Parameters
input_file: 20090724_LUd4_8_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: 16249
[x-link sites] used in any map: 5470 (33.66%)
[single hits in whole-genome, cDNA counts] total: 16249
[single hits in whole-genome, cDNA counts] used in any map: 5784 (33.69%)

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	1435	8.83%	26.23%	1477	8.60%	25.54%
intron-exon	-300; 300	1097	6.75%	20.05%	1127	6.56%	19.48%
5-ncRNA	-1000; 300	330	2.03%	6.03%	382	2.22%	6.60%
ncRNA-3	-300; 1000	487	3.00%	8.90%	545	3.17%	9.42%
ORF-3UTR	-300; 300	864	5.32%	15.80%	914	5.32%	15.80%
5UTR-ORF	-300; 300	30	0.18%	0.55%	31	0.18%	0.54%
inter-5UTR	-1000; 300	71	0.44%	1.30%	72	0.42%	1.24%
3UTR-inter	-300; 1000	976	6.01%	17.84%	1030	6.00%	17.81%
inter-5	-1000; 300	264	1.62%	4.83%	274	1.60%	4.74%
3-inter	-300; 1000	1407	8.66%	25.72%	1535	8.94%	26.54%
BP best in intron	-300; 100	570	3.51%	10.42%	580	3.38%	10.03%

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	1389	8.55%	25.39%	96.79%	1294	1.04436
anti	46	0.28%	0.84%	3.21%	36	0.0345865
both	1435	8.83%	26.23%	100.00%	1330	1.07895
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	1428	8.32%	24.69%	96.68%	1294	1.07368
anti	49	0.29%	0.85%	3.32%	36	0.0368421
both	1477	8.60%	25.54%	100.00%	1330	1.11053

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; 8	0; 8
chr2:198284903@-	-98; 300	SF3B1	6; 0	7; 0
chr1:186330752@-	-44; 300	TPR	4; 0	4; 0
chrX:151129695@-	-71; 300	GABRE	3; 0	3; 0
chr8:62596596@-	-75; 300	ASPH	3; 0	4; 0
chr7:128411528@+	-300; 107	CALU	3; 0	3; 0
chr5:39021139@-	-49; 300	RICTOR	3; 0	3; 0
chr3:41281934@+	-300; 300	CTNNB1	3; 0	3; 0
chr2:228207535@+	-38; 300	MFF	3; 0	3; 0
chr18:43595867@-	-162; 300	PSTPIP2	3; 0	3; 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; 8	0; 8
chr2:198284903@-	-98; 300	SF3B1	6; 0	7; 0
chr8:62596596@-	-75; 300	ASPH	3; 0	4; 0
chr12:50158717@+	-300; 300	TMBIM6	3; 0	4; 0
chr1:186330752@-	-44; 300	TPR	4; 0	4; 0
chrX:151129695@-	-71; 300	GABRE	3; 0	3; 0
chr7:72858312@-	-73; 300	BAZ1B	1; 0	3; 0
chr7:128411528@+	-300; 107	CALU	3; 0	3; 0
chr5:114878645@-	-272; 300	FEM1C	2; 0	3; 0
chr5:39021139@-	-49; 300	RICTOR	3; 0	3; 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	1054	6.49%	19.27%	96.08%	957	1.05717
anti	43	0.26%	0.79%	3.92%	40	0.0431294
both	1097	6.75%	20.05%	100.00%	997	1.1003
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	1084	6.31%	18.74%	96.18%	957	1.08726
anti	43	0.25%	0.74%	3.82%	40	0.0431294
both	1127	6.56%	19.48%	100.00%	997	1.13039

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)
chr9:131456919@+	-292; 300	SET	11; 0	14; 0
chr5:179041959@-	-293; 300	HNRNPH1	9; 0	10; 0
chr10:112657785@+	-300; 300	PDCD4	9; 0	12; 0
chr4:41699176@+	-300; 300	LIMCH1	7; 0	10; 0
chr15:45009804@+	-300; 277	B2M	6; 0	7; 0
chr8:128753204@+	-241; 235	MYC	4; 0	4; 0
chr5:32711539@+	-300; 171	NPR3	4; 0	4; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	3; 0	3; 0
chr20:34327468@-	-276; 222	RBM39	3; 0	3; 0
chr15:69072480@-	-134; 300	ANP32A	3; 0	3; 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)
chr9:131456919@+	-292; 300	SET	11; 0	14; 0
chr10:112657785@+	-300; 300	PDCD4	9; 0	12; 0
chr5:179041959@-	-293; 300	HNRNPH1	9; 0	10; 0
chr4:41699176@+	-300; 300	LIMCH1	7; 0	10; 0
chr15:45009804@+	-300; 277	B2M	6; 0	7; 0
chr8:128753204@+	-241; 235	MYC	4; 0	4; 0
chr5:32711539@+	-300; 171	NPR3	4; 0	4; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	3; 0	3; 0
chr4:42072205@+	-300; 52	SLC30A9	2; 0	3; 0
chr20:34327468@-	-276; 222	RBM39	3; 0	3; 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	177	1.09%	3.24%	53.64%	88	0.898477
anti	153	0.94%	2.80%	46.36%	110	0.77665
both	330	2.03%	6.03%	100.00%	197	1.67513
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	211	1.23%	3.65%	55.24%	88	1.07107
anti	171	1.00%	2.96%	44.76%	110	0.86802
both	382	2.22%	6.60%	100.00%	197	1.93909

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	62; 0	91; 0
chr8:128231332@-	-1000; 139	AC020688.1	7; 0	7; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 6	0; 6
chr17:57918626@+	-338; 36	hsa-mir-21	6; 0	6; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	6; 0	9; 0
chr4:30795591@-	-1000; 24	RP11-619J20.1	0; 5	0; 5
chr7:4811073@-	-1000; 300	AC092610.1	0; 4	0; 5
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 4	0; 4
chr3:49571651@-	-1000; 300	AC104452.1	0; 4	0; 4
chr13:30083551@+	-1000; 300	AL596114.1	0; 4	0; 4

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	62; 0	91; 0
chr6:71444374@+	-1000; 146	RP11-160A9.2, SMAP1	0; 3	0; 17
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	6; 0	9; 0
chr8:128231332@-	-1000; 139	AC020688.1	7; 0	7; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 6	0; 6
chr17:57918626@+	-338; 36	hsa-mir-21	6; 0	6; 0
chr7:4811073@-	-1000; 300	AC092610.1	0; 4	0; 5
chr4:30795591@-	-1000; 24	RP11-619J20.1	0; 5	0; 5
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 4	0; 4
chr3:49571651@-	-1000; 300	AC104452.1	0; 4	0; 4

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	381	2.34%	6.97%	78.23%	211	1.31834
anti	106	0.65%	1.94%	21.77%	78	0.366782
both	487	3.00%	8.90%	100.00%	289	1.68512
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	434	2.53%	7.50%	79.63%	211	1.50173
anti	111	0.65%	1.92%	20.37%	78	0.384083
both	545	3.17%	9.42%	100.00%	289	1.88581

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	97; 0	126; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 9	0; 12
chrUn_gl000220:118417@+	-300; 1000	28S	8; 0	10; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	6; 0	8; 0
chr9:74622795@-	-128; 1000	RP11-346E17.4	4; 0	4; 0
chr7:44507903@+	-204; 1000	AC004453.8	4; 0	4; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	4; 0	4; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 4	0; 5
chr2:191798136@-	-300; 1000	AC067945.1	0; 4	0; 4
chr12:49412980@+	-300; 1000	AC011603.2	0; 4	0; 4

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	97; 0	126; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 9	0; 12
chrUn_gl000220:118417@+	-300; 1000	28S	8; 0	10; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	6; 0	8; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 4	0; 5
chr1:171639418@-	-194; 1000	RP4-560B9.2	2; 0	5; 0
chr9:74622795@-	-128; 1000	RP11-346E17.4	4; 0	4; 0
chr9:12972840@-	-298; 1000	RP11-382H24.3	3; 0	4; 0
chr7:44507903@+	-204; 1000	AC004453.8	4; 0	4; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	4; 0	4; 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	854	5.26%	15.61%	98.84%	555	1.5115
anti	10	0.06%	0.18%	1.16%	10	0.0176991
both	864	5.32%	15.80%	100.00%	565	1.5292
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	904	5.26%	15.63%	98.91%	555	1.6
anti	10	0.06%	0.17%	1.09%	10	0.0176991
both	914	5.32%	15.80%	100.00%	565	1.6177

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	16; 0	18; 0
chr3:149087560@-	-53; 300	TM4SF1	9; 0	9; 0
chr1:35650053@-	-70; 300	SFPQ	8; 0	8; 0
chr7:128409221@+	-53; 300	CALU	7; 0	7; 0
chr21:44836618@-	-189; 300	SIK1	7; 0	7; 0
chr14:62213803@+	-76; 300	HIF1A	7; 0	8; 0
chr1:54497690@-	-144; 172	TMEM59	7; 0	7; 0
chr7:148700882@-	-209; 300	PDIA4	6; 0	6; 0
chr22:38881684@-	-300; 300	DDX17	6; 0	6; 0
chr2:189876774@+	-211; 300	COL3A1	6; 0	8; 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	16; 0	18; 0
chr3:149087560@-	-53; 300	TM4SF1	9; 0	9; 0
chr2:189876774@+	-211; 300	COL3A1	6; 0	8; 0
chr14:62213803@+	-76; 300	HIF1A	7; 0	8; 0
chr14:50360982@+	-264; 254	ARF6	5; 0	8; 0
chr1:35650053@-	-70; 300	SFPQ	8; 0	8; 0
chr1:207533847@+	-300; 231	CD55	6; 0	8; 0
chr7:128409221@+	-53; 300	CALU	7; 0	7; 0
chr5:122359566@-	-66; 300	PPIC	4; 0	7; 0
chr21:44836618@-	-189; 300	SIK1	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 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	24	0.15%	0.44%	80.00%	23	0.857143
anti	6	0.04%	0.11%	20.00%	5	0.214286
both	30	0.18%	0.55%	100.00%	28	1.07143
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	24	0.14%	0.41%	77.42%	23	0.857143
anti	7	0.04%	0.12%	22.58%	5	0.25
both	31	0.18%	0.54%	100.00%	28	1.10714

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)
chr7:112424879@-	-64; 300	TMEM168	2; 0	2; 0
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 2	0; 2
chrX:47082893@+	-300; 132	PCTK1	1; 0	1; 0
chr9:114937514@-	-87; 51	SUSD1	1; 0	1; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr6:31508971@-	-66; 265	BAT1	1; 0	1; 0
chr6:166401613@+	-250; 300	AL132661.1	0; 1	0; 1
chr6:43139364@+	-223; 271	SRF	1; 0	1; 0
chr6:33168574@+	-177; 300	SLC39A7	1; 0	1; 0
chr5:34915781@+	-151; 110	BRIX1	0; 1	0; 2

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)
chr7:112424879@-	-64; 300	TMEM168	2; 0	2; 0
chr5:34915781@+	-151; 110	BRIX1	0; 1	0; 2
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 2	0; 2
chrX:47082893@+	-300; 132	PCTK1	1; 0	1; 0
chr9:114937514@-	-87; 51	SUSD1	1; 0	1; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr6:31508971@-	-66; 265	BAT1	1; 0	1; 0
chr6:166401613@+	-250; 300	AL132661.1	0; 1	0; 1
chr6:43139364@+	-223; 271	SRF	1; 0	1; 0
chr6:33168574@+	-177; 300	SLC39A7	1; 0	1; 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	23	0.14%	0.42%	32.39%	21	0.370968
anti	48	0.30%	0.88%	67.61%	41	0.774194
both	71	0.44%	1.30%	100.00%	62	1.14516
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	23	0.13%	0.40%	31.94%	21	0.370968
anti	49	0.29%	0.85%	68.06%	41	0.790323
both	72	0.42%	1.24%	100.00%	62	1.16129

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; 4	0; 4
chr17:7387865@+	-741; 109	POLR2A	3; 0	3; 0
chr12:54673914@-	-1000; 62	CBX5	0; 3	0; 3
chr3:129035116@-	-1000; 186	H1FX	0; 2	0; 2
chr19:49122547@+	-1000; 126	SPHK2	0; 2	0; 2
chrX:151999510@+	-1000; 75	NSDHL	0; 1	0; 1
chr9:140100118@+	-1000; 55	NDOR1	0; 1	0; 1
chr9:130374543@+	-1000; 69	STXBP1	1; 0	1; 0
chr9:108210076@+	-1000; 124	FSD1L	0; 1	0; 1
chr9:34179010@+	-1000; 114	UBAP1	1; 0	1; 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; 4	0; 4
chr17:7387865@+	-741; 109	POLR2A	3; 0	3; 0
chr12:54673914@-	-1000; 62	CBX5	0; 3	0; 3
chr4:83295655@-	-1000; 103	HNRNPD	0; 1	0; 2
chr3:129035116@-	-1000; 186	H1FX	0; 2	0; 2
chr19:49122547@+	-1000; 126	SPHK2	0; 2	0; 2
chrX:151999510@+	-1000; 75	NSDHL	0; 1	0; 1
chr9:140100118@+	-1000; 55	NDOR1	0; 1	0; 1
chr9:130374543@+	-1000; 69	STXBP1	1; 0	1; 0
chr9:108210076@+	-1000; 124	FSD1L	0; 1	0; 1

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	851	5.24%	15.56%	87.19%	595	1.25702
anti	125	0.77%	2.29%	12.81%	87	0.184638
both	976	6.01%	17.84%	100.00%	677	1.44165
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	901	5.25%	15.58%	87.48%	595	1.33087
anti	129	0.75%	2.23%	12.52%	87	0.190547
both	1030	6.00%	17.81%	100.00%	677	1.52142

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)
chr17:4848945@-	-123; 1000	PFN1	11; 0	17; 0
chr21:44834393@-	-300; 1000	SIK1	8; 0	9; 0
chr1:100548933@+	-300; 1000	HIAT1	3; 5	3; 5
chr17:79845715@-	-144; 1000	THOC4	7; 0	8; 0
chr17:55757299@+	-195; 1000	MSI2	7; 0	7; 0
chr16:18802989@-	-300; 667	ARL6IP1	7; 0	7; 0
chr14:62214976@+	-300; 1000	HIF1A	7; 0	9; 0
chr8:42978323@+	-152; 1000	AC113191.2	6; 0	7; 0
chr18:8639380@+	-300; 1000	RAB12	6; 0	6; 0
chr17:79476997@-	-300; 1000	ACTG1	6; 0	7; 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)
chr17:4848945@-	-123; 1000	PFN1	11; 0	17; 0
chr21:44834393@-	-300; 1000	SIK1	8; 0	9; 0
chr14:62214976@+	-300; 1000	HIF1A	7; 0	9; 0
chr17:79845715@-	-144; 1000	THOC4	7; 0	8; 0
chr1:100548933@+	-300; 1000	HIAT1	3; 5	3; 5
chr8:42978323@+	-152; 1000	AC113191.2	6; 0	7; 0
chr17:79476997@-	-300; 1000	ACTG1	6; 0	7; 0
chr17:55757299@+	-195; 1000	MSI2	7; 0	7; 0
chr16:87863620@-	-300; 1000	SLC7A5	5; 0	7; 0
chr16:18802989@-	-300; 667	ARL6IP1	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 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	75	0.46%	1.37%	28.41%	58	0.388601
anti	189	1.16%	3.46%	71.59%	136	0.979275
both	264	1.62%	4.83%	100.00%	193	1.36788
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	79	0.46%	1.37%	28.83%	58	0.409326
anti	195	1.14%	3.37%	71.17%	136	1.01036
both	274	1.60%	4.74%	100.00%	193	1.41969

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; 13	0; 15
chr8:128231332@-	-1000; 139	AC020688.1	7; 0	7; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 6	0; 6
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	6; 0	9; 0
chr7:4811073@-	-1000; 300	AC092610.1	0; 4	0; 5
chr6:166401114@+	-1000; 249	AL132661.1	0; 4	0; 4
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 4	0; 4
chr3:49571651@-	-1000; 300	AC104452.1	0; 4	0; 4
chr13:30083551@+	-1000; 300	AL596114.1	0; 4	0; 4
chr17:7387865@+	-741; 109	POLR2A	3; 0	3; 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; 13	0; 15
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	6; 0	9; 0
chr8:128231332@-	-1000; 139	AC020688.1	7; 0	7; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 6	0; 6
chr7:4811073@-	-1000; 300	AC092610.1	0; 4	0; 5
chr6:166401114@+	-1000; 249	AL132661.1	0; 4	0; 4
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 4	0; 4
chr3:49571651@-	-1000; 300	AC104452.1	0; 4	0; 4
chr13:30083551@+	-1000; 300	AL596114.1	0; 4	0; 4
chr17:7387865@+	-741; 109	POLR2A	3; 0	3; 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	1168	7.19%	21.35%	83.01%	739	1.32426
anti	239	1.47%	4.37%	16.99%	149	0.270975
both	1407	8.66%	25.72%	100.00%	882	1.59524
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	1281	7.46%	22.15%	83.45%	739	1.45238
anti	254	1.48%	4.39%	16.55%	149	0.287982
both	1535	8.94%	26.54%	100.00%	882	1.74036

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	97; 0	126; 0
chr1:169101767@-	-127; 1000	NME7	0; 20	0; 22
chr7:5566780@-	-300; 1000	ACTB	15; 0	36; 0
chr17:4848945@-	-123; 1000	PFN1	11; 0	17; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 9	0; 12
chrUn_gl000220:118417@+	-300; 1000	28S	8; 0	10; 0
chr21:44834393@-	-300; 1000	SIK1	8; 0	9; 0
chr1:100548933@+	-300; 1000	HIAT1	3; 5	3; 5
chr17:79845715@-	-144; 1000	THOC4	7; 0	8; 0
chr17:55757299@+	-195; 1000	MSI2	7; 0	7; 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	97; 0	126; 0
chr7:5566780@-	-300; 1000	ACTB	15; 0	36; 0
chr1:169101767@-	-127; 1000	NME7	0; 20	0; 22
chr17:4848945@-	-123; 1000	PFN1	11; 0	17; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 9	0; 12
chrUn_gl000220:118417@+	-300; 1000	28S	8; 0	10; 0
chr21:44834393@-	-300; 1000	SIK1	8; 0	9; 0
chr14:62214976@+	-300; 1000	HIF1A	7; 0	9; 0
chr6:44221831@-	-300; 1000	SLC35B2	0; 4	0; 8
chr17:79845715@-	-144; 1000	THOC4	7; 0	8; 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	547	3.37%	10.00%	95.96%	511	1.02434
anti	23	0.14%	0.42%	4.04%	23	0.0430712
both	570	3.51%	10.42%	100.00%	534	1.06742
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	556	3.24%	9.61%	95.86%	511	1.0412
anti	24	0.14%	0.41%	4.14%	23	0.0449438
both	580	3.38%	10.03%	100.00%	534	1.08614

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)
chr5:43543440@-	-300; 100	PAIP1	5; 0	5; 0
chr2:191537788@+	-300; 36	NAB1	4; 0	4; 0
chr5:65318955@+	-300; 100	ERBB2IP	3; 0	3; 0
chr11:71710833@+	-300; 100	IL18BP	3; 0	3; 0
chr1:70697488@+	-300; 100	SFRS11	3; 0	3; 0
chrX:2864196@-	-300; 22	ARSE	2; 0	2; 0
chr6:136499677@+	-300; 100	PDE7B	2; 0	2; 0
chr6:76357382@+	-300; 62	SENP6	2; 0	2; 0
chr5:179041984@-	-268; 25	HNRNPH1	2; 0	2; 0
chr5:106723912@-	-300; 100	EFNA5	2; 0	2; 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)
chr5:43543440@-	-300; 100	PAIP1	5; 0	5; 0
chr2:191537788@+	-300; 36	NAB1	4; 0	4; 0
chr5:65318955@+	-300; 100	ERBB2IP	3; 0	3; 0
chr11:71710833@+	-300; 100	IL18BP	3; 0	3; 0
chr1:70697488@+	-300; 100	SFRS11	3; 0	3; 0
chrX:2864196@-	-300; 22	ARSE	2; 0	2; 0
chr7:55459161@+	-300; 100	LANCL2	1; 0	2; 0
chr7:30670981@+	-300; 80	GARS	1; 0	2; 0
chr6:136499677@+	-300; 100	PDE7B	2; 0	2; 0
chr6:76357382@+	-300; 62	SENP6	2; 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.