Parameters
input_file: 20090724_LUd3_4_hg19_ensembl59_S_iCLIP_TIAL1_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: 811679
[x-link sites] used in any map: 243651 (30.02%)
[single hits (=G+T), cDNA counts] total: 811679
[single hits (=G+T), cDNA counts] used in any map: 281223 (31.10%)

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	81623	10.06%	33.50%	86806	9.60%	30.87%
intron-exon	-300; 300	59563	7.34%	24.45%	63935	7.07%	22.73%
5-ncRNA	-1000; 300	11284	1.39%	4.63%	15383	1.70%	5.47%
ncRNA-3	-300; 1000	11872	1.46%	4.87%	17896	1.98%	6.36%
ORF-3UTR	-300; 300	30860	3.80%	12.67%	39905	4.41%	14.19%
5UTR-ORF	-300; 300	1909	0.24%	0.78%	2037	0.23%	0.72%
inter-5UTR	-1000; 300	3343	0.41%	1.37%	3841	0.42%	1.37%
3UTR-inter	-300; 1000	31537	3.89%	12.94%	39092	4.32%	13.90%
inter-5	-1000; 300	10711	1.32%	4.40%	12831	1.42%	4.56%
3-inter	-300; 1000	41638	5.13%	17.09%	55550	6.14%	19.75%
BP best in intron	-300; 100	33929	4.18%	13.93%	35246	3.90%	12.53%

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	79855	9.84%	32.77%	97.83%	39268	1.98689
anti	1768	0.22%	0.73%	2.17%	1168	0.0439899
both	81623	10.06%	33.50%	100.00%	40191	2.03088
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	84653	9.36%	30.10%	97.52%	39268	2.10627
anti	2153	0.24%	0.77%	2.48%	1168	0.0535692
both	86806	9.60%	30.87%	100.00%	40191	2.15984

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)
chr1:45976739@+	-281; 300	MMACHC	0; 114	0; 352
chr3:41281934@+	-300; 300	CTNNB1	78; 0	155; 0
chr7:128411528@+	-300; 107	CALU	68; 0	233; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 67	0; 129
chr16:2819285@+	-144; 300	SRRM2	64; 0	77; 0
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	88; 0
chr17:57915758@+	-52; 300	TMEM49	40; 0	64; 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)
chr1:45976739@+	-281; 300	MMACHC	0; 114	0; 352
chr7:128411528@+	-300; 107	CALU	68; 0	233; 0
chr3:41281934@+	-300; 300	CTNNB1	78; 0	155; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 67	0; 129
chr12:50158717@+	-300; 300	TMBIM6	45; 0	88; 0
chr5:10401598@+	-300; 185	MARCH6	57; 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
chr7:139025365@+	-85; 256	C7orf55	6; 1	63; 1

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	57572	7.09%	23.63%	96.66%	31950	1.74081
anti	1991	0.25%	0.82%	3.34%	1393	0.060202
both	59563	7.34%	24.45%	100.00%	33072	1.80101
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	61791	6.83%	21.97%	96.65%	31950	1.86838
anti	2144	0.24%	0.76%	3.35%	1393	0.0648283
both	63935	7.07%	22.73%	100.00%	33072	1.93321

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)
chr15:45009804@+	-300; 277	B2M	122; 0	399; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	97; 0	187; 0
chr9:131456919@+	-292; 300	SET	82; 0	334; 0
chr5:179041959@-	-293; 300	HNRNPH1	66; 0	186; 0
chr17:57915655@+	-300; 51	TMEM49	61; 0	104; 0
chr2:47387942@-	-300; 300	CALM2	56; 0	107; 0
chr7:5568349@-	-150; 219	ACTB	55; 0	99; 0
chr17:57917128@+	-300; 72	TMEM49	54; 0	85; 0
chr8:128753204@+	-241; 235	MYC	51; 0	124; 0
chr1:26227577@-	-160; 260	STMN1	50; 0	95; 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)
chr15:45009804@+	-300; 277	B2M	122; 0	399; 0
chr9:131456919@+	-292; 300	SET	82; 0	334; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	97; 0	187; 0
chr5:179041959@-	-293; 300	HNRNPH1	66; 0	186; 0
chr8:128753204@+	-241; 235	MYC	51; 0	124; 0
chr2:47387942@-	-300; 300	CALM2	56; 0	107; 0
chr10:112657785@+	-300; 300	PDCD4	45; 0	107; 0
chr17:57915655@+	-300; 51	TMEM49	61; 0	104; 0
chr7:5568349@-	-150; 219	ACTB	55; 0	99; 0
chr1:26227577@-	-160; 260	STMN1	50; 0	95; 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	4770	0.59%	1.96%	42.27%	1847	1.18568
anti	6514	0.80%	2.67%	57.73%	2292	1.61919
both	11284	1.39%	4.63%	100.00%	4023	2.80487
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	8034	0.89%	2.86%	52.23%	1847	1.99702
anti	7349	0.81%	2.61%	47.77%	2292	1.82675
both	15383	1.70%	5.47%	100.00%	4023	3.82376

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	636; 0	2462; 0
chr8:128231332@-	-1000; 139	AC020688.1	218; 3	346; 3
chr3:49571651@-	-1000; 300	AC104452.1	0; 133	0; 191
chrUn_gl000220:109077@+	-758; 300	18S	102; 0	253; 0
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
chr2:70315685@-	-1000; 62	AC136007.2	0; 65	0; 94
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 65	0; 88

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	636; 0	2462; 0
chr8:128231332@-	-1000; 139	AC020688.1	218; 3	346; 3
chrUn_gl000220:109077@+	-758; 300	18S	102; 0	253; 0
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
chr14:74055600@-	-1000; 36	AC005225.1	6; 0	119; 0
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 79	0; 113
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	103; 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	6317	0.78%	2.59%	53.21%	2188	1.53437
anti	5555	0.68%	2.28%	46.79%	2032	1.34928
both	11872	1.46%	4.87%	100.00%	4117	2.88365
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	11777	1.30%	4.19%	65.81%	2188	2.86058
anti	6119	0.68%	2.18%	34.19%	2032	1.48628
both	17896	1.98%	6.36%	100.00%	4117	4.34685

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	891; 0	3814; 0
chrUn_gl000220:110946@+	-300; 539	18S	142; 0	549; 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
chrY:21154137@-	-229; 1000	CD24L4, NCRNA00185	74; 0	114; 0
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 72	0; 88
chr2:191798136@-	-300; 1000	AC067945.1	0; 70	0; 85
chr8:128220109@-	-300; 1000	AC020688.1	68; 0	76; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 68	0; 133

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	891; 0	3814; 0
chrUn_gl000220:110946@+	-300; 539	18S	142; 0	549; 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; 68	0; 133
chrY:21154137@-	-229; 1000	CD24L4, NCRNA00185	74; 0	114; 0
chr8:144939422@+	-300; 1000	AC105049.1	0; 78	0; 105
chr1:28835512@-	-182; 1000	AL513497.3	0; 67	0; 98

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	30321	3.74%	12.44%	98.25%	5027	5.81419
anti	539	0.07%	0.22%	1.75%	298	0.103356
both	30860	3.80%	12.67%	100.00%	5215	5.91755
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	39330	4.35%	13.99%	98.56%	5027	7.54171
anti	575	0.06%	0.20%	1.44%	298	0.110259
both	39905	4.41%	14.19%	100.00%	5215	7.65197

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)
chr19:13054727@+	-101; 288	CALR	157; 0	840; 0
chr3:149087560@-	-53; 300	TM4SF1	119; 0	353; 0
chr5:179156650@+	-145; 300	CANX	109; 0	230; 0
chr1:35650053@-	-70; 300	SFPQ	105; 0	216; 0
chr14:62213803@+	-76; 300	HIF1A	103; 0	231; 0
chr10:102120690@+	-100; 300	SCD	103; 0	279; 0
chr9:86584111@-	-92; 300	HNRNPK	84; 0	127; 0
chr6:30692174@+	-300; 300	TUBB	84; 0	167; 0
chr21:27253823@-	-129; 300	APP	83; 0	141; 0
chrX:114884310@+	-165; 300	PLS3	81; 0	117; 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)
chr19:13054727@+	-101; 288	CALR	157; 0	840; 0
chr3:149087560@-	-53; 300	TM4SF1	119; 0	353; 0
chr17:4849191@-	-50; 123	PFN1	66; 0	317; 0
chr10:102120690@+	-100; 300	SCD	103; 0	279; 0
chr14:62213803@+	-76; 300	HIF1A	103; 0	231; 0
chr5:179156650@+	-145; 300	CANX	109; 0	230; 0
chr1:35650053@-	-70; 300	SFPQ	105; 0	216; 0
chr1:156109094@+	-112; 233	LMNA	75; 0	184; 0
chr6:30692174@+	-300; 300	TUBB	84; 0	167; 0
chr7:148700882@-	-209; 300	PDIA4	67; 0	166; 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	1741	0.21%	0.71%	91.20%	854	1.90899
anti	168	0.02%	0.07%	8.80%	69	0.184211
both	1909	0.24%	0.78%	100.00%	912	2.0932
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	1853	0.20%	0.66%	90.97%	854	2.0318
anti	184	0.02%	0.07%	9.03%	69	0.201754
both	2037	0.23%	0.72%	100.00%	912	2.23355

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)
chr17:4851688@-	-300; 66	PFN1	46; 0	67; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 39	0; 52
chr8:101733810@-	-252; 96	PABPC1	35; 0	51; 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 (=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)
chr17:4851688@-	-300; 66	PFN1	46; 0	67; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 39	0; 52
chr8:101733810@-	-252; 96	PABPC1	35; 0	51; 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	1120	0.14%	0.46%	33.50%	662	0.696951
anti	2223	0.27%	0.91%	66.50%	1055	1.38332
both	3343	0.41%	1.37%	100.00%	1607	2.08027
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	1303	0.14%	0.46%	33.92%	662	0.810828
anti	2538	0.28%	0.90%	66.08%	1055	1.57934
both	3841	0.42%	1.37%	100.00%	1607	2.39017

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)
chr6:166401114@+	-1000; 249	AL132661.1	0; 117	0; 199
chr11:62623517@+	-1000; 112	SLC3A2	0; 51	0; 63
chr8:101734314@-	-1000; 252	PABPC1	44; 0	170; 0
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 33	0; 42
chr5:32788944@+	-844; 281	C5orf23	30; 0	34; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 28	0; 33
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

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)
chr6:166401114@+	-1000; 249	AL132661.1	0; 117	0; 199
chr8:101734314@-	-1000; 252	PABPC1	44; 0	170; 0
chr13:41635409@+	-1000; 200	WBP4	0; 13	0; 72
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; 28	0; 33
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

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	26764	3.30%	10.98%	84.87%	4907	4.76992
anti	4773	0.59%	1.96%	15.13%	1120	0.850651
both	31537	3.89%	12.94%	100.00%	5611	5.62057
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	33085	3.66%	11.76%	84.63%	4907	5.89645
anti	6007	0.66%	2.14%	15.37%	1120	1.07058
both	39092	4.32%	13.90%	100.00%	5611	6.96703

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)
chr19:39220830@-	-300; 1000	CAPN12	0; 188	0; 348
chr8:128753674@+	-235; 1000	MYC	115; 0	368; 0
chr15:45010359@+	-278; 1000	B2M	97; 0	212; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 91	0; 162
chr12:20833881@+	-300; 1000	PDE3A	90; 0	134; 0
chr16:18802989@-	-300; 667	ARL6IP1	88; 0	148; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 85	0; 122
chr14:62214976@+	-300; 1000	HIF1A	81; 0	147; 0
chr19:13055304@+	-289; 674	CALR	79; 0	163; 0
chr17:7215782@+	-300; 1000	EIF5A	69; 5	167; 5

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)
chr8:128753674@+	-235; 1000	MYC	115; 0	368; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 188	0; 348
chr17:4848518@+	-104; 1000	RNF167	2; 69	2; 320
chr15:45010359@+	-278; 1000	B2M	97; 0	212; 0
chr11:65622306@-	-249; 1000	CFL1	61; 0	205; 0
chr17:7215782@+	-300; 1000	EIF5A	69; 5	167; 5
chr19:13055304@+	-289; 674	CALR	79; 0	163; 0
chr17:38613983@+	-300; 1000	IGFBP4	47; 0	163; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 91	0; 162
chr17:79845715@-	-144; 1000	THOC4	64; 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 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	2861	0.35%	1.17%	26.71%	1448	0.67018
anti	7850	0.97%	3.22%	73.29%	3024	1.83884
both	10711	1.32%	4.40%	100.00%	4269	2.50902
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	3765	0.42%	1.34%	29.34%	1448	0.88194
anti	9066	1.00%	3.22%	70.66%	3024	2.12368
both	12831	1.42%	4.56%	100.00%	4269	3.00562

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)
chr8:128231332@-	-1000; 139	AC020688.1	218; 3	346; 3
chr3:49571651@-	-1000; 300	AC104452.1	0; 133	0; 191
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 116	0; 254
chr6:166401114@+	-1000; 249	AL132661.1	0; 115	0; 197
chrUn_gl000220:109077@+	-758; 300	18S	102; 0	253; 0
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
chr2:70315685@-	-1000; 62	AC136007.2	0; 65	0; 94
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 65	0; 88

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)
chr8:128231332@-	-1000; 139	AC020688.1	218; 3	346; 3
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 116	0; 254
chrUn_gl000220:109077@+	-758; 300	18S	102; 0	253; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 115	0; 197
chr3:49571651@-	-1000; 300	AC104452.1	0; 133	0; 191
chr8:101734314@-	-1000; 252	PABPC1	44; 0	170; 0
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

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	32223	3.97%	13.23%	77.39%	6273	3.92198
anti	9415	1.16%	3.86%	22.61%	2486	1.14593
both	41638	5.13%	17.09%	100.00%	8216	5.06792
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	44118	4.88%	15.69%	79.42%	6273	5.36977
anti	11432	1.26%	4.07%	20.58%	2486	1.39143
both	55550	6.14%	19.75%	100.00%	8216	6.7612

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	891; 0	3814; 0
chr1:169101767@-	-127; 1000	NME7	0; 231	0; 442
chr19:39220830@-	-300; 1000	CAPN12	0; 188	0; 348
chrUn_gl000220:110946@+	-300; 539	18S	142; 0	549; 0
chr8:128753674@+	-235; 1000	MYC	115; 0	368; 0
chr15:45010359@+	-278; 1000	B2M	97; 0	212; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 91	0; 162
chr12:20833881@+	-300; 1000	PDE3A	90; 0	134; 0
chr16:18802989@-	-300; 667	ARL6IP1	88; 0	148; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 85	0; 122

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	891; 0	3814; 0
chrUn_gl000220:110946@+	-300; 539	18S	142; 0	549; 0
chr7:5566780@-	-300; 1000	ACTB	84; 0	491; 0
chr1:169101767@-	-127; 1000	NME7	0; 231	0; 442
chr8:128753674@+	-235; 1000	MYC	115; 0	368; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 188	0; 348
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	61; 0	205; 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	32683	4.03%	13.41%	96.33%	20928	1.5026
anti	1246	0.15%	0.51%	3.67%	962	0.0572847
both	33929	4.18%	13.93%	100.00%	21751	1.55988
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	33905	3.75%	12.06%	96.20%	20928	1.55878
anti	1341	0.15%	0.48%	3.80%	962	0.0616523
both	35246	3.90%	12.53%	100.00%	21751	1.62043

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)
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 (=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)
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.