	4212	1.70%	10.76%
ORF-3UTR	-300; 300	1622	0.69%	4.54%	1741	0.70%	4.45%
5UTR-ORF	-300; 300	252	0.11%	0.70%	276	0.11%	0.70%
inter-5UTR	-1000; 300	915	0.39%	2.56%	1012	0.41%	2.58%
3UTR-inter	-300; 1000	2347	1.00%	6.56%	2530	1.02%	6.46%
inter-5	-1000; 300	2838	1.21%	7.94%	3289	1.32%	8.40%
3-inter	-300; 1000	4243	1.82%	11.87%	4908	1.98%	12.53%
BP best in intron	-300; 100	9382	4.02%	26.24%	9859	3.97%	25.18%

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	9466	4.05%	26.47%	96.31%	7431	1.22284
anti	363	0.16%	1.02%	3.69%	326	0.0468932
both	9829	4.21%	27.49%	100.00%	7741	1.26973
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	9941	4.00%	25.39%	96.29%	7431	1.2842
anti	383	0.15%	0.98%	3.71%	326	0.0494768
both	10324	4.16%	26.36%	100.00%	7741	1.33368

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 in whole-genome, 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
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
chr5:78909906@+	-75; 300	PAPD4	7; 0	8; 0
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 in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, 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
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
chr14:62188541@+	-43; 300	HIF1A	7; 0	9; 0
chr11:10828365@-	-33; 300	EIF4G2	7; 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	8785	3.76%	24.57%	95.14%	6936	1.20129
anti	449	0.19%	1.26%	4.86%	386	0.0613975
both	9234	3.95%	25.82%	100.00%	7313	1.26268
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	9224	3.71%	23.55%	95.19%	6936	1.26132
anti	466	0.19%	1.19%	4.81%	386	0.0637221
both	9690	3.90%	24.74%	100.00%	7313	1.32504

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 in whole-genome, cDNA counts] (same; anti)
chr1:1413405@+	-300; 300	ATAD3B	18; 0	25; 0
chr17:57915655@+	-300; 51	TMEM49	15; 0	19; 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
chr9:131456919@+	-292; 300	SET	11; 0	12; 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 in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, 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
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
chr9:131456919@+	-292; 300	SET	11; 0	12; 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	1572	0.67%	4.40%	48.65%	794	0.859486
anti	1659	0.71%	4.64%	51.35%	1059	0.907053
both	3231	1.38%	9.04%	100.00%	1829	1.76654
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	2325	0.94%	5.94%	57.27%	794	1.27119
anti	1735	0.70%	4.43%	42.73%	1059	0.948606
both	4060	1.63%	10.37%	100.00%	1829	2.21979

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 in whole-genome, cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	150; 0	339; 0
chr8:128231332@-	-1000; 139	AC020688.1	64; 1	100; 1
chr17:57918626@+	-338; 36	hsa-mir-21	48; 0	222; 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
chr20:47895476@+	-101; 44	C20orf199, SNORD12-ENSG00000209042	13; 0	47; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	11; 0	32; 0
chr1:145382396@-	-1000; 171	RP11-458D21.1	1; 10	1; 11

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	150; 0	339; 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
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
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	14; 0	29; 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	1789	0.77%	5.00%	52.40%	849	0.953117
anti	1625	0.70%	4.54%	47.60%	1036	0.865743
both	3414	1.46%	9.55%	100.00%	1877	1.81886
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	2499	1.01%	6.38%	59.33%	849	1.33138
anti	1713	0.69%	4.37%	40.67%	1036	0.912627
both	4212	1.70%	10.76%	100.00%	1877	2.24401

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 in whole-genome, 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
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
chr11:10823012@-	-71; 189	EIF4G2, snoU97	15; 0	48; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, 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
chr1:11968328@+	-60; 1000	U5-ENSG00000199347	21; 0	35; 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	1538	0.66%	4.30%	94.82%	955	1.51081
anti	84	0.04%	0.23%	5.18%	70	0.0825147
both	1622	0.69%	4.54%	100.00%	1018	1.59332
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	1653	0.67%	4.22%	94.95%	955	1.62377
anti	88	0.04%	0.22%	5.05%	70	0.086444
both	1741	0.70%	4.45%	100.00%	1018	1.71022

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 in whole-genome, cDNA counts] (same; anti)
chr17:57917272@+	-72; 300	TMEM49	29; 0	36; 0
chr12:46754890@-	-51; 300	SLC38A2	17; 0	27; 0
chr1:35650053@-	-70; 300	SFPQ	14; 0	16; 0
chr17:4849191@-	-50; 123	PFN1	11; 0	26; 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
chr19:1037899@+	-138; 300	CNN2	9; 0	9; 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 in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr17:57917272@+	-72; 300	TMEM49	29; 0	36; 0
chr12:46754890@-	-51; 300	SLC38A2	17; 0	27; 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
chrX:70794505@+	-300; 300	OGT	9; 0	9; 0
chr22:38881684@-	-300; 300	DDX17	8; 0	9; 0
chr19:1037899@+	-138; 300	CNN2	9; 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%	0.65%	91.67%	160	1.32759
anti	21	0.01%	0.06%	8.33%	14	0.12069
both	252	0.11%	0.70%	100.00%	174	1.44828
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	255	0.10%	0.65%	92.39%	160	1.46552
anti	21	0.01%	0.05%	7.61%	14	0.12069
both	276	0.11%	0.70%	100.00%	174	1.58621

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 in whole-genome, 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 in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, 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	259	0.11%	0.72%	28.31%	175	0.445017
anti	656	0.28%	1.83%	71.69%	420	1.12715
both	915	0.39%	2.56%	100.00%	582	1.57216
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	270	0.11%	0.69%	26.68%	175	0.463918
anti	742	0.30%	1.89%	73.32%	420	1.27491
both	1012	0.41%	2.58%	100.00%	582	1.73883

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 in whole-genome, 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 in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, 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	1800	0.77%	5.03%	76.69%	1160	1.19601
anti	547	0.23%	1.53%	23.31%	373	0.363455
both	2347	1.00%	6.56%	100.00%	1505	1.55947
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	1944	0.78%	4.96%	76.84%	1160	1.29169
anti	586	0.24%	1.50%	23.16%	373	0.389369
both	2530	1.02%	6.46%	100.00%	1505	1.68106

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 in whole-genome, 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 in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, 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	743	0.32%	2.08%	26.18%	428	0.436289
anti	2095	0.90%	5.86%	73.82%	1309	1.23018
both	2838	1.21%	7.94%	100.00%	1703	1.66647
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	926	0.37%	2.36%	28.15%	428	0.543746
anti	2363	0.95%	6.03%	71.85%	1309	1.38755
both	3289	1.32%	8.40%	100.00%	1703	1.9313

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 in whole-genome, cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 68	0; 190
chr8:128231332@-	-1000; 139	AC020688.1	64; 1	100; 1
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
chr1:145382396@-	-1000; 171	RP11-458D21.1	1; 10	1; 11
chr8:33370702@-	-1000; 286	C8orf41	1; 9	1; 11

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 68	0; 190
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
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
chr10:103124791@-	-1000; 95	U2-ENSG00000222414	5; 0	16; 0

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	2560	1.10%	7.16%	60.33%	1495	1.02277
anti	1683	0.72%	4.71%	39.67%	1045	0.672393
both	4243	1.82%	11.87%	100.00%	2503	1.69517
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	3096	1.25%	7.91%	63.08%	1495	1.23692
anti	1812	0.73%	4.63%	36.92%	1045	0.723931
both	4908	1.98%	12.53%	100.00%	2503	1.96085

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 in whole-genome, 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
chr7:5566780@-	-300; 1000	ACTB	37; 0	103; 0
chr17:16344889@-	-300; 1000	C17orf76	0; 24	0; 48
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
chr1:169101767@-	-127; 1000	NME7	0; 12	0; 12

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	196; 0	449; 0
chr7:5566780@-	-300; 1000	ACTB	37; 0	103; 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; 48
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
chr17:79476997@-	-300; 1000	ACTG1	10; 0	17; 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	9026	3.86%	25.24%	96.21%	7064	1.22469
anti	356	0.15%	1.00%	3.79%	319	0.0483039
both	9382	4.02%	26.24%	100.00%	7370	1.273
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [BPs] in map	[single hits in whole-genome, cDNA counts] per unique [BP]
same	9486	3.82%	24.22%	96.22%	7064	1.28711
anti	373	0.15%	0.95%	3.78%	319	0.0506106
both	9859	3.97%	25.18%	100.00%	7370	1.33772

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 in whole-genome, cDNA counts] (same; anti)
chr17:57915352@+	-300; 100	TMEM49	15; 0	32; 0
chr21:44842114@-	-300; 100	SIK1	12; 0	17; 0
chr9:33259146@-	-300; 100	AL161445.1	11; 0	15; 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
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
chr2:182783120@+	-300; 100	SSFA2	7; 0	7; 0

Top 10 BPs with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr17:57915352@+	-300; 100	TMEM49	15; 0	32; 0
chr21:44842114@-	-300; 100	SIK1	12; 0	17; 0
chr9:33259146@-	-300; 100	AL161445.1	11; 0	15; 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.