Parameters
input_file: 20090715_LUh6_3_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: 125279
[x-link sites] used in any map: 19281 (15.39%)
[single hits in whole-genome, cDNA counts] total: 125279
[single hits in whole-genome, cDNA counts] used in any map: 20920 (15.82%)

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	5251	4.19%	27.23%	5504	4.16%	26.31%
intron-exon	-300; 300	4731	3.78%	24.54%	4934	3.73%	23.59%
5-ncRNA	-1000; 300	1863	1.49%	9.66%	2300	1.74%	10.99%
ncRNA-3	-300; 1000	1916	1.53%	9.94%	2298	1.74%	10.98%
ORF-3UTR	-300; 300	854	0.68%	4.43%	903	0.68%	4.32%
5UTR-ORF	-300; 300	137	0.11%	0.71%	147	0.11%	0.70%
inter-5UTR	-1000; 300	491	0.39%	2.55%	547	0.41%	2.61%
3UTR-inter	-300; 1000	1306	1.04%	6.77%	1383	1.05%	6.61%
inter-5	-1000; 300	1595	1.27%	8.27%	1859	1.41%	8.89%
3-inter	-300; 1000	2396	1.91%	12.43%	2664	2.02%	12.73%
BP best in intron	-300; 100	5039	4.02%	26.13%	5262	3.98%	25.15%

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	5041	4.02%	26.14%	96.00%	4234	1.14308
anti	210	0.17%	1.09%	4.00%	177	0.047619
both	5251	4.19%	27.23%	100.00%	4410	1.1907
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	5284	4.00%	25.26%	96.00%	4234	1.19819
anti	220	0.17%	1.05%	4.00%	177	0.0498866
both	5504	4.16%	26.31%	100.00%	4410	1.24807

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	27; 0	47; 0
chr5:78909906@+	-75; 300	PAPD4	8; 0	10; 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 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	27; 0	47; 0
chr5:78909906@+	-75; 300	PAPD4	8; 0	10; 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	4500	3.59%	23.34%	95.12%	3856	1.11001
anti	231	0.18%	1.20%	4.88%	205	0.0569808
both	4731	3.78%	24.54%	100.00%	4054	1.167
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	4698	3.55%	22.46%	95.22%	3856	1.15886
anti	236	0.18%	1.13%	4.78%	205	0.0582141
both	4934	3.73%	23.59%	100.00%	4054	1.21707

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	10; 0	20; 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
chr9:131456919@+	-292; 300	SET	5; 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)
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
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
chr5:1320845@-	-300; 262	CLPTM1L	3; 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	965	0.77%	5.00%	51.80%	519	0.813659
anti	898	0.72%	4.66%	48.20%	673	0.757167
both	1863	1.49%	9.66%	100.00%	1186	1.57083
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	1352	1.02%	6.46%	58.78%	519	1.13997
anti	948	0.72%	4.53%	41.22%	673	0.799325
both	2300	1.74%	10.99%	100.00%	1186	1.93929

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	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
chr17:41445449@-	-1000; 87	AC087650.5	22; 0	34; 0
chr20:47896855@+	-555; 45	C20orf199, SNORD12-ENSG00000222365	16; 0	83; 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
chr12:7052978@+	-748; 31	U7-ENSG00000238923	7; 0	22; 0
chrM:576@+	-288; 35	J01415.1	1; 5	1; 5

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	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
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
chr10:103124791@-	-1000; 95	U2-ENSG00000222414	5; 0	21; 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	1027	0.82%	5.33%	53.60%	513	0.880789
anti	889	0.71%	4.61%	46.40%	657	0.762436
both	1916	1.53%	9.94%	100.00%	1166	1.64322
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	1374	1.04%	6.57%	59.79%	513	1.17839
anti	924	0.70%	4.42%	40.21%	657	0.792453
both	2298	1.74%	10.98%	100.00%	1166	1.97084

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	121; 0	219; 0
chrUn_gl000220:118417@+	-300; 1000	28S	30; 0	47; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 25	0; 31
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
chr1:45187456@-	-59; 1000	U5-ENSG00000199377	11; 0	14; 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	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
chr11:10823012@-	-71; 189	EIF4G2, snoU97	10; 0	17; 0
chr1:11968328@+	-60; 1000	U5-ENSG00000199347	11; 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 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	813	0.65%	4.22%	95.20%	583	1.31129
anti	41	0.03%	0.21%	4.80%	37	0.066129
both	854	0.68%	4.43%	100.00%	620	1.37742
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	858	0.65%	4.10%	95.02%	583	1.38387
anti	45	0.03%	0.22%	4.98%	37	0.0725806
both	903	0.68%	4.32%	100.00%	620	1.45645

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	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 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	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	120	0.10%	0.62%	87.59%	92	1.14286
anti	17	0.01%	0.09%	12.41%	13	0.161905
both	137	0.11%	0.71%	100.00%	105	1.30476
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	130	0.10%	0.62%	88.44%	92	1.2381
anti	17	0.01%	0.08%	11.56%	13	0.161905
both	147	0.11%	0.70%	100.00%	105	1.4

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)
chr6:31508971@-	-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 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)
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	129	0.10%	0.67%	26.27%	107	0.351499
anti	362	0.29%	1.88%	73.73%	262	0.986376
both	491	0.39%	2.55%	100.00%	367	1.33787
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	137	0.10%	0.65%	25.05%	107	0.373297
anti	410	0.31%	1.96%	74.95%	262	1.11717
both	547	0.41%	2.61%	100.00%	367	1.49046

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)
chr20:47894962@-	-1000; 248	ZNFX1	0; 11	0; 43
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 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; 11	0; 43
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	1011	0.81%	5.24%	77.41%	748	1.05203
anti	295	0.24%	1.53%	22.59%	225	0.306972
both	1306	1.04%	6.77%	100.00%	961	1.359
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	1073	0.81%	5.13%	77.58%	748	1.11655
anti	310	0.23%	1.48%	22.42%	225	0.322581
both	1383	1.05%	6.61%	100.00%	961	1.43913

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	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; 6
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 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	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
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
chr19:39220830@-	-300; 1000	CAPN12	0; 6	0; 6

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	446	0.36%	2.31%	27.96%	265	0.411819
anti	1149	0.92%	5.96%	72.04%	823	1.06094
both	1595	1.27%	8.27%	100.00%	1083	1.47276
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	563	0.43%	2.69%	30.29%	265	0.519852
anti	1296	0.98%	6.20%	69.71%	823	1.19668
both	1859	1.41%	8.89%	100.00%	1083	1.71653

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; 53	0; 117
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	61; 1
chr17:41445449@-	-1000; 87	AC087650.5	22; 0	34; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 11	0; 43
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
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 6	0; 7
chr12:120729705@-	-597; 70	U4-ENSG00000202538	6; 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)
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; 11	0; 43
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
chr15:65588388@+	-1000; 58	U5-ENSG00000199568	5; 0	12; 0
chr12:120729705@-	-597; 70	U4-ENSG00000202538	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 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	1477	1.18%	7.66%	61.64%	951	0.93481
anti	919	0.73%	4.77%	38.36%	648	0.581646
both	2396	1.91%	12.43%	100.00%	1580	1.51646
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	1701	1.29%	8.13%	63.85%	951	1.07658
anti	963	0.73%	4.60%	36.15%	648	0.609494
both	2664	2.02%	12.73%	100.00%	1580	1.68608

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	121; 0	219; 0
chrUn_gl000220:118417@+	-300; 1000	28S	30; 0	47; 0
chr7:5566780@-	-300; 1000	ACTB	27; 0	61; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 25	0; 31
chr17:16344889@-	-300; 1000	C17orf76	0; 23	0; 29
chr17:57917950@+	-300; 338	TMEM49	22; 0	33; 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
chr9:35657749@-	-132; 1000	RNase_MRP-ENSG00000199916	9; 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)
chr11:65271080@+	-300; 1000	MALAT1	121; 0	219; 0
chr7:5566780@-	-300; 1000	ACTB	27; 0	61; 0
chrUn_gl000220:118417@+	-300; 1000	28S	30; 0	47; 0
chr17:57917950@+	-300; 338	TMEM49	22; 0	33; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 25	0; 31
chr17:16344889@-	-300; 1000	C17orf76	0; 23	0; 29
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
chr17:80209542@+	-213; 1000	AC132872.1	0; 11	0; 11

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	4835	3.86%	25.08%	95.95%	4038	1.14546
anti	204	0.16%	1.06%	4.05%	187	0.0483298
both	5039	4.02%	26.13%	100.00%	4221	1.19379
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	5051	3.82%	24.14%	95.99%	4038	1.19664
anti	211	0.16%	1.01%	4.01%	187	0.0499882
both	5262	3.98%	25.15%	100.00%	4221	1.24662

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)
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 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	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.