Parameters
input_file: 20090724_LUd3_5_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: 36252
[x-link sites] used in any map: 11620 (32.05%)
[single hits (=G+T), cDNA counts] total: 36252
[single hits (=G+T), cDNA counts] used in any map: 12375 (32.31%)

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	3417	9.43%	29.41%	3520	9.19%	28.44%
intron-exon	-300; 300	2529	6.98%	21.76%	2602	6.79%	21.03%
5-ncRNA	-1000; 300	736	2.03%	6.33%	813	2.12%	6.57%
ncRNA-3	-300; 1000	816	2.25%	7.02%	942	2.46%	7.61%
ORF-3UTR	-300; 300	1714	4.73%	14.75%	1830	4.78%	14.79%
5UTR-ORF	-300; 300	90	0.25%	0.77%	93	0.24%	0.75%
inter-5UTR	-1000; 300	222	0.61%	1.91%	244	0.64%	1.97%
3UTR-inter	-300; 1000	1709	4.71%	14.71%	1833	4.79%	14.81%
inter-5	-1000; 300	682	1.88%	5.87%	728	1.90%	5.88%
3-inter	-300; 1000	2467	6.81%	21.23%	2797	7.30%	22.60%
BP best in intron	-300; 100	1352	3.73%	11.64%	1394	3.64%	11.26%

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	3332	9.19%	28.67%	97.51%	3041	1.06863
anti	85	0.23%	0.73%	2.49%	77	0.0272611
both	3417	9.43%	29.41%	100.00%	3118	1.09589
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	3430	8.96%	27.72%	97.44%	3041	1.10006
anti	90	0.23%	0.73%	2.56%	77	0.0288647
both	3520	9.19%	28.44%	100.00%	3118	1.12893

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)
chr3:41281934@+	-300; 300	CTNNB1	13; 0	14; 0
chr11:85374566@-	-182; 300	CREBZF	8; 0	8; 0
chr7:128411528@+	-300; 107	CALU	6; 0	8; 0
chr4:24529096@-	-284; 300	DHX15	5; 0	5; 0
chr1:45976739@+	-281; 300	MMACHC	0; 5	0; 6
chr5:177637967@-	-300; 300	AGXT2L2	0; 4	0; 4
chr5:10401598@+	-300; 185	MARCH6	4; 0	4; 0
chr2:133015100@-	-221; 224	NCRNA00164	4; 0	4; 0
chr2:68405987@-	-300; 300	PPP3R1	4; 0	5; 0
chr2:61413216@+	-51; 182	AHSA2	4; 0	5; 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)
chr3:41281934@+	-300; 300	CTNNB1	13; 0	14; 0
chr7:128411528@+	-300; 107	CALU	6; 0	8; 0
chr15:45007922@+	-151; 300	B2M	3; 0	8; 0
chr11:85374566@-	-182; 300	CREBZF	8; 0	8; 0
chr1:45976739@+	-281; 300	MMACHC	0; 5	0; 6
chr4:24529096@-	-284; 300	DHX15	5; 0	5; 0
chr2:68405987@-	-300; 300	PPP3R1	4; 0	5; 0
chr2:61413216@+	-51; 182	AHSA2	4; 0	5; 0
chr13:111555820@-	-33; 300	ANKRD10	4; 0	5; 0
chr6:18225699@-	-124; 192	DEK	3; 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 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	2435	6.72%	20.96%	96.28%	2167	1.08174
anti	94	0.26%	0.81%	3.72%	84	0.0417592
both	2529	6.98%	21.76%	100.00%	2251	1.1235
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	2506	6.54%	20.25%	96.31%	2167	1.11328
anti	96	0.25%	0.78%	3.69%	84	0.0426477
both	2602	6.79%	21.03%	100.00%	2251	1.15593

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)
chr9:131456919@+	-292; 300	SET	24; 0	34; 0
chr15:45009804@+	-300; 277	B2M	11; 0	12; 0
chr5:179041959@-	-293; 300	HNRNPH1	10; 0	12; 0
chr17:57915655@+	-300; 51	TMEM49	10; 0	10; 0
chr10:112657785@+	-300; 300	PDCD4	10; 0	10; 0
chr7:5568349@-	-150; 219	ACTB	6; 0	6; 0
chr16:29821927@-	-300; 92	AC009133.4	0; 6	0; 6
chr7:26230747@-	-300; 68	HNRNPA2B1	5; 0	5; 0
chr5:172461401@+	-300; 249	ATP6V0E1	5; 0	5; 0
chr17:1248792@-	-300; 300	YWHAE	5; 0	5; 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)
chr9:131456919@+	-292; 300	SET	24; 0	34; 0
chr5:179041959@-	-293; 300	HNRNPH1	10; 0	12; 0
chr15:45009804@+	-300; 277	B2M	11; 0	12; 0
chr17:57915655@+	-300; 51	TMEM49	10; 0	10; 0
chr10:112657785@+	-300; 300	PDCD4	10; 0	10; 0
chr7:5568349@-	-150; 219	ACTB	6; 0	6; 0
chr16:29821927@-	-300; 92	AC009133.4	0; 6	0; 6
chr7:26230747@-	-300; 68	HNRNPA2B1	5; 0	5; 0
chr5:172461401@+	-300; 249	ATP6V0E1	5; 0	5; 0
chr17:1248792@-	-300; 300	YWHAE	5; 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	379	1.05%	3.26%	51.49%	199	0.823913
anti	357	0.98%	3.07%	48.51%	262	0.776087
both	736	2.03%	6.33%	100.00%	460	1.6
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	447	1.17%	3.61%	54.98%	199	0.971739
anti	366	0.96%	2.96%	45.02%	262	0.795652
both	813	2.12%	6.57%	100.00%	460	1.76739

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	69; 0	84; 0
chr17:57918626@+	-338; 36	hsa-mir-21	19; 0	34; 0
chrUn_gl000220:109077@+	-758; 300	18S	16; 0	16; 0
chr13:30083551@+	-1000; 300	AL596114.1	0; 13	0; 14
chrUn_gl000220:113347@+	-585; 300	28S	11; 0	12; 0
chr8:128231332@-	-1000; 139	AC020688.1	11; 0	11; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 10	0; 11
chr12:7052978@+	-748; 31	U7-ENSG00000238923	9; 0	16; 0
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 7	0; 7
chr5:25190790@+	-1000; 176	RP11-184E9.1	0; 5	0; 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)
chr11:65269806@+	-1000; 29	MALAT1	69; 0	84; 0
chr17:57918626@+	-338; 36	hsa-mir-21	19; 0	34; 0
chrUn_gl000220:109077@+	-758; 300	18S	16; 0	16; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	9; 0	16; 0
chr13:30083551@+	-1000; 300	AL596114.1	0; 13	0; 14
chrUn_gl000220:113347@+	-585; 300	28S	11; 0	12; 0
chr8:128231332@-	-1000; 139	AC020688.1	11; 0	11; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 10	0; 11
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	4; 0	7; 0
chr12:13593934@-	-1000; 59	5S_rRNA-ENSG00000201476	1; 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 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	545	1.50%	4.69%	66.79%	283	1.11224
anti	271	0.75%	2.33%	33.21%	208	0.553061
both	816	2.25%	7.02%	100.00%	490	1.66531
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	665	1.74%	5.37%	70.59%	283	1.35714
anti	277	0.72%	2.24%	29.41%	208	0.565306
both	942	2.46%	7.61%	100.00%	490	1.92245

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	148; 0	219; 0
chrUn_gl000220:110946@+	-300; 539	18S	20; 0	28; 0
chrUn_gl000220:118417@+	-300; 1000	28S	18; 0	21; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 13	0; 13
chr3:14530617@-	-300; 1000	GRIP2	0; 8	0; 9
chr11:10823012@-	-71; 189	EIF4G2, snoU97	6; 0	6; 0
chr1:148604906@-	-83; 1000	U1-ENSG00000207205	6; 0	7; 0
chr1:21070455@+	-63; 1000	RP5-930J4.4	0; 6	0; 6
chr1:17733878@+	-33; 1000	RP1-20B21.4	0; 6	0; 6
chrY:21154137@-	-229; 1000	CD24L4, NCRNA00185	5; 0	5; 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)
chr11:65271080@+	-300; 1000	MALAT1	148; 0	219; 0
chrUn_gl000220:110946@+	-300; 539	18S	20; 0	28; 0
chrUn_gl000220:118417@+	-300; 1000	28S	18; 0	21; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 13	0; 13
chr3:14530617@-	-300; 1000	GRIP2	0; 8	0; 9
chr14:74055527@-	-37; 1000	AC005225.1	2; 0	9; 0
chr1:148604906@-	-83; 1000	U1-ENSG00000207205	6; 0	7; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	5; 0	6; 0
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	4; 0	6; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	2; 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 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	1680	4.63%	14.46%	98.02%	957	1.70732
anti	34	0.09%	0.29%	1.98%	27	0.0345528
both	1714	4.73%	14.75%	100.00%	984	1.74187
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	1793	4.68%	14.49%	97.98%	957	1.82215
anti	37	0.10%	0.30%	2.02%	27	0.0376016
both	1830	4.78%	14.79%	100.00%	984	1.85976

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	37; 0	55; 0
chr1:54497690@-	-144; 172	TMEM59	22; 0	34; 0
chr3:149087560@-	-53; 300	TM4SF1	21; 0	29; 0
chrX:70520705@+	-300; 156	NONO	15; 0	19; 0
chr6:30692174@+	-300; 300	TUBB	15; 0	17; 0
chr2:136872205@-	-300; 144	CXCR4	14; 0	15; 0
chr10:102120690@+	-100; 300	SCD	13; 0	15; 0
chr1:35650053@-	-70; 300	SFPQ	11; 0	12; 0
chr5:122359566@-	-66; 300	PPIC	10; 0	12; 0
chr20:48741591@-	-62; 300	TMEM189	10; 0	11; 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	37; 0	55; 0
chr1:54497690@-	-144; 172	TMEM59	22; 0	34; 0
chr3:149087560@-	-53; 300	TM4SF1	21; 0	29; 0
chrX:70520705@+	-300; 156	NONO	15; 0	19; 0
chr6:30692174@+	-300; 300	TUBB	15; 0	17; 0
chr2:136872205@-	-300; 144	CXCR4	14; 0	15; 0
chr10:102120690@+	-100; 300	SCD	13; 0	15; 0
chr5:122359566@-	-66; 300	PPIC	10; 0	12; 0
chr17:4849191@-	-50; 123	PFN1	8; 0	12; 0
chr1:35650053@-	-70; 300	SFPQ	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 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	83	0.23%	0.71%	92.22%	75	1.05063
anti	7	0.02%	0.06%	7.78%	4	0.0886076
both	90	0.25%	0.77%	100.00%	79	1.13924
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	86	0.22%	0.69%	92.47%	75	1.08861
anti	7	0.02%	0.06%	7.53%	4	0.0886076
both	93	0.24%	0.75%	100.00%	79	1.17722

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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 4	0; 4
chr6:24718895@-	-300; 64	C6orf62	3; 0	3; 0
chr6:33168574@+	-177; 300	SLC39A7	2; 0	2; 0
chr3:98620169@-	-182; 102	DCBLD2	2; 0	2; 0
chr22:38884251@-	-142; 187	DDX17	2; 0	2; 0
chr2:136873508@-	-152; 300	CXCR4	2; 0	2; 0
chr12:40499609@-	-141; 278	SLC2A13	2; 0	2; 0
chr1:12677352@-	-192; 97	DHRS3	2; 0	2; 0
chrX:48434573@+	-51; 117	RBM3	1; 0	1; 0
chr9:131709581@-	-215; 300	DOLK	1; 0	1; 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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 4	0; 4
chr6:24718895@-	-300; 64	C6orf62	3; 0	3; 0
chr8:101733810@-	-252; 96	PABPC1	1; 0	2; 0
chr6:42237327@-	-129; 300	TRERF1	1; 0	2; 0
chr6:33168574@+	-177; 300	SLC39A7	2; 0	2; 0
chr5:179050164@-	-215; 158	HNRNPH1	1; 0	2; 0
chr3:98620169@-	-182; 102	DCBLD2	2; 0	2; 0
chr22:38884251@-	-142; 187	DDX17	2; 0	2; 0
chr2:136873508@-	-152; 300	CXCR4	2; 0	2; 0
chr12:40499609@-	-141; 278	SLC2A13	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.

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	83	0.23%	0.71%	37.39%	67	0.488235
anti	139	0.38%	1.20%	62.61%	103	0.817647
both	222	0.61%	1.91%	100.00%	170	1.30588
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	97	0.25%	0.78%	39.75%	67	0.570588
anti	147	0.38%	1.19%	60.25%	103	0.864706
both	244	0.64%	1.97%	100.00%	170	1.43529

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)
chr8:101734314@-	-1000; 252	PABPC1	14; 0	25; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 11
chr8:33370702@-	-1000; 286	C8orf41	0; 6	0; 6
chr20:47894962@-	-1000; 248	ZNFX1	0; 4	0; 5
chr13:41635409@+	-1000; 200	WBP4	0; 4	0; 6
chr11:62623517@+	-1000; 112	SLC3A2	0; 4	0; 4
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 4	0; 4
chr6:30585485@+	-1000; 67	MRPS18B	0; 3	0; 3
chr1:173837219@+	-1000; 87	ZBTB37	0; 3	0; 5
chr9:100745637@+	-1000; 100	ANP32B	2; 0	2; 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)
chr8:101734314@-	-1000; 252	PABPC1	14; 0	25; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 11
chr8:33370702@-	-1000; 286	C8orf41	0; 6	0; 6
chr13:41635409@+	-1000; 200	WBP4	0; 4	0; 6
chr20:47894962@-	-1000; 248	ZNFX1	0; 4	0; 5
chr1:173837219@+	-1000; 87	ZBTB37	0; 3	0; 5
chr11:62623517@+	-1000; 112	SLC3A2	0; 4	0; 4
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 4	0; 4
chr6:30585485@+	-1000; 67	MRPS18B	0; 3	0; 3
chr17:4843462@-	-1000; 129	SLC25A11	0; 2	0; 3

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	1435	3.96%	12.35%	83.97%	890	1.36407
anti	274	0.76%	2.36%	16.03%	172	0.260456
both	1709	4.71%	14.71%	100.00%	1052	1.62452
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	1540	4.02%	12.44%	84.02%	890	1.46388
anti	293	0.77%	2.37%	15.98%	172	0.278517
both	1833	4.79%	14.81%	100.00%	1052	1.7424

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)
chr17:79845715@-	-144; 1000	THOC4	18; 0	33; 0
chr13:113978542@-	-129; 1000	GRTP1	0; 15	0; 20
chr18:25530928@-	-300; 1000	CDH2	13; 0	16; 0
chr13:30083545@-	-300; 1000	SLC7A1	13; 0	14; 0
chr19:18390561@-	-300; 1000	JUND	11; 0	20; 0
chr17:79476997@-	-300; 1000	ACTG1	10; 0	24; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 9	0; 9
chr17:4848518@+	-104; 1000	RNF167	1; 8	1; 12
chr14:62214976@+	-300; 1000	HIF1A	9; 0	12; 0
chr12:104744062@+	-300; 1000	TXNRD1	9; 0	11; 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)
chr17:79845715@-	-144; 1000	THOC4	18; 0	33; 0
chr17:79476997@-	-300; 1000	ACTG1	10; 0	24; 0
chr19:18390561@-	-300; 1000	JUND	11; 0	20; 0
chr13:113978542@-	-129; 1000	GRTP1	0; 15	0; 20
chr18:25530928@-	-300; 1000	CDH2	13; 0	16; 0
chr13:30083545@-	-300; 1000	SLC7A1	13; 0	14; 0
chr17:4848518@+	-104; 1000	RNF167	1; 8	1; 12
chr14:62214976@+	-300; 1000	HIF1A	9; 0	12; 0
chr12:104744062@+	-300; 1000	TXNRD1	9; 0	11; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 8	0; 10

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	220	0.61%	1.89%	32.26%	149	0.463158
anti	462	1.27%	3.98%	67.74%	326	0.972632
both	682	1.88%	5.87%	100.00%	475	1.43579
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	247	0.64%	2.00%	33.93%	149	0.52
anti	481	1.26%	3.89%	66.07%	326	1.01263
both	728	1.90%	5.88%	100.00%	475	1.53263

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)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 19	0; 22
chrUn_gl000220:109077@+	-758; 300	18S	16; 0	16; 0
chr8:101734314@-	-1000; 252	PABPC1	14; 0	25; 0
chr13:30083551@+	-1000; 300	AL596114.1	0; 13	0; 14
chrUn_gl000220:113347@+	-585; 300	28S	11; 0	12; 0
chr8:128231332@-	-1000; 139	AC020688.1	11; 0	11; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 11
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 10	0; 11
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 7	0; 7
chr8:33370702@-	-1000; 286	C8orf41	0; 5	0; 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)
chr8:101734314@-	-1000; 252	PABPC1	14; 0	25; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 19	0; 22
chrUn_gl000220:109077@+	-758; 300	18S	16; 0	16; 0
chr13:30083551@+	-1000; 300	AL596114.1	0; 13	0; 14
chrUn_gl000220:113347@+	-585; 300	28S	11; 0	12; 0
chr8:128231332@-	-1000; 139	AC020688.1	11; 0	11; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 11
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 10	0; 11
chr12:13593934@-	-1000; 59	5S_rRNA-ENSG00000201476	1; 0	7; 0
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 7	0; 7

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	1941	5.35%	16.70%	78.68%	1105	1.36883
anti	526	1.45%	4.53%	21.32%	325	0.370945
both	2467	6.81%	21.23%	100.00%	1418	1.73977
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	2238	5.84%	18.08%	80.01%	1105	1.57828
anti	559	1.46%	4.52%	19.99%	325	0.394217
both	2797	7.30%	22.60%	100.00%	1418	1.9725

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	148; 0	219; 0
chr1:169101767@-	-127; 1000	NME7	0; 35	0; 40
chr7:5566780@-	-300; 1000	ACTB	30; 0	110; 0
chrUn_gl000220:110946@+	-300; 539	18S	20; 0	28; 0
chrUn_gl000220:118417@+	-300; 1000	28S	18; 0	21; 0
chr17:79845715@-	-144; 1000	THOC4	18; 0	33; 0
chr13:113978542@-	-129; 1000	GRTP1	0; 15	0; 20
chr6:44221831@-	-300; 1000	SLC35B2	0; 13	0; 14
chr18:25530928@-	-300; 1000	CDH2	13; 0	16; 0
chr13:30083545@-	-300; 1000	SLC7A1	13; 0	14; 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)
chr11:65271080@+	-300; 1000	MALAT1	148; 0	219; 0
chr7:5566780@-	-300; 1000	ACTB	30; 0	110; 0
chr1:169101767@-	-127; 1000	NME7	0; 35	0; 40
chr17:79845715@-	-144; 1000	THOC4	18; 0	33; 0
chrUn_gl000220:110946@+	-300; 539	18S	20; 0	28; 0
chr17:79476997@-	-300; 1000	ACTG1	10; 0	24; 0
chrUn_gl000220:118417@+	-300; 1000	28S	18; 0	21; 0
chr19:18390561@-	-300; 1000	JUND	11; 0	20; 0
chr13:113978542@-	-129; 1000	GRTP1	0; 15	0; 20
chr18:25530928@-	-300; 1000	CDH2	13; 0	16; 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	1296	3.57%	11.15%	95.86%	1221	1.01727
anti	56	0.15%	0.48%	4.14%	53	0.043956
both	1352	3.73%	11.64%	100.00%	1274	1.06122
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	1335	3.49%	10.79%	95.77%	1221	1.04788
anti	59	0.15%	0.48%	4.23%	53	0.0463108
both	1394	3.64%	11.26%	100.00%	1274	1.09419

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)
chr2:61413393@+	-229; 100	AHSA2	5; 0	6; 0
chr5:10401919@+	-300; 100	MARCH6	4; 0	4; 0
chr5:179048854@-	-300; 100	HNRNPH1	3; 0	3; 0
chr5:65454855@+	-300; 100	SFRS12	3; 0	3; 0
chr4:123818859@-	-300; 27	NUDT6	0; 3	0; 3
chr19:10251082@-	-147; 79	DNMT1	3; 0	3; 0
chr17:35564817@-	-300; 100	ACACA	3; 0	3; 0
chr16:31199583@+	-300; 60	FUS	3; 0	3; 0
chr13:113840277@-	-300; 100	PCID2	3; 0	4; 0
chr12:105589775@-	-300; 100	APPL2	3; 0	3; 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)
chr2:61413393@+	-229; 100	AHSA2	5; 0	6; 0
chr5:10401919@+	-300; 100	MARCH6	4; 0	4; 0
chr13:113840277@-	-300; 100	PCID2	3; 0	4; 0
chr5:179048854@-	-300; 100	HNRNPH1	3; 0	3; 0
chr5:102601485@+	-300; 100	C5orf30	2; 0	3; 0
chr5:65454855@+	-300; 100	SFRS12	3; 0	3; 0
chr4:123818859@-	-300; 27	NUDT6	0; 3	0; 3
chr19:10251082@-	-147; 79	DNMT1	3; 0	3; 0
chr17:35564817@-	-300; 100	ACACA	3; 0	3; 0
chr17:2092017@-	-300; 100	SMG6	0; 1	0; 3

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