Parameters
input_file: 20090715_LUh6_3_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: 129900
[x-link sites] used in any map: 19832 (15.27%)
[single hits (=G+T), cDNA counts] total: 129900
[single hits (=G+T), cDNA counts] used in any map: 21511 (15.68%)

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	5381	4.14%	27.13%	5642	4.11%	26.23%
intron-exon	-300; 300	4839	3.73%	24.40%	5046	3.68%	23.46%
5-ncRNA	-1000; 300	1951	1.50%	9.84%	2401	1.75%	11.16%
ncRNA-3	-300; 1000	1985	1.53%	10.01%	2377	1.73%	11.05%
ORF-3UTR	-300; 300	876	0.67%	4.42%	927	0.68%	4.31%
5UTR-ORF	-300; 300	139	0.11%	0.70%	149	0.11%	0.69%
inter-5UTR	-1000; 300	496	0.38%	2.50%	554	0.40%	2.58%
3UTR-inter	-300; 1000	1337	1.03%	6.74%	1417	1.03%	6.59%
inter-5	-1000; 300	1665	1.28%	8.40%	1943	1.42%	9.03%
3-inter	-300; 1000	2467	1.90%	12.44%	2745	2.00%	12.76%
BP best in intron	-300; 100	5188	3.99%	26.16%	5413	3.95%	25.16%

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	5151	3.97%	25.97%	95.73%	4317	1.14238
anti	230	0.18%	1.16%	4.27%	195	0.0510091
both	5381	4.14%	27.13%	100.00%	4509	1.19339
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	5401	3.94%	25.11%	95.73%	4317	1.19783
anti	241	0.18%	1.12%	4.27%	195	0.0534487
both	5642	4.11%	26.23%	100.00%	4509	1.25128

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	27; 0	47; 0
chr5:78909906@+	-75; 300	PAPD4	9; 0	11; 0
chr5:58468626@-	-39; 300	PDE4D	7; 0	7; 0
chr17:46919896@+	-167; 300	CALCOCO2	7; 0	8; 0
chr16:67315087@+	-47; 191	PLEKHG4	7; 0	7; 0
chr12:20523178@+	-300; 300	PDE3A	7; 0	9; 0
chrX:54591087@+	-64; 164	GNL3L	6; 0	6; 0
chr13:27828604@+	-124; 238	RPL21	6; 0	7; 0
chr12:123739580@+	-300; 300	C12orf65	0; 6	0; 6
chr1:46072352@+	-100; 300	NASP	6; 0	6; 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	27; 0	47; 0
chr5:78909906@+	-75; 300	PAPD4	9; 0	11; 0
chr12:20523178@+	-300; 300	PDE3A	7; 0	9; 0
chr17:46919896@+	-167; 300	CALCOCO2	7; 0	8; 0
chr5:58468626@-	-39; 300	PDE4D	7; 0	7; 0
chr16:67315087@+	-47; 191	PLEKHG4	7; 0	7; 0
chr13:27828604@+	-124; 238	RPL21	6; 0	7; 0
chrX:54591087@+	-64; 164	GNL3L	6; 0	6; 0
chr9:21818201@+	-84; 300	MTAP	5; 0	6; 0
chr6:31804294@+	-112; 162	C6orf48	4; 0	6; 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	4574	3.52%	23.06%	94.52%	3900	1.10831
anti	265	0.20%	1.34%	5.48%	235	0.0642113
both	4839	3.73%	24.40%	100.00%	4127	1.17252
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	4773	3.48%	22.19%	94.59%	3900	1.15653
anti	273	0.20%	1.27%	5.41%	235	0.0661497
both	5046	3.68%	23.46%	100.00%	4127	1.22268

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	10; 0	20; 0
chr9:131456919@+	-292; 300	SET	7; 0	7; 0
chr5:179041959@-	-293; 300	HNRNPH1	7; 0	8; 0
chr2:182783049@+	-300; 74	SSFA2	7; 0	7; 0
chr12:54678332@+	-116; 300	HNRNPA1	7; 0	12; 0
chr1:21101497@-	-222; 300	HP1BP3	7; 0	10; 0
chr6:13974440@+	-300; 77	RNF182	6; 0	7; 0
chr17:57915655@+	-300; 51	TMEM49	6; 0	6; 0
chr13:111556688@-	-300; 156	ANKRD10	6; 0	6; 0
chr13:111933550@+	-263; 144	ARHGEF7	6; 0	6; 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	10; 0	20; 0
chr12:54678332@+	-116; 300	HNRNPA1	7; 0	12; 0
chr1:21101497@-	-222; 300	HP1BP3	7; 0	10; 0
chr5:179041959@-	-293; 300	HNRNPH1	7; 0	8; 0
chr9:131456919@+	-292; 300	SET	7; 0	7; 0
chr6:13974440@+	-300; 77	RNF182	6; 0	7; 0
chr3:47702944@-	-300; 81	SMARCC1	5; 0	7; 0
chr2:182783049@+	-300; 74	SSFA2	7; 0	7; 0
chr17:62496890@-	-300; 112	DDX5	5; 0	7; 0
chr7:23391204@-	-300; 141	IGF2BP3	5; 0	6; 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	1032	0.79%	5.20%	52.90%	538	0.848684
anti	919	0.71%	4.63%	47.10%	687	0.755757
both	1951	1.50%	9.84%	100.00%	1216	1.60444
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	1432	1.04%	6.66%	59.64%	538	1.17763
anti	969	0.71%	4.50%	40.36%	687	0.796875
both	2401	1.75%	11.16%	100.00%	1216	1.97451

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	86; 0	159; 0
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	61; 1
chr17:57918626@+	-338; 36	hsa-mir-21	33; 0	81; 0
chrUn_gl000220:109077@+	-758; 300	18S	25; 0	34; 0
chr17:41445449@-	-1000; 87	AC087650.5	22; 0	34; 0
chr20:47896855@+	-555; 45	C20orf199, SNORD12-ENSG00000222365	16; 0	83; 0
chrUn_gl000220:113347@+	-585; 300	28S	14; 0	15; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	11; 0	25; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	11; 0	18; 0
chr20:47895476@+	-101; 44	C20orf199, SNORD12-ENSG00000209042	10; 0	42; 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	86; 0	159; 0
chr20:47896855@+	-555; 45	C20orf199, SNORD12-ENSG00000222365	16; 0	83; 0
chr17:57918626@+	-338; 36	hsa-mir-21	33; 0	81; 0
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	61; 1
chr20:47895476@+	-101; 44	C20orf199, SNORD12-ENSG00000209042	10; 0	42; 0
chrUn_gl000220:109077@+	-758; 300	18S	25; 0	34; 0
chr17:41445449@-	-1000; 87	AC087650.5	22; 0	34; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	11; 0	25; 0
chr1:11969983@-	-628; 60	U5-ENSG00000201801	6; 0	23; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	7; 0	22; 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	1066	0.82%	5.38%	53.70%	531	0.883914
anti	919	0.71%	4.63%	46.30%	681	0.762023
both	1985	1.53%	10.01%	100.00%	1206	1.64594
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	1422	1.04%	6.61%	59.82%	531	1.1791
anti	955	0.70%	4.44%	40.18%	681	0.791874
both	2377	1.73%	11.05%	100.00%	1206	1.97098

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	121; 0	219; 0
chrUn_gl000220:118417@+	-300; 1000	28S	30; 0	47; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 25	0; 31
chrUn_gl000220:110946@+	-300; 539	18S	16; 0	22; 0
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	16; 0	26; 0
chr1:11969863@-	-60; 1000	U5-ENSG00000201801	16; 0	67; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	15; 0	27; 0
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	11; 1	87; 1
chr17:80209542@+	-213; 1000	AC132872.1	0; 11	0; 11
chr1:45196725@-	-58; 1000	U5-ENSG00000200169	11; 0	12; 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	121; 0	219; 0
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	11; 1	87; 1
chr1:11969863@-	-60; 1000	U5-ENSG00000201801	16; 0	67; 0
chrUn_gl000220:118417@+	-300; 1000	28S	30; 0	47; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 25	0; 31
chr11:62609089@-	-96; 978	U2-ENSG00000222328	15; 0	27; 0
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	16; 0	26; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	8; 0	25; 0
chrUn_gl000220:110946@+	-300; 539	18S	16; 0	22; 0
chr11:10823012@-	-71; 189	EIF4G2, snoU97	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 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	835	0.64%	4.21%	95.32%	598	1.31496
anti	41	0.03%	0.21%	4.68%	37	0.0645669
both	876	0.67%	4.42%	100.00%	635	1.37953
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	882	0.64%	4.10%	95.15%	598	1.38898
anti	45	0.03%	0.21%	4.85%	37	0.0708661
both	927	0.68%	4.31%	100.00%	635	1.45984

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	20; 0	26; 0
chr17:4849191@-	-50; 123	PFN1	8; 0	13; 0
chr19:1037899@+	-138; 300	CNN2	7; 0	7; 0
chr9:33113448@-	-68; 300	B4GALT1	6; 0	6; 0
chr3:55503877@-	-300; 116	WNT5A	6; 0	6; 0
chr2:232319617@-	-180; 300	NCL	6; 0	6; 0
chr2:189876774@+	-211; 300	COL3A1	6; 0	7; 0
chr19:19105798@-	-145; 252	SFRS14	6; 0	6; 0
chr16:69744875@-	-154; 300	NQO1	6; 0	6; 0
chr12:46754890@-	-51; 300	SLC38A2	6; 0	6; 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	20; 0	26; 0
chr17:4849191@-	-50; 123	PFN1	8; 0	13; 0
chr2:189876774@+	-211; 300	COL3A1	6; 0	7; 0
chr19:1037899@+	-138; 300	CNN2	7; 0	7; 0
chr1:245017433@-	-93; 300	HNRNPU	6; 0	7; 0
chr1:32374252@-	-154; 300	PTP4A2	6; 0	7; 0
chr9:33113448@-	-68; 300	B4GALT1	6; 0	6; 0
chr5:90666613@-	-300; 300	ARRDC3	5; 0	6; 0
chr3:55503877@-	-300; 116	WNT5A	6; 0	6; 0
chr2:232319617@-	-180; 300	NCL	6; 0	6; 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	121	0.09%	0.61%	87.05%	93	1.13084
anti	18	0.01%	0.09%	12.95%	14	0.168224
both	139	0.11%	0.70%	100.00%	107	1.29907
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	131	0.10%	0.61%	87.92%	93	1.2243
anti	18	0.01%	0.08%	12.08%	14	0.168224
both	149	0.11%	0.69%	100.00%	107	1.39252

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)
chr6:31508971@-	-66; 265	BAT1	4; 0	7; 0
chr2:23746960@-	-127; 70	AC011239.1-ENSG00000224361	0; 4	0; 4
chr17:43226557@+	-300; 300	HEXIM1	4; 0	5; 0
chr13:45010763@-	-109; 62	TSC22D1	4; 0	5; 0
chr7:1608974@-	-300; 108	PSMG3	3; 0	3; 0
chr10:114710515@+	-254; 94	TCF7L2	3; 0	3; 0
chr1:46597623@-	-300; 53	PIK3R3	3; 0	3; 0
chr9:21334857@-	-286; 300	KLHL9	2; 0	2; 0
chr7:105925396@-	-121; 62	PBEF1	2; 0	2; 0
chr6:31725905@+	-300; 82	MSH5	2; 0	2; 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)
chr6:31508971@-	-66; 265	BAT1	4; 0	7; 0
chr17:43226557@+	-300; 300	HEXIM1	4; 0	5; 0
chr13:45010763@-	-109; 62	TSC22D1	4; 0	5; 0
chr2:23746960@-	-127; 70	AC011239.1-ENSG00000224361	0; 4	0; 4
chr7:1608974@-	-300; 108	PSMG3	3; 0	3; 0
chr19:49468764@+	-100; 51	FTL	2; 0	3; 0
chr10:114710515@+	-254; 94	TCF7L2	3; 0	3; 0
chr1:46597623@-	-300; 53	PIK3R3	3; 0	3; 0
chr9:21334857@-	-286; 300	KLHL9	2; 0	2; 0
chr8:124268185@-	-113; 300	ZHX1	1; 0	2; 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	131	0.10%	0.66%	26.41%	109	0.3531
anti	365	0.28%	1.84%	73.59%	264	0.983827
both	496	0.38%	2.50%	100.00%	371	1.33693
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	139	0.10%	0.65%	25.09%	109	0.374663
anti	415	0.30%	1.93%	74.91%	264	1.1186
both	554	0.40%	2.58%	100.00%	371	1.49326

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)
chr20:47894962@-	-1000; 248	ZNFX1	0; 12	0; 44
chr1:173837219@+	-1000; 87	ZBTB37	0; 8	0; 9
chr8:33370702@-	-1000; 286	C8orf41	0; 7	0; 7
chr6:166401114@+	-1000; 249	AL132661.1	0; 7	0; 8
chr11:62623517@+	-1000; 112	SLC3A2	0; 6	0; 6
chr7:1610640@-	-1000; 266	PSMG3	0; 5	0; 6
chr3:158450484@-	-1000; 140	RARRES1	0; 5	0; 6
chr20:17949555@+	-1000; 114	C20orf72	0; 5	0; 5
chr2:242256475@-	-1000; 95	HDLBP	0; 5	0; 5
chr2:27579867@-	-1000; 131	GTF3C2	0; 5	0; 7

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; 12	0; 44
chr1:173837219@+	-1000; 87	ZBTB37	0; 8	0; 9
chr6:166401114@+	-1000; 249	AL132661.1	0; 7	0; 8
chr8:33370702@-	-1000; 286	C8orf41	0; 7	0; 7
chr2:27579867@-	-1000; 131	GTF3C2	0; 5	0; 7
chr7:1610640@-	-1000; 266	PSMG3	0; 5	0; 6
chr3:158450484@-	-1000; 140	RARRES1	0; 5	0; 6
chr11:62623517@+	-1000; 112	SLC3A2	0; 6	0; 6
chr11:3011092@+	-1000; 300	AC131971.1	0; 5	0; 6
chr8:56987068@-	-1000; 63	RPS20	2; 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 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	1037	0.80%	5.23%	77.56%	764	1.05708
anti	300	0.23%	1.51%	22.44%	229	0.30581
both	1337	1.03%	6.74%	100.00%	981	1.3629
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	1099	0.80%	5.11%	77.56%	764	1.12029
anti	318	0.23%	1.48%	22.44%	229	0.324159
both	1417	1.03%	6.59%	100.00%	981	1.44444

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	22; 0	33; 0
chr19:34891236@+	-148; 1000	GPI	11; 0	12; 0
chr17:4848518@+	-104; 1000	RNF167	0; 9	0; 14
chr5:10435491@+	-300; 1000	MARCH6	7; 0	8; 0
chr19:54972979@-	-144; 1000	LENG9	0; 7	0; 8
chr17:79476997@-	-300; 1000	ACTG1	7; 0	8; 0
chr22:36677325@-	-300; 1000	MYH9	6; 0	6; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 6	0; 7
chr16:87863620@-	-300; 1000	SLC7A5	6; 0	6; 0
chr11:47489944@-	-248; 1000	CELF1	6; 0	6; 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	22; 0	33; 0
chr17:4848518@+	-104; 1000	RNF167	0; 9	0; 14
chr19:34891236@+	-148; 1000	GPI	11; 0	12; 0
chr5:10435491@+	-300; 1000	MARCH6	7; 0	8; 0
chr19:54972979@-	-144; 1000	LENG9	0; 7	0; 8
chr17:79476997@-	-300; 1000	ACTG1	7; 0	8; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 6	0; 7
chr12:10851674@-	-288; 1000	CSDA	5; 0	7; 0
chr22:36677325@-	-300; 1000	MYH9	6; 0	6; 0
chr2:20649206@+	-300; 798	RHOB	5; 0	6; 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	498	0.38%	2.51%	29.91%	279	0.450271
anti	1167	0.90%	5.88%	70.09%	835	1.05515
both	1665	1.28%	8.40%	100.00%	1106	1.50542
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	627	0.46%	2.91%	32.27%	279	0.566908
anti	1316	0.96%	6.12%	67.73%	835	1.18987
both	1943	1.42%	9.03%	100.00%	1106	1.75678

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; 53	0; 117
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	61; 1
chrUn_gl000220:109077@+	-758; 300	18S	25; 0	34; 0
chr17:41445449@-	-1000; 87	AC087650.5	22; 0	34; 0
chrUn_gl000220:113347@+	-585; 300	28S	14; 0	15; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 12	0; 44
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	11; 0	18; 0
chr1:173837219@+	-1000; 87	ZBTB37	0; 8	0; 9
chr6:166401114@+	-1000; 249	AL132661.1	0; 6	0; 7
chr3:120025572@+	-1000; 300	RP11-174O3.1	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)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 53	0; 117
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	61; 1
chr20:47894962@-	-1000; 248	ZNFX1	0; 12	0; 44
chrUn_gl000220:109077@+	-758; 300	18S	25; 0	34; 0
chr17:41445449@-	-1000; 87	AC087650.5	22; 0	34; 0
chr1:11969983@-	-628; 60	U5-ENSG00000201801	6; 0	23; 0
chr10:103124791@-	-1000; 95	U2-ENSG00000222414	5; 0	21; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	11; 0	18; 0
chr1:11968208@+	-1000; 60	U5-ENSG00000199347	4; 0	18; 0
chrUn_gl000220:113347@+	-585; 300	28S	14; 0	15; 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	1526	1.17%	7.69%	61.86%	974	0.943723
anti	941	0.72%	4.74%	38.14%	662	0.581942
both	2467	1.90%	12.44%	100.00%	1617	1.52566
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	1757	1.28%	8.17%	64.01%	974	1.08658
anti	988	0.72%	4.59%	35.99%	662	0.611008
both	2745	2.00%	12.76%	100.00%	1617	1.69759

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	121; 0	219; 0
chrUn_gl000220:118417@+	-300; 1000	28S	30; 0	47; 0
chr7:5566780@-	-300; 1000	ACTB	27; 0	62; 0
chr17:16344889@-	-300; 1000	C17orf76	0; 25	0; 31
chr1:28835512@-	-182; 1000	AL513497.3	0; 25	0; 31
chr17:57917950@+	-300; 338	TMEM49	22; 0	33; 0
chrUn_gl000220:110946@+	-300; 539	18S	16; 0	22; 0
chr19:34891236@+	-148; 1000	GPI	11; 0	12; 0
chr17:80209542@+	-213; 1000	AC132872.1	0; 11	0; 11
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	10; 0	13; 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	121; 0	219; 0
chr7:5566780@-	-300; 1000	ACTB	27; 0	62; 0
chrUn_gl000220:118417@+	-300; 1000	28S	30; 0	47; 0
chr17:57917950@+	-300; 338	TMEM49	22; 0	33; 0
chr17:16344889@-	-300; 1000	C17orf76	0; 25	0; 31
chr1:28835512@-	-182; 1000	AL513497.3	0; 25	0; 31
chrUn_gl000220:110946@+	-300; 539	18S	16; 0	22; 0
chr17:4848518@+	-104; 1000	RNF167	0; 9	0; 14
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	10; 0	13; 0
chr19:34891236@+	-148; 1000	GPI	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 "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	4931	3.80%	24.86%	95.05%	4116	1.13435
anti	257	0.20%	1.30%	4.95%	237	0.0591212
both	5188	3.99%	26.16%	100.00%	4347	1.19347
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	5148	3.75%	23.93%	95.10%	4116	1.18427
anti	265	0.19%	1.23%	4.90%	237	0.0609616
both	5413	3.95%	25.16%	100.00%	4347	1.24523

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)
chr5:170817954@+	-235; 100	NPM1	7; 0	9; 0
chr21:44842114@-	-300; 100	SIK1	7; 0	8; 0
chr17:57915352@+	-300; 100	TMEM49	6; 0	11; 0
chr16:53337220@+	-300; 100	CHD9	6; 0	6; 0
chr11:47829005@-	-300; 100	NUP160	6; 0	10; 0
chr11:67814704@+	-300; 100	TCIRG1	6; 0	6; 0
chr1:28835317@+	-300; 22	SNHG3	6; 0	6; 0
chr9:125758092@+	-300; 100	RABGAP1	5; 0	5; 0
chr7:23391241@-	-300; 37	IGF2BP3	5; 0	6; 0
chr7:117825342@+	-300; 100	LSM8	5; 0	5; 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	6; 0	11; 0
chr11:47829005@-	-300; 100	NUP160	6; 0	10; 0
chr5:170817954@+	-235; 100	NPM1	7; 0	9; 0
chr21:44842114@-	-300; 100	SIK1	7; 0	8; 0
chr16:70571951@+	-300; 100	SNORD111-ENSG00000221066	5; 0	8; 0
chr6:36568740@+	-300; 100	SFRS3	5; 0	7; 0
chr17:62496969@-	-300; 79	DDX5	5; 0	7; 0
chr12:20768952@+	-300; 100	PDE3A	5; 0	7; 0
chr7:23391241@-	-300; 37	IGF2BP3	5; 0	6; 0
chr5:179048854@-	-300; 100	HNRNPH1	5; 0	6; 0

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