Parameters
input_file: 20090724_LUd3_4_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: 788834
[x-link sites] used in any map: 238397 (30.22%)
[single hits in whole-genome, cDNA counts] total: 788834
[single hits in whole-genome, cDNA counts] used in any map: 273413 (31.28%)

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	80801	10.24%	33.89%	85809	9.82%	31.38%
intron-exon	-300; 300	58797	7.45%	24.66%	62960	7.20%	23.03%
5-ncRNA	-1000; 300	10826	1.37%	4.54%	14563	1.67%	5.33%
ncRNA-3	-300; 1000	11249	1.43%	4.72%	16661	1.91%	6.09%
ORF-3UTR	-300; 300	29718	3.77%	12.47%	38312	4.38%	14.01%
5UTR-ORF	-300; 300	1883	0.24%	0.79%	2009	0.23%	0.73%
inter-5UTR	-1000; 300	3274	0.42%	1.37%	3592	0.41%	1.31%
3UTR-inter	-300; 1000	30426	3.86%	12.76%	37531	4.29%	13.73%
inter-5	-1000; 300	10331	1.31%	4.33%	12078	1.38%	4.42%
3-inter	-300; 1000	40072	5.08%	16.81%	52891	6.05%	19.34%
BP best in intron	-300; 100	33482	4.24%	14.04%	34752	3.98%	12.71%

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	79114	10.03%	33.19%	97.91%	39030	1.98201
anti	1687	0.21%	0.71%	2.09%	1117	0.0422638
both	80801	10.24%	33.89%	100.00%	39916	2.02428
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	83785	9.59%	30.64%	97.64%	39030	2.09903
anti	2024	0.23%	0.74%	2.36%	1117	0.0507065
both	85809	9.82%	31.38%	100.00%	39916	2.14974

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; 101	0; 303
chr3:41281934@+	-300; 300	CTNNB1	78; 0	155; 0
chr7:128411528@+	-300; 107	CALU	68; 0	233; 0
chr16:2819285@+	-144; 300	SRRM2	64; 0	77; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 61	0; 123
chr5:10401598@+	-300; 185	MARCH6	57; 0	87; 0
chr2:191800015@+	-300; 300	GLS	47; 0	82; 0
chr5:179047674@-	-181; 300	HNRNPH1	46; 0	51; 0
chr12:50158717@+	-300; 300	TMBIM6	45; 0	87; 0
chr17:57915758@+	-52; 300	TMEM49	40; 0	64; 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; 101	0; 303
chr7:128411528@+	-300; 107	CALU	68; 0	233; 0
chr3:41281934@+	-300; 300	CTNNB1	78; 0	155; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 61	0; 123
chr5:10401598@+	-300; 185	MARCH6	57; 0	87; 0
chr12:50158717@+	-300; 300	TMBIM6	45; 0	87; 0
chr2:191800015@+	-300; 300	GLS	47; 0	82; 0
chr1:165624857@+	-127; 300	MGST3	31; 0	81; 0
chr16:2819285@+	-144; 300	SRRM2	64; 0	77; 0
chr5:147650475@+	-75; 300	SPINK5L3	39; 0	64; 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	56911	7.21%	23.87%	96.79%	31720	1.73615
anti	1886	0.24%	0.79%	3.21%	1312	0.0575351
both	58797	7.45%	24.66%	100.00%	32780	1.79369
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	60936	6.97%	22.29%	96.79%	31720	1.85894
anti	2024	0.23%	0.74%	3.21%	1312	0.061745
both	62960	7.20%	23.03%	100.00%	32780	1.92068

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	122; 0	399; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	97; 0	187; 0
chr5:179041959@-	-293; 300	HNRNPH1	63; 0	180; 0
chr17:57915655@+	-300; 51	TMEM49	61; 0	104; 0
chr9:131456919@+	-292; 300	SET	55; 0	282; 0
chr17:57917128@+	-300; 72	TMEM49	54; 0	85; 0
chr2:47387942@-	-300; 300	CALM2	53; 0	94; 0
chr8:128753204@+	-241; 235	MYC	51; 0	124; 0
chr1:26227577@-	-160; 260	STMN1	50; 0	95; 0
chr7:5568349@-	-150; 219	ACTB	46; 0	85; 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	122; 0	399; 0
chr9:131456919@+	-292; 300	SET	55; 0	282; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	97; 0	187; 0
chr5:179041959@-	-293; 300	HNRNPH1	63; 0	180; 0
chr8:128753204@+	-241; 235	MYC	51; 0	124; 0
chr10:112657785@+	-300; 300	PDCD4	44; 0	106; 0
chr17:57915655@+	-300; 51	TMEM49	61; 0	104; 0
chr1:26227577@-	-160; 260	STMN1	50; 0	95; 0
chr2:47387942@-	-300; 300	CALM2	53; 0	94; 0
chr7:5568349@-	-150; 219	ACTB	46; 0	85; 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	4487	0.57%	1.88%	41.45%	1777	1.14875
anti	6339	0.80%	2.66%	58.55%	2237	1.62289
both	10826	1.37%	4.54%	100.00%	3906	2.77163
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	7426	0.85%	2.72%	50.99%	1777	1.90118
anti	7137	0.82%	2.61%	49.01%	2237	1.82719
both	14563	1.67%	5.33%	100.00%	3906	3.72837

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	636; 0	2462; 0
chr8:128231332@-	-1000; 139	AC020688.1	218; 3	346; 3
chr3:49571651@-	-1000; 300	AC104452.1	0; 133	0; 191
chr1:205685227@+	-1000; 300	AC119673.2	0; 101	0; 153
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 90	0; 135
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 79	0; 113
chr17:57918626@+	-338; 36	hsa-mir-21	71; 0	203; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 65	0; 88
chr2:70315685@-	-1000; 62	AC136007.2	0; 59	0; 87
chr13:30083551@+	-1000; 300	AL596114.1	0; 56	0; 84

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	636; 0	2462; 0
chr8:128231332@-	-1000; 139	AC020688.1	218; 3	346; 3
chr17:57918626@+	-338; 36	hsa-mir-21	71; 0	203; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 133	0; 191
chr1:205685227@+	-1000; 300	AC119673.2	0; 101	0; 153
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 90	0; 135
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 79	0; 113
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	103; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 65	0; 88
chr2:70315685@-	-1000; 62	AC136007.2	0; 59	0; 87

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	5845	0.74%	2.45%	51.96%	2075	1.47452
anti	5404	0.69%	2.27%	48.04%	1978	1.36327
both	11249	1.43%	4.72%	100.00%	3964	2.83779
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	10715	1.23%	3.92%	64.31%	2075	2.70308
anti	5946	0.68%	2.17%	35.69%	1978	1.5
both	16661	1.91%	6.09%	100.00%	3964	4.20308

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	891; 0	3814; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 108	0; 165
chr8:144939422@+	-300; 1000	AC105049.1	0; 78	0; 105
chrUn_gl000220:118417@+	-300; 1000	28S	75; 0	177; 0
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 72	0; 88
chr2:191798136@-	-300; 1000	AC067945.1	0; 69	0; 84
chr10:112658486@-	-300; 1000	NCRNA00081	0; 67	0; 132
chr1:28835512@-	-182; 1000	AL513497.3	0; 67	0; 98
chr8:128220109@-	-300; 1000	AC020688.1	66; 0	74; 0
chr1:21070455@+	-63; 1000	RP5-930J4.4	0; 62	0; 78

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	891; 0	3814; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	30; 0	297; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	58; 0	271; 0
chrUn_gl000220:118417@+	-300; 1000	28S	75; 0	177; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 108	0; 165
chr10:112658486@-	-300; 1000	NCRNA00081	0; 67	0; 132
chr8:144939422@+	-300; 1000	AC105049.1	0; 78	0; 105
chr1:28835512@-	-182; 1000	AL513497.3	0; 67	0; 98
chr9:35657749@-	-132; 1000	RNase_MRP-ENSG00000199916	36; 0	93; 0
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 72	0; 88

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	29193	3.70%	12.25%	98.23%	4976	5.65975
anti	525	0.07%	0.22%	1.77%	290	0.101784
both	29718	3.77%	12.47%	100.00%	5158	5.76154
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	37754	4.32%	13.81%	98.54%	4976	7.3195
anti	558	0.06%	0.20%	1.46%	290	0.108181
both	38312	4.38%	14.01%	100.00%	5158	7.42769

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	156; 0	837; 0
chr3:149087560@-	-53; 300	TM4SF1	119; 0	353; 0
chr5:179156650@+	-145; 300	CANX	109; 0	230; 0
chr1:35650053@-	-70; 300	SFPQ	104; 0	211; 0
chr14:62213803@+	-76; 300	HIF1A	103; 0	231; 0
chr21:27253823@-	-129; 300	APP	83; 0	141; 0
chrX:114884310@+	-165; 300	PLS3	81; 0	117; 0
chr2:136872205@-	-300; 144	CXCR4	79; 0	142; 0
chr2:189876774@+	-211; 300	COL3A1	78; 0	148; 0
chr1:156109094@+	-112; 233	LMNA	75; 0	184; 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	156; 0	837; 0
chr3:149087560@-	-53; 300	TM4SF1	119; 0	353; 0
chr17:4849191@-	-50; 123	PFN1	66; 0	317; 0
chr14:62213803@+	-76; 300	HIF1A	103; 0	231; 0
chr5:179156650@+	-145; 300	CANX	109; 0	230; 0
chr1:35650053@-	-70; 300	SFPQ	104; 0	211; 0
chr10:102120690@+	-100; 300	SCD	67; 0	193; 0
chr1:156109094@+	-112; 233	LMNA	75; 0	184; 0
chr7:148700882@-	-209; 300	PDIA4	67; 0	166; 0
chr1:54497690@-	-144; 172	TMEM59	68; 0	153; 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	1718	0.22%	0.72%	91.24%	850	1.89625
anti	165	0.02%	0.07%	8.76%	67	0.182119
both	1883	0.24%	0.79%	100.00%	906	2.07837
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	1828	0.21%	0.67%	90.99%	850	2.01766
anti	181	0.02%	0.07%	9.01%	67	0.199779
both	2009	0.23%	0.73%	100.00%	906	2.21744

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)
chr17:4851688@-	-300; 66	PFN1	46; 0	67; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 39	0; 52
chr8:101733810@-	-252; 96	PABPC1	31; 0	47; 0
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 31	0; 33
chr22:38884251@-	-142; 187	DDX17	20; 0	22; 0
chr2:61764828@-	-277; 66	XPO1	19; 0	21; 0
chr6:24718895@-	-300; 64	C6orf62	16; 0	19; 0
chr6:64286785@+	-92; 52	PTP4A1	16; 0	17; 0
chr2:211421442@+	-91; 70	CPS1	15; 0	15; 0
chr17:43226557@+	-300; 300	HEXIM1	15; 0	20; 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)
chr17:4851688@-	-300; 66	PFN1	46; 0	67; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 39	0; 52
chr8:101733810@-	-252; 96	PABPC1	31; 0	47; 0
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 31	0; 33
chr22:38884251@-	-142; 187	DDX17	20; 0	22; 0
chr2:61764828@-	-277; 66	XPO1	19; 0	21; 0
chr17:43226557@+	-300; 300	HEXIM1	15; 0	20; 0
chr6:24718895@-	-300; 64	C6orf62	16; 0	19; 0
chr6:64286785@+	-92; 52	PTP4A1	16; 0	17; 0
chr2:211421442@+	-91; 70	CPS1	15; 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 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	1082	0.14%	0.45%	33.05%	654	0.68179
anti	2192	0.28%	0.92%	66.95%	1042	1.38122
both	3274	0.42%	1.37%	100.00%	1587	2.06301
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	1145	0.13%	0.42%	31.88%	654	0.721487
anti	2447	0.28%	0.89%	68.12%	1042	1.5419
both	3592	0.41%	1.31%	100.00%	1587	2.26339

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; 117	0; 199
chr11:62623517@+	-1000; 112	SLC3A2	0; 51	0; 63
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 33	0; 42
chr5:32788944@+	-844; 281	C5orf23	30; 0	34; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 27	0; 32
chr8:71485680@+	-1000; 300	AC120194.1	0; 23	0; 26
chr7:26240781@+	-1000; 200	CBX3	0; 23	0; 26
chr4:77997141@-	-1000; 184	CCNI	20; 0	27; 0
chr17:7387865@+	-741; 109	POLR2A	19; 1	24; 1
chr8:101734314@-	-1000; 252	PABPC1	18; 0	25; 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)
chr6:166401114@+	-1000; 249	AL132661.1	0; 117	0; 199
chr11:62623517@+	-1000; 112	SLC3A2	0; 51	0; 63
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 33	0; 42
chr5:32788944@+	-844; 281	C5orf23	30; 0	34; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 27	0; 32
chr4:77997141@-	-1000; 184	CCNI	20; 0	27; 0
chr11:66115160@-	-1000; 72	AP001107.2	0; 9	0; 27
chr8:71485680@+	-1000; 300	AC120194.1	0; 23	0; 26
chr7:26240781@+	-1000; 200	CBX3	0; 23	0; 26
chr8:101734314@-	-1000; 252	PABPC1	18; 0	25; 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	25828	3.27%	10.83%	84.89%	4861	4.64532
anti	4598	0.58%	1.93%	15.11%	1104	0.826978
both	30426	3.86%	12.76%	100.00%	5560	5.4723
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	31784	3.64%	11.62%	84.69%	4861	5.71655
anti	5747	0.66%	2.10%	15.31%	1104	1.03363
both	37531	4.29%	13.73%	100.00%	5560	6.75018

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; 175	0; 334
chr8:128753674@+	-235; 1000	MYC	114; 0	366; 0
chr15:45010359@+	-278; 1000	B2M	97; 0	212; 0
chr12:20833881@+	-300; 1000	PDE3A	90; 0	134; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 85	0; 122
chr14:62214976@+	-300; 1000	HIF1A	81; 0	147; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 79	0; 145
chr16:18802989@-	-300; 667	ARL6IP1	78; 0	122; 0
chr17:4848518@+	-104; 1000	RNF167	2; 69	2; 320
chr19:57805436@+	-300; 1000	ZNF460	68; 0	82; 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)
chr8:128753674@+	-235; 1000	MYC	114; 0	366; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 175	0; 334
chr17:4848518@+	-104; 1000	RNF167	2; 69	2; 320
chr15:45010359@+	-278; 1000	B2M	97; 0	212; 0
chr11:65622306@-	-249; 1000	CFL1	56; 0	197; 0
chr17:38613983@+	-300; 1000	IGFBP4	47; 0	162; 0
chr17:79845715@-	-144; 1000	THOC4	64; 0	153; 0
chr14:62214976@+	-300; 1000	HIF1A	81; 0	147; 0
chr17:79476997@-	-300; 1000	ACTG1	56; 0	145; 0
chr16:87863620@-	-300; 1000	SLC7A5	66; 0	145; 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	2642	0.33%	1.11%	25.57%	1403	0.63236
anti	7689	0.97%	3.23%	74.43%	2972	1.84035
both	10331	1.31%	4.33%	100.00%	4178	2.47271
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	3256	0.37%	1.19%	26.96%	1403	0.77932
anti	8822	1.01%	3.23%	73.04%	2972	2.11154
both	12078	1.38%	4.42%	100.00%	4178	2.89086

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	218; 3	346; 3
chr3:49571651@-	-1000; 300	AC104452.1	0; 133	0; 191
chr6:166401114@+	-1000; 249	AL132661.1	0; 115	0; 197
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 113	0; 250
chr1:205685227@+	-1000; 300	AC119673.2	0; 101	0; 153
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 90	0; 135
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 79	0; 113
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 65	0; 88
chr2:70315685@-	-1000; 62	AC136007.2	0; 59	0; 87
chr13:30083551@+	-1000; 300	AL596114.1	0; 56	0; 84

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)
chr8:128231332@-	-1000; 139	AC020688.1	218; 3	346; 3
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 113	0; 250
chr6:166401114@+	-1000; 249	AL132661.1	0; 115	0; 197
chr3:49571651@-	-1000; 300	AC104452.1	0; 133	0; 191
chr1:205685227@+	-1000; 300	AC119673.2	0; 101	0; 153
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 90	0; 135
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 79	0; 113
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	103; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 65	0; 88
chr2:70315685@-	-1000; 62	AC136007.2	0; 59	0; 87

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	30955	3.92%	12.98%	77.25%	6170	3.82727
anti	9117	1.16%	3.82%	22.75%	2441	1.12723
both	40072	5.08%	16.81%	100.00%	8088	4.9545
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	41892	4.79%	15.32%	79.20%	6170	5.17953
anti	10999	1.26%	4.02%	20.80%	2441	1.35992
both	52891	6.05%	19.34%	100.00%	8088	6.53944

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	891; 0	3814; 0
chr1:169101767@-	-127; 1000	NME7	0; 231	0; 442
chr19:39220830@-	-300; 1000	CAPN12	0; 175	0; 334
chr8:128753674@+	-235; 1000	MYC	114; 0	366; 0
chr15:45010359@+	-278; 1000	B2M	97; 0	212; 0
chr12:20833881@+	-300; 1000	PDE3A	90; 0	134; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 85	0; 122
chr14:62214976@+	-300; 1000	HIF1A	81; 0	147; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 79	0; 145
chr16:18802989@-	-300; 667	ARL6IP1	78; 0	122; 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	891; 0	3814; 0
chr1:169101767@-	-127; 1000	NME7	0; 231	0; 442
chr8:128753674@+	-235; 1000	MYC	114; 0	366; 0
chr7:5566780@-	-300; 1000	ACTB	59; 0	359; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 175	0; 334
chr17:4848518@+	-104; 1000	RNF167	2; 69	2; 320
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	30; 0	297; 0
chr15:45010359@+	-278; 1000	B2M	97; 0	212; 0
chr11:65622306@-	-249; 1000	CFL1	56; 0	197; 0
chrUn_gl000220:118417@+	-300; 1000	28S	75; 0	177; 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	32341	4.10%	13.57%	96.59%	20723	1.50605
anti	1141	0.14%	0.48%	3.41%	881	0.053134
both	33482	4.24%	14.04%	100.00%	21474	1.55919
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	33548	3.84%	12.27%	96.54%	20723	1.56226
anti	1204	0.14%	0.44%	3.46%	881	0.0560678
both	34752	3.98%	12.71%	100.00%	21474	1.61833

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)
chr14:70237083@+	-300; 98	SFRS5	48; 0	65; 0
chr1:1326494@-	-300; 100	CCNL2	39; 0	53; 0
chr5:179046653@-	-300; 100	HNRNPH1	37; 0	46; 0
chr5:10401919@+	-300; 100	MARCH6	36; 0	58; 0
chr3:186506588@+	-298; 100	EIF4A2	33; 0	43; 0
chr5:179045370@-	-300; 47	HNRNPH1	32; 0	53; 0
chr5:179048854@-	-300; 100	HNRNPH1	29; 0	37; 0
chr15:66783435@-	-300; 100	SNAPC5	0; 29	0; 35
chr22:38884242@-	-300; 100	DDX17	28; 0	31; 0
chr20:34326966@-	-300; 28	RBM39	28; 0	34; 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)
chr14:70237083@+	-300; 98	SFRS5	48; 0	65; 0
chr9:86584384@-	-300; 90	HNRNPK	12; 0	59; 0
chr5:10401919@+	-300; 100	MARCH6	36; 0	58; 0
chr5:179045370@-	-300; 47	HNRNPH1	32; 0	53; 0
chr1:1326494@-	-300; 100	CCNL2	39; 0	53; 0
chr5:179046653@-	-300; 100	HNRNPH1	37; 0	46; 0
chr2:61413393@+	-229; 100	AHSA2	22; 0	44; 0
chr3:186506588@+	-298; 100	EIF4A2	33; 0	43; 0
chr5:179048854@-	-300; 100	HNRNPH1	29; 0	37; 0
chr16:31199583@+	-300; 60	FUS	26; 0	36; 0

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