Parameters
input_file: 20090724_LUd4_7_hg19_ensembl59_G_iCLIP_TIAL1_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: 263346
[x-link sites] used in any map: 79346 (30.13%)
[single hits in whole-genome, cDNA counts] total: 263346
[single hits in whole-genome, cDNA counts] used in any map: 88379 (30.74%)

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	25113	9.54%	31.65%	26385	9.18%	29.85%
intron-exon	-300; 300	18972	7.20%	23.91%	20072	6.98%	22.71%
5-ncRNA	-1000; 300	3895	1.48%	4.91%	5216	1.81%	5.90%
ncRNA-3	-300; 1000	4452	1.69%	5.61%	6439	2.24%	7.29%
ORF-3UTR	-300; 300	10715	4.07%	13.50%	12221	4.25%	13.83%
5UTR-ORF	-300; 300	460	0.17%	0.58%	481	0.17%	0.54%
inter-5UTR	-1000; 300	913	0.35%	1.15%	976	0.34%	1.10%
3UTR-inter	-300; 1000	11087	4.21%	13.97%	12562	4.37%	14.21%
inter-5	-1000; 300	3263	1.24%	4.11%	3712	1.29%	4.20%
3-inter	-300; 1000	14898	5.66%	18.78%	18280	6.36%	20.68%
BP best in intron	-300; 100	10584	4.02%	13.34%	11015	3.83%	12.46%

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	24520	9.31%	30.90%	97.64%	17296	1.38829
anti	593	0.23%	0.75%	2.36%	422	0.0335749
both	25113	9.54%	31.65%	100.00%	17662	1.42187
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	25686	8.93%	29.06%	97.35%	17296	1.45431
anti	699	0.24%	0.79%	2.65%	422	0.0395765
both	26385	9.18%	29.85%	100.00%	17662	1.49389

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)
chr1:45976739@+	-281; 300	MMACHC	0; 61	0; 132
chr7:128411528@+	-300; 107	CALU	39; 0	84; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 29	0; 37
chr3:41281934@+	-300; 300	CTNNB1	29; 0	45; 0
chr2:191800015@+	-300; 300	GLS	26; 0	29; 0
chr6:18225699@-	-124; 192	DEK	24; 0	26; 0
chr12:50158717@+	-300; 300	TMBIM6	21; 0	33; 0
chr5:147650475@+	-75; 300	SPINK5L3	20; 0	24; 0
chr5:179048241@-	-78; 103	HNRNPH1	19; 0	30; 0
chr5:10401598@+	-300; 185	MARCH6	19; 0	27; 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)
chr1:45976739@+	-281; 300	MMACHC	0; 61	0; 132
chr7:128411528@+	-300; 107	CALU	39; 0	84; 0
chr3:41281934@+	-300; 300	CTNNB1	29; 0	45; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 29	0; 37
chr12:50158717@+	-300; 300	TMBIM6	21; 0	33; 0
chr5:179048241@-	-78; 103	HNRNPH1	19; 0	30; 0
chr2:191800015@+	-300; 300	GLS	26; 0	29; 0
chr1:165624857@+	-127; 300	MGST3	15; 0	29; 0
chr5:10401598@+	-300; 185	MARCH6	19; 0	27; 0
chr6:18225699@-	-124; 192	DEK	24; 0	26; 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	18365	6.97%	23.15%	96.80%	13354	1.33051
anti	607	0.23%	0.77%	3.20%	487	0.0439759
both	18972	7.20%	23.91%	100.00%	13803	1.37448
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	19433	6.76%	21.99%	96.82%	13354	1.40788
anti	639	0.22%	0.72%	3.18%	487	0.0462943
both	20072	6.98%	22.71%	100.00%	13803	1.45418

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)
chr15:45009804@+	-300; 277	B2M	69; 0	125; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	45; 0	58; 0
chr5:179041959@-	-293; 300	HNRNPH1	41; 0	96; 0
chr9:131456919@+	-292; 300	SET	37; 0	93; 0
chr8:128753204@+	-241; 235	MYC	26; 0	49; 0
chr10:112657785@+	-300; 300	PDCD4	24; 0	37; 0
chr2:47387942@-	-300; 300	CALM2	23; 0	33; 0
chr1:165697357@-	-300; 292	TMCO1	23; 0	34; 0
chr2:211542610@+	-300; 300	CPS1	21; 0	28; 0
chr2:189876353@+	-300; 210	COL3A1	21; 0	24; 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)
chr15:45009804@+	-300; 277	B2M	69; 0	125; 0
chr5:179041959@-	-293; 300	HNRNPH1	41; 0	96; 0
chr9:131456919@+	-292; 300	SET	37; 0	93; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	45; 0	58; 0
chr8:128753204@+	-241; 235	MYC	26; 0	49; 0
chr10:112657785@+	-300; 300	PDCD4	24; 0	37; 0
chr1:165697357@-	-300; 292	TMCO1	23; 0	34; 0
chr2:47387942@-	-300; 300	CALM2	23; 0	33; 0
chr2:211542610@+	-300; 300	CPS1	21; 0	28; 0
chr17:57917128@+	-300; 72	TMEM49	20; 0	26; 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	1869	0.71%	2.36%	47.98%	792	1.03776
anti	2026	0.77%	2.55%	52.02%	1036	1.12493
both	3895	1.48%	4.91%	100.00%	1801	2.16269
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	3033	1.06%	3.43%	58.15%	792	1.68406
anti	2183	0.76%	2.47%	41.85%	1036	1.2121
both	5216	1.81%	5.90%	100.00%	1801	2.89617

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	480; 0	1321; 0
chr8:128231332@-	-1000; 139	AC020688.1	104; 1	127; 1
chr3:49571651@-	-1000; 300	AC104452.1	0; 46	0; 54
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 42	0; 44
chr17:57918626@+	-338; 36	hsa-mir-21	40; 0	98; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 35	0; 42
chr1:205685227@+	-1000; 300	AC119673.2	0; 29	0; 34
chr2:70315685@-	-1000; 62	AC136007.2	0; 28	0; 37
chr6:72113323@-	-1000; 35	C6orf155, hsa-mir-30a	27; 0	34; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 24	0; 28

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	480; 0	1321; 0
chr8:128231332@-	-1000; 139	AC020688.1	104; 1	127; 1
chr17:57918626@+	-338; 36	hsa-mir-21	40; 0	98; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	15; 0	62; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 46	0; 54
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 42	0; 44
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 35	0; 42
chr2:70315685@-	-1000; 62	AC136007.2	0; 28	0; 37
chr6:72113323@-	-1000; 35	C6orf155, hsa-mir-30a	27; 0	34; 0
chr1:205685227@+	-1000; 300	AC119673.2	0; 29	0; 34

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	2760	1.05%	3.48%	61.99%	1164	1.35228
anti	1692	0.64%	2.13%	38.01%	906	0.829005
both	4452	1.69%	5.61%	100.00%	2041	2.18128
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	4633	1.61%	5.24%	71.95%	1164	2.26997
anti	1806	0.63%	2.04%	28.05%	906	0.88486
both	6439	2.24%	7.29%	100.00%	2041	3.15483

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	625; 0	1780; 0
chrUn_gl000220:118417@+	-300; 1000	28S	48; 0	118; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	47; 0	158; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 37	0; 42
chr10:112658486@-	-300; 1000	NCRNA00081	0; 35	0; 48
chr1:28835512@-	-182; 1000	AL513497.3	0; 28	0; 36
chr8:128220109@-	-300; 1000	AC020688.1	25; 0	28; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 25	0; 34
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 25	0; 25
chr17:57918698@+	-36; 1000	hsa-mir-21	21; 0	23; 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	625; 0	1780; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	47; 0	158; 0
chrUn_gl000220:118417@+	-300; 1000	28S	48; 0	118; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	18; 0	88; 0
chr1:45187456@-	-59; 1000	U5-ENSG00000199377	16; 0	51; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 35	0; 48
chr15:65597130@+	-58; 1000	U5-ENSG00000200156	18; 0	44; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 37	0; 42
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	16; 0	41; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	12; 0	38; 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	10550	4.01%	13.30%	98.46%	3155	3.25216
anti	165	0.06%	0.21%	1.54%	116	0.0508631
both	10715	4.07%	13.50%	100.00%	3244	3.30302
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	12048	4.19%	13.63%	98.58%	3155	3.71393
anti	173	0.06%	0.20%	1.42%	116	0.0533292
both	12221	4.25%	13.83%	100.00%	3244	3.76726

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)
chr19:13054727@+	-101; 288	CALR	90; 0	181; 0
chr3:149087560@-	-53; 300	TM4SF1	62; 0	106; 0
chr14:62213803@+	-76; 300	HIF1A	53; 0	82; 0
chr5:179156650@+	-145; 300	CANX	50; 0	72; 0
chr21:27253823@-	-129; 300	APP	42; 0	57; 0
chr7:148700882@-	-209; 300	PDIA4	40; 0	77; 0
chr1:35650053@-	-70; 300	SFPQ	39; 0	68; 0
chr7:6501391@-	-300; 300	KDELR2	38; 0	43; 0
chr1:156109094@+	-112; 233	LMNA	38; 0	51; 0
chr17:56082650@-	-155; 300	SFRS1	37; 0	47; 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)
chr19:13054727@+	-101; 288	CALR	90; 0	181; 0
chr3:149087560@-	-53; 300	TM4SF1	62; 0	106; 0
chr17:4849191@-	-50; 123	PFN1	35; 0	89; 0
chr14:62213803@+	-76; 300	HIF1A	53; 0	82; 0
chr7:148700882@-	-209; 300	PDIA4	40; 0	77; 0
chr5:179156650@+	-145; 300	CANX	50; 0	72; 0
chr1:35650053@-	-70; 300	SFPQ	39; 0	68; 0
chr21:27253823@-	-129; 300	APP	42; 0	57; 0
chr1:156109094@+	-112; 233	LMNA	38; 0	51; 0
chr17:56082650@-	-155; 300	SFRS1	37; 0	47; 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	391	0.15%	0.49%	85.00%	267	1.33447
anti	69	0.03%	0.09%	15.00%	28	0.235495
both	460	0.17%	0.58%	100.00%	293	1.56997
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	404	0.14%	0.46%	83.99%	267	1.37884
anti	77	0.03%	0.09%	16.01%	28	0.262799
both	481	0.17%	0.54%	100.00%	293	1.64164

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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 16	0; 21
chr7:135612307@+	-300; 127	AC015987.2	0; 13	0; 14
chr8:101733810@-	-252; 96	PABPC1	10; 0	10; 0
chr6:24718895@-	-300; 64	C6orf62	9; 0	11; 0
chr17:43226557@+	-300; 300	HEXIM1	7; 0	8; 0
chr5:138643104@+	-89; 300	MATR3	6; 0	7; 0
chr17:4851688@-	-300; 66	PFN1	6; 0	6; 0
chr14:24408733@+	-300; 99	C14orf167	0; 6	0; 6
chr11:3012265@+	-300; 90	AC131971.1	0; 6	0; 6
chr2:136873508@-	-152; 300	CXCR4	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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 16	0; 21
chr7:135612307@+	-300; 127	AC015987.2	0; 13	0; 14
chr6:24718895@-	-300; 64	C6orf62	9; 0	11; 0
chr8:101733810@-	-252; 96	PABPC1	10; 0	10; 0
chr17:43226557@+	-300; 300	HEXIM1	7; 0	8; 0
chr5:138643104@+	-89; 300	MATR3	6; 0	7; 0
chr17:4851688@-	-300; 66	PFN1	6; 0	6; 0
chr14:24408733@+	-300; 99	C14orf167	0; 6	0; 6
chr11:3012265@+	-300; 90	AC131971.1	0; 6	0; 6
chr22:38884251@-	-142; 187	DDX17	4; 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	262	0.10%	0.33%	28.70%	194	0.435216
anti	651	0.25%	0.82%	71.30%	422	1.0814
both	913	0.35%	1.15%	100.00%	602	1.51661
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	269	0.09%	0.30%	27.56%	194	0.446844
anti	707	0.25%	0.80%	72.44%	422	1.17442
both	976	0.34%	1.10%	100.00%	602	1.62126

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; 44	0; 57
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 17	0; 22
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 16
chr11:62623517@+	-1000; 112	SLC3A2	0; 12	0; 12
chr5:147647742@+	-1000; 164	SPINK5L3	10; 0	10; 0
chr7:26240781@+	-1000; 200	CBX3	0; 9	0; 10
chr5:32788944@+	-844; 281	C5orf23	9; 0	10; 0
chr8:101734314@-	-1000; 252	PABPC1	7; 0	7; 0
chr5:175815975@-	-1000; 188	NOP16	0; 7	0; 8
chr8:33370702@-	-1000; 286	C8orf41	0; 6	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)
chr6:166401114@+	-1000; 249	AL132661.1	0; 44	0; 57
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 17	0; 22
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 16
chr11:62623517@+	-1000; 112	SLC3A2	0; 12	0; 12
chr7:26240781@+	-1000; 200	CBX3	0; 9	0; 10
chr5:147647742@+	-1000; 164	SPINK5L3	10; 0	10; 0
chr5:32788944@+	-844; 281	C5orf23	9; 0	10; 0
chr5:175815975@-	-1000; 188	NOP16	0; 7	0; 8
chr11:66115160@-	-1000; 72	AP001107.2	0; 6	0; 8
chr8:101734314@-	-1000; 252	PABPC1	7; 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	9610	3.65%	12.11%	86.68%	3223	2.63794
anti	1477	0.56%	1.86%	13.32%	566	0.405435
both	11087	4.21%	13.97%	100.00%	3643	3.04337
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	10840	3.77%	12.27%	86.29%	3223	2.97557
anti	1722	0.60%	1.95%	13.71%	566	0.472687
both	12562	4.37%	14.21%	100.00%	3643	3.44826

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)
chr19:39220830@-	-300; 1000	CAPN12	0; 70	0; 112
chr8:128753674@+	-235; 1000	MYC	59; 0	111; 0
chr15:45010359@+	-278; 1000	B2M	54; 0	81; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 40	0; 45
chr19:57805436@+	-300; 1000	ZNF460	39; 0	41; 0
chr12:104744062@+	-300; 1000	TXNRD1	38; 0	53; 0
chr16:87863620@-	-300; 1000	SLC7A5	37; 0	62; 0
chr16:18802989@-	-300; 667	ARL6IP1	37; 0	50; 0
chr12:20833881@+	-300; 1000	PDE3A	36; 0	44; 0
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 89

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)
chr19:39220830@-	-300; 1000	CAPN12	0; 70	0; 112
chr8:128753674@+	-235; 1000	MYC	59; 0	111; 0
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 89
chr15:45010359@+	-278; 1000	B2M	54; 0	81; 0
chr16:87863620@-	-300; 1000	SLC7A5	37; 0	62; 0
chr17:79845715@-	-144; 1000	THOC4	24; 0	61; 0
chr12:104744062@+	-300; 1000	TXNRD1	38; 0	53; 0
chr9:124095121@+	-120; 1000	GSN	23; 0	51; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 34	1; 50
chr16:18802989@-	-300; 667	ARL6IP1	37; 0	50; 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	811	0.31%	1.02%	24.85%	501	0.45613
anti	2452	0.93%	3.09%	75.15%	1313	1.37908
both	3263	1.24%	4.11%	100.00%	1778	1.83521
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	961	0.33%	1.09%	25.89%	501	0.540495
anti	2751	0.96%	3.11%	74.11%	1313	1.54724
both	3712	1.29%	4.20%	100.00%	1778	2.08774

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)
chr8:128231332@-	-1000; 139	AC020688.1	104; 1	127; 1
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 66	0; 147
chr3:49571651@-	-1000; 300	AC104452.1	0; 46	0; 54
chr6:166401114@+	-1000; 249	AL132661.1	0; 44	0; 57
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 42	0; 44
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 35	0; 42
chr1:205685227@+	-1000; 300	AC119673.2	0; 29	0; 34
chr2:70315685@-	-1000; 62	AC136007.2	0; 28	0; 37
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 24	0; 28
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 24	0; 30

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; 66	0; 147
chr8:128231332@-	-1000; 139	AC020688.1	104; 1	127; 1
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	15; 0	62; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 44	0; 57
chr3:49571651@-	-1000; 300	AC104452.1	0; 46	0; 54
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 42	0; 44
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 35	0; 42
chr2:70315685@-	-1000; 62	AC136007.2	0; 28	0; 37
chr1:205685227@+	-1000; 300	AC119673.2	0; 29	0; 34
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 24	0; 30

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	11941	4.53%	15.05%	80.15%	3980	2.38629
anti	2957	1.12%	3.73%	19.85%	1210	0.590927
both	14898	5.66%	18.78%	100.00%	5004	2.97722
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	14911	5.19%	16.87%	81.57%	3980	2.97982
anti	3369	1.17%	3.81%	18.43%	1210	0.673261
both	18280	6.36%	20.68%	100.00%	5004	3.65308

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	625; 0	1780; 0
chr1:169101767@-	-127; 1000	NME7	0; 91	0; 139
chr19:39220830@-	-300; 1000	CAPN12	0; 70	0; 112
chr8:128753674@+	-235; 1000	MYC	59; 0	111; 0
chr15:45010359@+	-278; 1000	B2M	54; 0	81; 0
chrUn_gl000220:118417@+	-300; 1000	28S	48; 0	118; 0
chr7:5566780@-	-300; 1000	ACTB	47; 0	161; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 40	0; 45
chr19:57805436@+	-300; 1000	ZNF460	39; 0	41; 0
chr4:57897324@+	-130; 1000	POLR2B	4; 34	4; 51

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	625; 0	1780; 0
chr7:5566780@-	-300; 1000	ACTB	47; 0	161; 0
chr1:169101767@-	-127; 1000	NME7	0; 91	0; 139
chrUn_gl000220:118417@+	-300; 1000	28S	48; 0	118; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 70	0; 112
chr8:128753674@+	-235; 1000	MYC	59; 0	111; 0
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 89
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	18; 0	88; 0
chr15:45010359@+	-278; 1000	B2M	54; 0	81; 0
chr1:153516087@-	-156; 923	S100A4	24; 0	68; 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	10193	3.87%	12.85%	96.31%	8153	1.20485
anti	391	0.15%	0.49%	3.69%	321	0.0462175
both	10584	4.02%	13.34%	100.00%	8460	1.25106
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	10611	3.69%	12.01%	96.33%	8153	1.25426
anti	404	0.14%	0.46%	3.67%	321	0.0477541
both	11015	3.83%	12.46%	100.00%	8460	1.30201

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)
chr5:179045370@-	-300; 47	HNRNPH1	20; 0	22; 0
chr5:147653879@+	-300; 28	SPINK5L3	18; 0	20; 0
chr1:70697488@+	-300; 100	SFRS11	17; 0	18; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	15; 0	15; 0
chr16:31199583@+	-300; 60	FUS	15; 0	16; 0
chr2:61413393@+	-229; 100	AHSA2	14; 0	17; 0
chr1:1326494@-	-300; 100	CCNL2	13; 0	15; 0
chr5:179046653@-	-300; 100	HNRNPH1	12; 0	15; 0
chr5:179048854@-	-300; 100	HNRNPH1	11; 0	13; 0
chr16:277586@-	-300; 100	LUC7L	11; 0	11; 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)
chr9:86584384@-	-300; 90	HNRNPK	10; 0	33; 0
chr5:179045370@-	-300; 47	HNRNPH1	20; 0	22; 0
chr5:147653879@+	-300; 28	SPINK5L3	18; 0	20; 0
chr1:70697488@+	-300; 100	SFRS11	17; 0	18; 0
chr2:61413393@+	-229; 100	AHSA2	14; 0	17; 0
chr16:31199583@+	-300; 60	FUS	15; 0	16; 0
chr1:28835317@+	-300; 22	SNHG3	9; 0	16; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	15; 0	15; 0
chr5:179046653@-	-300; 100	HNRNPH1	12; 0	15; 0
chr1:1326494@-	-300; 100	CCNL2	13; 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.