Parameters
input_file: 20090724_LUd3_5_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: 0

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 34406
[x-link sites] used in any map: 11177 (32.49%)
[single hits in whole-genome, cDNA counts] total: 34406
[single hits in whole-genome, cDNA counts] used in any map: 11860 (32.78%)

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	3350	9.74%	29.97%	3448	9.53%	29.07%
intron-exon	-300; 300	2476	7.20%	22.15%	2547	7.04%	21.48%
5-ncRNA	-1000; 300	669	1.94%	5.99%	737	2.04%	6.21%
ncRNA-3	-300; 1000	755	2.19%	6.75%	862	2.38%	7.27%
ORF-3UTR	-300; 300	1629	4.73%	14.57%	1740	4.81%	14.67%
5UTR-ORF	-300; 300	89	0.26%	0.80%	92	0.25%	0.78%
inter-5UTR	-1000; 300	201	0.58%	1.80%	208	0.57%	1.75%
3UTR-inter	-300; 1000	1638	4.76%	14.66%	1760	4.86%	14.84%
inter-5	-1000; 300	621	1.80%	5.56%	651	1.80%	5.49%
3-inter	-300; 1000	2349	6.83%	21.02%	2647	7.32%	22.32%
BP best in intron	-300; 100	1316	3.82%	11.77%	1357	3.75%	11.44%

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	3272	9.51%	29.27%	97.67%	2989	1.06928
anti	78	0.23%	0.70%	2.33%	71	0.0254902
both	3350	9.74%	29.97%	100.00%	3060	1.09477
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	3367	9.31%	28.39%	97.65%	2989	1.10033
anti	81	0.22%	0.68%	2.35%	71	0.0264706
both	3448	9.53%	29.07%	100.00%	3060	1.1268

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)
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
chr5:10401598@+	-300; 185	MARCH6	4; 0	4; 0
chr2:68405987@-	-300; 300	PPP3R1	4; 0	5; 0
chr2:61413216@+	-51; 182	AHSA2	4; 0	5; 0
chr16:31196500@+	-121; 159	FUS	4; 0	4; 0
chr13:111555820@-	-33; 300	ANKRD10	4; 0	5; 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)
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	2390	6.95%	21.38%	96.53%	2134	1.08096
anti	86	0.25%	0.77%	3.47%	77	0.0388964
both	2476	7.20%	22.15%	100.00%	2211	1.11986
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	2460	6.80%	20.74%	96.58%	2134	1.11262
anti	87	0.24%	0.73%	3.42%	77	0.0393487
both	2547	7.04%	21.48%	100.00%	2211	1.15197

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	21; 0	31; 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
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
chr9:114982652@-	-300; 102	ROD1	4; 0	4; 0
chr7:5568349@-	-150; 219	ACTB	4; 0	4; 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	21; 0	31; 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
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
chr9:114982652@-	-300; 102	ROD1	4; 0	4; 0
chr7:5568349@-	-150; 219	ACTB	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 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	332	0.96%	2.97%	49.63%	181	0.772093
anti	337	0.98%	3.02%	50.37%	250	0.783721
both	669	1.94%	5.99%	100.00%	430	1.55581
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	392	1.08%	3.31%	53.19%	181	0.911628
anti	345	0.95%	2.91%	46.81%	250	0.802326
both	737	2.04%	6.21%	100.00%	430	1.71395

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	19; 0	34; 0
chr13:30083551@+	-1000; 300	AL596114.1	0; 13	0; 14
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
chr3:49571651@-	-1000; 300	AC104452.1	0; 5	0; 5
chr18:9923916@+	-1000; 51	5S_rRNA-ENSG00000223138, VAPA	5; 0	6; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	5; 0	5; 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)
chr11:65269806@+	-1000; 29	MALAT1	69; 0	84; 0
chr17:57918626@+	-338; 36	hsa-mir-21	19; 0	34; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	9; 0	16; 0
chr13:30083551@+	-1000; 300	AL596114.1	0; 13	0; 14
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
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 7	0; 7
chr2:212400377@+	-1000; 58	5S_rRNA-ENSG00000199585	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 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	495	1.44%	4.43%	65.56%	263	1.06911
anti	260	0.76%	2.33%	34.44%	201	0.561555
both	755	2.19%	6.75%	100.00%	463	1.63067
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	596	1.65%	5.03%	69.14%	263	1.28726
anti	266	0.74%	2.24%	30.86%	201	0.574514
both	862	2.38%	7.27%	100.00%	463	1.86177

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	148; 0	219; 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
chr1:21070455@+	-63; 1000	RP5-930J4.4	0; 6	0; 6
chr8:144939422@+	-300; 1000	AC105049.1	0; 5	0; 5
chr8:33371096@+	-52; 1000	snoU13-ENSG00000239039	5; 0	5; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	5; 0	6; 0
chr17:80561428@-	-92; 1000	AC124283.1	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)
chr11:65271080@+	-300; 1000	MALAT1	148; 0	219; 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
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	5; 0	6; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	2; 0	6; 0
chr11:10823012@-	-71; 189	EIF4G2, snoU97	6; 0	6; 0
chr1:171639418@-	-194; 1000	RP4-560B9.2	5; 0	6; 0
chr1:21070455@+	-63; 1000	RP5-930J4.4	0; 6	0; 6
chr8:144939422@+	-300; 1000	AC105049.1	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 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	1597	4.64%	14.29%	98.04%	928	1.67576
anti	32	0.09%	0.29%	1.96%	25	0.0335782
both	1629	4.73%	14.57%	100.00%	953	1.70934
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	1705	4.71%	14.38%	97.99%	928	1.78909
anti	35	0.10%	0.30%	2.01%	25	0.0367261
both	1740	4.81%	14.67%	100.00%	953	1.82581

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	36; 0	54; 0
chr1:54497690@-	-144; 172	TMEM59	22; 0	34; 0
chr3:149087560@-	-53; 300	TM4SF1	21; 0	29; 0
chr2:136872205@-	-300; 144	CXCR4	14; 0	15; 0
chr6:30692174@+	-300; 300	TUBB	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
chr7:80374206@-	-208; 300	SEMA3C	8; 0	10; 0
chr5:179156650@+	-145; 300	CANX	8; 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	36; 0	54; 0
chr1:54497690@-	-144; 172	TMEM59	22; 0	34; 0
chr3:149087560@-	-53; 300	TM4SF1	21; 0	29; 0
chr6:30692174@+	-300; 300	TUBB	13; 0	15; 0
chr2:136872205@-	-300; 144	CXCR4	14; 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
chr20:48741591@-	-62; 300	TMEM189	10; 0	11; 0
chr7:80374206@-	-208; 300	SEMA3C	8; 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 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	0.24%	0.74%	93.26%	75	1.0641
anti	6	0.02%	0.05%	6.74%	3	0.0769231
both	89	0.26%	0.80%	100.00%	78	1.14103
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	86	0.24%	0.73%	93.48%	75	1.10256
anti	6	0.02%	0.05%	6.52%	3	0.0769231
both	92	0.25%	0.78%	100.00%	78	1.17949

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; 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 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; 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	68	0.20%	0.61%	33.83%	65	0.412121
anti	133	0.39%	1.19%	66.17%	100	0.806061
both	201	0.58%	1.80%	100.00%	165	1.21818
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	69	0.19%	0.58%	33.17%	65	0.418182
anti	139	0.38%	1.17%	66.83%	100	0.842424
both	208	0.57%	1.75%	100.00%	165	1.26061

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; 11
chr8:33370702@-	-1000; 286	C8orf41	0; 6	0; 6
chr20:47894962@-	-1000; 248	ZNFX1	0; 4	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
chr1:173837219@+	-1000; 87	ZBTB37	0; 3	0; 5
chr9:100745637@+	-1000; 100	ANP32B	2; 0	2; 0
chr6:88054599@+	-1000; 109	C6orf163	2; 0	2; 0
chr6:30294255@+	-1000; 258	TRIM39	0; 2	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)
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
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
chr9:100745637@+	-1000; 100	ANP32B	2; 0	2; 0
chr6:88054599@+	-1000; 109	C6orf163	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 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	1377	4.00%	12.32%	84.07%	860	1.36067
anti	261	0.76%	2.34%	15.93%	162	0.257905
both	1638	4.76%	14.66%	100.00%	1012	1.61858
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	1480	4.09%	12.48%	84.09%	860	1.46245
anti	280	0.77%	2.36%	15.91%	162	0.27668
both	1760	4.86%	14.84%	100.00%	1012	1.73913

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)
chr17:79845715@-	-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 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)
chr17:79845715@-	-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	175	0.51%	1.57%	28.18%	142	0.380435
anti	446	1.30%	3.99%	71.82%	318	0.969565
both	621	1.80%	5.56%	100.00%	460	1.35
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	188	0.52%	1.59%	28.88%	142	0.408696
anti	463	1.28%	3.90%	71.12%	318	1.00652
both	651	1.80%	5.49%	100.00%	460	1.41522

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; 19	0; 22
chr13:30083551@+	-1000; 300	AL596114.1	0; 13	0; 14
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
chr3:49571651@-	-1000; 300	AC104452.1	0; 5	0; 5
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	5; 0	5; 0
chr1:234742753@+	-1000; 300	RP4-781K5.2	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; 19	0; 22
chr13:30083551@+	-1000; 300	AL596114.1	0; 13	0; 14
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
chr2:212400377@+	-1000; 58	5S_rRNA-ENSG00000199585	2; 0	6; 0
chr8:33370702@-	-1000; 286	C8orf41	0; 5	0; 5
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	1846	5.37%	16.52%	78.59%	1066	1.35139
anti	503	1.46%	4.50%	21.41%	311	0.368228
both	2349	6.83%	21.02%	100.00%	1366	1.71962
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	2112	5.84%	17.81%	79.79%	1066	1.54612
anti	535	1.48%	4.51%	20.21%	311	0.391654
both	2647	7.32%	22.32%	100.00%	1366	1.93777

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	148; 0	219; 0
chr1:169101767@-	-127; 1000	NME7	0; 35	0; 40
chr7:5566780@-	-300; 1000	ACTB	24; 0	83; 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
chr18:25530928@-	-300; 1000	CDH2	13; 0	16; 0
chr13:30083545@-	-300; 1000	SLC7A1	13; 0	14; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 13	0; 13
chr19:18390561@-	-300; 1000	JUND	11; 0	20; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	148; 0	219; 0
chr7:5566780@-	-300; 1000	ACTB	24; 0	83; 0
chr1:169101767@-	-127; 1000	NME7	0; 35	0; 40
chr17:79845715@-	-144; 1000	THOC4	18; 0	33; 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
chr5:179041177@-	-300; 1000	HNRNPH1	9; 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 "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	1268	3.69%	11.34%	96.35%	1195	1.02258
anti	48	0.14%	0.43%	3.65%	45	0.0387097
both	1316	3.82%	11.77%	100.00%	1240	1.06129
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	1307	3.61%	11.02%	96.32%	1195	1.05403
anti	50	0.14%	0.42%	3.68%	45	0.0403226
both	1357	3.75%	11.44%	100.00%	1240	1.09435

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)
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
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
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)
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
chr17:35564817@-	-300; 100	ACACA	3; 0	3; 0
chr17:2092017@-	-300; 100	SMG6	0; 1	0; 3
chr16:31199583@+	-300; 60	FUS	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.