Parameters
input_file: 20090724_LUd3_2_hg19_ensembl59_G_iCLIP_TIA1_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: 0

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 30826
[x-link sites] used in any map: 9999 (32.44%)
[single hits in whole-genome, cDNA counts] total: 30826
[single hits in whole-genome, cDNA counts] used in any map: 10440 (32.43%)

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	2783	9.03%	27.83%	2852	8.86%	27.32%
intron-exon	-300; 300	2262	7.34%	22.62%	2322	7.21%	22.24%
5-ncRNA	-1000; 300	524	1.70%	5.24%	567	1.76%	5.43%
ncRNA-3	-300; 1000	611	1.98%	6.11%	678	2.11%	6.49%
ORF-3UTR	-300; 300	1570	5.09%	15.70%	1657	5.15%	15.87%
5UTR-ORF	-300; 300	83	0.27%	0.83%	85	0.26%	0.81%
inter-5UTR	-1000; 300	127	0.41%	1.27%	128	0.40%	1.23%
3UTR-inter	-300; 1000	1664	5.40%	16.64%	1748	5.43%	16.74%
inter-5	-1000; 300	456	1.48%	4.56%	485	1.51%	4.65%
3-inter	-300; 1000	2249	7.30%	22.49%	2423	7.53%	23.21%
BP best in intron	-300; 100	1215	3.94%	12.15%	1261	3.92%	12.08%

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	2707	8.78%	27.07%	97.27%	2476	1.07208
anti	76	0.25%	0.76%	2.73%	52	0.030099
both	2783	9.03%	27.83%	100.00%	2525	1.10218
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	2764	8.59%	26.48%	96.91%	2476	1.09465
anti	88	0.27%	0.84%	3.09%	52	0.0348515
both	2852	8.86%	27.32%	100.00%	2525	1.1295

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; 13	0; 23
chr7:128411528@+	-300; 107	CALU	10; 0	13; 0
chr3:41281934@+	-300; 300	CTNNB1	9; 0	9; 0
chr12:50158717@+	-300; 300	TMBIM6	9; 0	11; 0
chr6:18225699@-	-124; 192	DEK	7; 0	8; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 7	0; 7
chr5:10401598@+	-300; 185	MARCH6	7; 0	7; 0
chr7:90001542@+	-37; 300	GTPBP10	6; 0	6; 0
chr5:179048241@-	-78; 103	HNRNPH1	6; 0	7; 0
chr15:37393091@-	-204; 194	MEIS2	0; 5	0; 5

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:45976739@+	-281; 300	MMACHC	0; 13	0; 23
chr7:128411528@+	-300; 107	CALU	10; 0	13; 0
chr12:50158717@+	-300; 300	TMBIM6	9; 0	11; 0
chr3:41281934@+	-300; 300	CTNNB1	9; 0	9; 0
chr6:18225699@-	-124; 192	DEK	7; 0	8; 0
chr5:179048241@-	-78; 103	HNRNPH1	6; 0	7; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 7	0; 7
chr5:10401598@+	-300; 185	MARCH6	7; 0	7; 0
chr7:90001542@+	-37; 300	GTPBP10	6; 0	6; 0
chr15:37393091@-	-204; 194	MEIS2	0; 5	0; 5

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	2194	7.12%	21.94%	96.99%	1979	1.07813
anti	68	0.22%	0.68%	3.01%	57	0.0334152
both	2262	7.34%	22.62%	100.00%	2035	1.11155
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	2254	7.00%	21.59%	97.07%	1979	1.10762
anti	68	0.21%	0.65%	2.93%	57	0.0334152
both	2322	7.21%	22.24%	100.00%	2035	1.14103

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	18; 0	19; 0
chr9:131456919@+	-292; 300	SET	17; 0	22; 0
chr16:29821927@-	-300; 92	AC009133.4	0; 6	0; 6
chr10:112657785@+	-300; 300	PDCD4	6; 0	11; 0
chr1:26227577@-	-160; 260	STMN1	6; 0	6; 0
chr5:179041959@-	-293; 300	HNRNPH1	5; 0	6; 0
chr11:2966875@-	-300; 300	NAP1L4	5; 0	5; 0
chr11:4139549@+	-300; 71	RRM1	5; 0	6; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	4; 0	4; 0
chr5:180665662@-	-187; 212	GNB2L1	4; 0	6; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr9:131456919@+	-292; 300	SET	17; 0	22; 0
chr15:45009804@+	-300; 277	B2M	18; 0	19; 0
chr10:112657785@+	-300; 300	PDCD4	6; 0	11; 0
chr5:180665662@-	-187; 212	GNB2L1	4; 0	6; 0
chr5:179041959@-	-293; 300	HNRNPH1	5; 0	6; 0
chr16:29821927@-	-300; 92	AC009133.4	0; 6	0; 6
chr11:4139549@+	-300; 71	RRM1	5; 0	6; 0
chr1:26227577@-	-160; 260	STMN1	6; 0	6; 0
chr11:2966875@-	-300; 300	NAP1L4	5; 0	5; 0
chr1:87329287@-	-300; 219	RP4-604K5.1	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 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	265	0.86%	2.65%	50.57%	154	0.777126
anti	259	0.84%	2.59%	49.43%	187	0.759531
both	524	1.70%	5.24%	100.00%	341	1.53666
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	299	0.93%	2.86%	52.73%	154	0.876833
anti	268	0.83%	2.57%	47.27%	187	0.785924
both	567	1.76%	5.43%	100.00%	341	1.66276

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	69; 0	84; 0
chr17:57918626@+	-338; 36	hsa-mir-21	13; 0	15; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 12	0; 12
chr13:30083551@+	-1000; 300	AL596114.1	0; 10	0; 11
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	8; 0	13; 0
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 7	0; 7
chr8:128231332@-	-1000; 139	AC020688.1	6; 0	6; 0
chr3:129034234@+	-1000; 123	RP13-685P2.5	0; 6	0; 7
chr17:74730198@+	-119; 300	AC005837.2	0; 6	0; 7
chr3:49571651@-	-1000; 300	AC104452.1	0; 5	0; 5

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	69; 0	84; 0
chr17:57918626@+	-338; 36	hsa-mir-21	13; 0	15; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	8; 0	13; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 12	0; 12
chr13:30083551@+	-1000; 300	AL596114.1	0; 10	0; 11
chr3:129034234@+	-1000; 123	RP13-685P2.5	0; 6	0; 7
chr17:74730198@+	-119; 300	AC005837.2	0; 6	0; 7
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 7	0; 7
chr8:128231332@-	-1000; 139	AC020688.1	6; 0	6; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	4; 0	6; 0

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

RNAmap 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	393	1.27%	3.93%	64.32%	226	1.0155
anti	218	0.71%	2.18%	35.68%	162	0.563307
both	611	1.98%	6.11%	100.00%	387	1.57881
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	450	1.40%	4.31%	66.37%	226	1.16279
anti	228	0.71%	2.18%	33.63%	162	0.589147
both	678	2.11%	6.49%	100.00%	387	1.75194

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	99; 0	136; 0
chrUn_gl000220:118417@+	-300; 1000	28S	13; 0	19; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 9	0; 9
chr8:144939422@+	-300; 1000	AC105049.1	0; 6	0; 6
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	6; 0	8; 0
chr3:47705424@+	-155; 1000	RP11-395P16.1	0; 6	0; 6
chr10:112658486@-	-300; 1000	NCRNA00081	0; 6	0; 11
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	5; 0	7; 0
chr5:131528501@+	-274; 1000	AC063976.4	0; 4	0; 4
chr2:66666218@-	-178; 1000	AC092669.4	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	99; 0	136; 0
chrUn_gl000220:118417@+	-300; 1000	28S	13; 0	19; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 6	0; 11
chr3:14530617@-	-300; 1000	GRIP2	0; 9	0; 9
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	6; 0	8; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	5; 0	7; 0
chr8:144939422@+	-300; 1000	AC105049.1	0; 6	0; 6
chr3:47705424@+	-155; 1000	RP11-395P16.1	0; 6	0; 6
chr2:181737592@-	-274; 1000	FTHL20	3; 0	5; 0
chr5:131528501@+	-274; 1000	AC063976.4	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 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	1547	5.02%	15.47%	98.54%	874	1.7343
anti	23	0.07%	0.23%	1.46%	20	0.0257848
both	1570	5.09%	15.70%	100.00%	892	1.76009
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	1633	5.07%	15.64%	98.55%	874	1.83072
anti	24	0.07%	0.23%	1.45%	20	0.0269058
both	1657	5.15%	15.87%	100.00%	892	1.85762

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	24; 0	39; 0
chr3:149087560@-	-53; 300	TM4SF1	20; 0	24; 0
chr1:54497690@-	-144; 172	TMEM59	17; 0	20; 0
chr1:35650053@-	-70; 300	SFPQ	15; 0	16; 0
chr21:27253823@-	-129; 300	APP	12; 0	13; 0
chr7:148700882@-	-209; 300	PDIA4	11; 0	12; 0
chr6:30692174@+	-300; 300	TUBB	11; 0	12; 0
chr5:179156650@+	-145; 300	CANX	11; 0	11; 0
chr22:38881684@-	-300; 300	DDX17	11; 0	13; 0
chr14:62213803@+	-76; 300	HIF1A	11; 0	11; 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	24; 0	39; 0
chr3:149087560@-	-53; 300	TM4SF1	20; 0	24; 0
chr1:54497690@-	-144; 172	TMEM59	17; 0	20; 0
chr1:35650053@-	-70; 300	SFPQ	15; 0	16; 0
chr22:38881684@-	-300; 300	DDX17	11; 0	13; 0
chr21:27253823@-	-129; 300	APP	12; 0	13; 0
chr7:148700882@-	-209; 300	PDIA4	11; 0	12; 0
chr6:30692174@+	-300; 300	TUBB	11; 0	12; 0
chrX:102931085@-	-300; 300	MORF4L2	10; 0	11; 0
chr9:117360023@+	-87; 300	ATP6V1G1	7; 0	11; 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	72	0.23%	0.72%	86.75%	69	0.935065
anti	11	0.04%	0.11%	13.25%	8	0.142857
both	83	0.27%	0.83%	100.00%	77	1.07792
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	74	0.23%	0.71%	87.06%	69	0.961039
anti	11	0.03%	0.11%	12.94%	8	0.142857
both	85	0.26%	0.81%	100.00%	77	1.1039

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; 3	0; 3
chr7:135612307@+	-300; 127	AC015987.2	0; 2	0; 2
chr2:136873508@-	-152; 300	CXCR4	2; 0	2; 0
chr2:20251280@-	-254; 55	LAPTM4A	2; 0	2; 0
chr17:4851688@-	-300; 66	PFN1	2; 0	2; 0
chrX:106960040@-	-162; 61	TSC22D3	1; 0	1; 0
chrX:48434573@+	-51; 117	RBM3	1; 0	1; 0
chr9:117267080@-	-300; 300	DFNB31	1; 0	1; 0
chr9:89561693@-	-205; 300	GAS1	1; 0	1; 0
chr8:119123284@-	-300; 300	EXT1	1; 0	2; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 3	0; 3
chr8:119123284@-	-300; 300	EXT1	1; 0	2; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 2	0; 2
chr3:33155569@+	-50; 235	CRTAP	1; 0	2; 0
chr2:136873508@-	-152; 300	CXCR4	2; 0	2; 0
chr2:20251280@-	-254; 55	LAPTM4A	2; 0	2; 0
chr17:4851688@-	-300; 66	PFN1	2; 0	2; 0
chrX:106960040@-	-162; 61	TSC22D3	1; 0	1; 0
chrX:48434573@+	-51; 117	RBM3	1; 0	1; 0
chr9:117267080@-	-300; 300	DFNB31	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	38	0.12%	0.38%	29.92%	37	0.348624
anti	89	0.29%	0.89%	70.08%	72	0.816514
both	127	0.41%	1.27%	100.00%	109	1.16514
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	38	0.12%	0.36%	29.69%	37	0.348624
anti	90	0.28%	0.86%	70.31%	72	0.825688
both	128	0.40%	1.23%	100.00%	109	1.17431

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; 10	0; 10
chr15:89878025@-	-1000; 61	POLG	0; 3	0; 3
chr8:101734314@-	-1000; 252	PABPC1	2; 0	2; 0
chr8:33370702@-	-1000; 286	C8orf41	0; 2	0; 2
chr8:71485680@+	-1000; 300	AC120194.1	0; 2	0; 2
chr20:47894962@-	-1000; 248	ZNFX1	0; 2	0; 2
chr11:62623517@+	-1000; 112	SLC3A2	0; 2	0; 2
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 2	0; 2
chr1:185126211@+	-1000; 117	C1orf26	0; 2	0; 2
chrY:15592552@-	-1000; 300	UTY	0; 1	0; 1

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; 10	0; 10
chr15:89878025@-	-1000; 61	POLG	0; 3	0; 3
chr8:101734314@-	-1000; 252	PABPC1	2; 0	2; 0
chr8:33370702@-	-1000; 286	C8orf41	0; 2	0; 2
chr8:71485680@+	-1000; 300	AC120194.1	0; 2	0; 2
chr6:30294255@+	-1000; 258	TRIM39	0; 1	0; 2
chr20:47894962@-	-1000; 248	ZNFX1	0; 2	0; 2
chr11:62623517@+	-1000; 112	SLC3A2	0; 2	0; 2
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 2	0; 2
chr1:185126211@+	-1000; 117	C1orf26	0; 2	0; 2

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	1431	4.64%	14.31%	86.00%	898	1.37596
anti	233	0.76%	2.33%	14.00%	148	0.224038
both	1664	5.40%	16.64%	100.00%	1040	1.6
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	1501	4.66%	14.38%	85.87%	898	1.44327
anti	247	0.77%	2.37%	14.13%	148	0.2375
both	1748	5.43%	16.74%	100.00%	1040	1.68077

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)
chr13:113978542@-	-129; 1000	GRTP1	0; 18	0; 19
chr19:39220830@-	-300; 1000	CAPN12	0; 16	0; 16
chr9:124095121@+	-120; 1000	GSN	11; 0	12; 0
chr17:79476997@-	-300; 1000	ACTG1	11; 0	12; 0
chr8:128753674@+	-235; 1000	MYC	10; 0	11; 0
chr17:79845715@-	-144; 1000	THOC4	9; 0	13; 0
chr16:18802989@-	-300; 667	ARL6IP1	9; 0	9; 0
chr13:30083545@-	-300; 1000	SLC7A1	9; 0	10; 0
chr11:65622306@-	-249; 1000	CFL1	9; 0	12; 0
chr3:145787225@-	-300; 127	PLOD2	8; 0	10; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr13:113978542@-	-129; 1000	GRTP1	0; 18	0; 19
chr19:39220830@-	-300; 1000	CAPN12	0; 16	0; 16
chr17:79845715@-	-144; 1000	THOC4	9; 0	13; 0
chr9:124095121@+	-120; 1000	GSN	11; 0	12; 0
chr17:79476997@-	-300; 1000	ACTG1	11; 0	12; 0
chr11:65622306@-	-249; 1000	CFL1	9; 0	12; 0
chr8:128753674@+	-235; 1000	MYC	10; 0	11; 0
chr3:145787225@-	-300; 127	PLOD2	8; 0	10; 0
chr17:4848518@+	-104; 1000	RNF167	0; 4	0; 10
chr13:30083545@-	-300; 1000	SLC7A1	9; 0	10; 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	114	0.37%	1.14%	25.00%	100	0.336283
anti	342	1.11%	3.42%	75.00%	240	1.00885
both	456	1.48%	4.56%	100.00%	339	1.34513
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	128	0.40%	1.23%	26.39%	100	0.377581
anti	357	1.11%	3.42%	73.61%	240	1.0531
both	485	1.51%	4.65%	100.00%	339	1.43068

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; 20	0; 26
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 12	0; 12
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 10
chr13:30083551@+	-1000; 300	AL596114.1	0; 10	0; 11
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	8; 0	13; 0
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 7	0; 7
chr8:128231332@-	-1000; 139	AC020688.1	6; 0	6; 0
chr3:129034234@+	-1000; 123	RP13-685P2.5	0; 6	0; 7
chr17:74730198@+	-119; 300	AC005837.2	0; 6	0; 7
chr3:49571651@-	-1000; 300	AC104452.1	0; 5	0; 5

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 20	0; 26
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	8; 0	13; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 12	0; 12
chr13:30083551@+	-1000; 300	AL596114.1	0; 10	0; 11
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 10
chr3:129034234@+	-1000; 123	RP13-685P2.5	0; 6	0; 7
chr17:74730198@+	-119; 300	AC005837.2	0; 6	0; 7
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 7	0; 7
chr8:128231332@-	-1000; 139	AC020688.1	6; 0	6; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 5	0; 5

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	1810	5.87%	18.10%	80.48%	1090	1.32795
anti	439	1.42%	4.39%	19.52%	282	0.322084
both	2249	7.30%	22.49%	100.00%	1363	1.65004
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	1963	6.10%	18.80%	81.02%	1090	1.44021
anti	460	1.43%	4.41%	18.98%	282	0.337491
both	2423	7.53%	23.21%	100.00%	1363	1.7777

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	99; 0	136; 0
chr7:5566780@-	-300; 1000	ACTB	22; 0	42; 0
chr1:169101767@-	-127; 1000	NME7	0; 20	0; 20
chr13:113978542@-	-129; 1000	GRTP1	0; 18	0; 19
chr19:39220830@-	-300; 1000	CAPN12	0; 16	0; 16
chr1:153516087@-	-156; 923	S100A4	14; 0	19; 0
chrUn_gl000220:118417@+	-300; 1000	28S	13; 0	19; 0
chr9:124095121@+	-120; 1000	GSN	11; 0	12; 0
chr17:79476997@-	-300; 1000	ACTG1	11; 0	12; 0
chr8:128753674@+	-235; 1000	MYC	10; 0	11; 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	99; 0	136; 0
chr7:5566780@-	-300; 1000	ACTB	22; 0	42; 0
chr1:169101767@-	-127; 1000	NME7	0; 20	0; 20
chrUn_gl000220:118417@+	-300; 1000	28S	13; 0	19; 0
chr13:113978542@-	-129; 1000	GRTP1	0; 18	0; 19
chr1:153516087@-	-156; 923	S100A4	14; 0	19; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 16	0; 16
chr17:79845715@-	-144; 1000	THOC4	9; 0	13; 0
chr9:124095121@+	-120; 1000	GSN	11; 0	12; 0
chr17:79476997@-	-300; 1000	ACTG1	11; 0	12; 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	1186	3.85%	11.86%	97.61%	1117	1.03762
anti	29	0.09%	0.29%	2.39%	26	0.0253718
both	1215	3.94%	12.15%	100.00%	1143	1.06299
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	1232	3.83%	11.80%	97.70%	1117	1.07787
anti	29	0.09%	0.28%	2.30%	26	0.0253718
both	1261	3.92%	12.08%	100.00%	1143	1.10324

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)
chr5:10401919@+	-300; 100	MARCH6	8; 0	8; 0
chr9:86584384@-	-300; 90	HNRNPK	5; 0	7; 0
chr11:4139437@+	-300; 100	RRM1	5; 0	6; 0
chr12:32861040@+	-300; 44	DNM1L	0; 4	0; 4
chr5:179048854@-	-300; 100	HNRNPH1	3; 0	4; 0
chr5:111067169@-	-300; 100	C5orf13	3; 0	3; 0
chr17:38288172@+	-113; 100	MSL1	3; 0	3; 0
chr14:70237083@+	-300; 98	SFRS5	3; 0	3; 0
chr13:111303470@-	-300; 24	CARS2	3; 0	3; 0
chr1:1326494@-	-300; 100	CCNL2	3; 0	3; 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)
chr5:10401919@+	-300; 100	MARCH6	8; 0	8; 0
chr9:86584384@-	-300; 90	HNRNPK	5; 0	7; 0
chr11:4139437@+	-300; 100	RRM1	5; 0	6; 0
chr5:179048854@-	-300; 100	HNRNPH1	3; 0	4; 0
chr12:32861040@+	-300; 44	DNM1L	0; 4	0; 4
chrX:153225889@-	-300; 25	HCFC1	1; 0	3; 0
chr5:179045370@-	-300; 47	HNRNPH1	2; 0	3; 0
chr5:111067169@-	-300; 100	C5orf13	3; 0	3; 0
chr3:180326196@+	-178; 100	TTC14	2; 0	3; 0
chr2:61413393@+	-229; 100	AHSA2	2; 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.