Parameters
input_file: 20090724_LUd3_3_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: 432373
[x-link sites] used in any map: 136510 (31.57%)
[single hits in whole-genome, cDNA counts] total: 432373
[single hits in whole-genome, cDNA counts] used in any map: 155342 (32.71%)

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	49155	11.37%	36.01%	52523	11.06%	33.81%
intron-exon	-300; 300	32412	7.50%	23.74%	34648	7.30%	22.30%
5-ncRNA	-1000; 300	6399	1.48%	4.69%	9372	1.97%	6.03%
ncRNA-3	-300; 1000	6595	1.53%	4.83%	9627	2.03%	6.20%
ORF-3UTR	-300; 300	16921	3.91%	12.40%	20576	4.33%	13.25%
5UTR-ORF	-300; 300	973	0.23%	0.71%	1034	0.22%	0.67%
inter-5UTR	-1000; 300	1837	0.42%	1.35%	2123	0.45%	1.37%
3UTR-inter	-300; 1000	16141	3.73%	11.82%	19136	4.03%	12.32%
inter-5	-1000; 300	5852	1.35%	4.29%	7234	1.52%	4.66%
3-inter	-300; 1000	21645	5.01%	15.86%	27488	5.79%	17.70%
BP best in intron	-300; 100	18106	4.19%	13.26%	18857	3.97%	12.14%

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	48203	11.15%	35.31%	98.06%	28637	1.64971
anti	952	0.22%	0.70%	1.94%	693	0.0325815
both	49155	11.37%	36.01%	100.00%	29219	1.6823
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	51315	10.81%	33.03%	97.70%	28637	1.75622
anti	1208	0.25%	0.78%	2.30%	693	0.041343
both	52523	11.06%	33.81%	100.00%	29219	1.79756

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; 67	0; 267
chr3:41281934@+	-300; 300	CTNNB1	50; 0	87; 0
chr7:128411528@+	-300; 107	CALU	48; 0	116; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 40	0; 60
chr2:191800015@+	-300; 300	GLS	36; 0	46; 0
chr5:10401598@+	-300; 185	MARCH6	35; 0	61; 0
chr3:186506209@+	-300; 300	EIF4A2	31; 0	33; 0
chr12:50158717@+	-300; 300	TMBIM6	31; 0	70; 0
chr6:18225699@-	-124; 192	DEK	29; 0	35; 0
chr5:179047674@-	-181; 300	HNRNPH1	23; 0	27; 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; 67	0; 267
chr7:128411528@+	-300; 107	CALU	48; 0	116; 0
chr3:41281934@+	-300; 300	CTNNB1	50; 0	87; 0
chr12:50158717@+	-300; 300	TMBIM6	31; 0	70; 0
chr5:10401598@+	-300; 185	MARCH6	35; 0	61; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 40	0; 60
chr7:139025365@+	-85; 256	C7orf55	7; 0	48; 0
chr2:191800015@+	-300; 300	GLS	36; 0	46; 0
chr17:57915758@+	-52; 300	TMEM49	23; 0	40; 0
chr5:179048241@-	-78; 103	HNRNPH1	19; 0	37; 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	31396	7.26%	23.00%	96.87%	20529	1.48094
anti	1016	0.23%	0.74%	3.13%	762	0.0479245
both	32412	7.50%	23.74%	100.00%	21200	1.52887
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	33579	7.07%	21.62%	96.91%	20529	1.58392
anti	1069	0.23%	0.69%	3.09%	762	0.0504245
both	34648	7.30%	22.30%	100.00%	21200	1.63434

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	82; 0	202; 0
chr9:131456919@+	-292; 300	SET	41; 0	132; 0
chr8:128753204@+	-241; 235	MYC	41; 0	63; 0
chr5:179041959@-	-293; 300	HNRNPH1	41; 0	103; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	38; 0	81; 0
chr2:211542610@+	-300; 300	CPS1	34; 0	48; 0
chr17:57915655@+	-300; 51	TMEM49	29; 0	45; 0
chr1:165697357@-	-300; 292	TMCO1	29; 0	37; 0
chr1:26227577@-	-160; 260	STMN1	28; 0	60; 0
chr7:6502805@-	-300; 300	KDELR2	27; 0	56; 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)
chr15:45009804@+	-300; 277	B2M	82; 0	202; 0
chr9:131456919@+	-292; 300	SET	41; 0	132; 0
chr5:179041959@-	-293; 300	HNRNPH1	41; 0	103; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	38; 0	81; 0
chr11:64540976@-	-300; 241	SF1	17; 0	68; 0
chr8:128753204@+	-241; 235	MYC	41; 0	63; 0
chr17:57917128@+	-300; 72	TMEM49	27; 0	63; 0
chr1:26227577@-	-160; 260	STMN1	28; 0	60; 0
chr7:6502805@-	-300; 300	KDELR2	27; 0	56; 0
chr10:112657785@+	-300; 300	PDCD4	25; 0	53; 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	2957	0.68%	2.17%	46.21%	1244	1.06712
anti	3442	0.80%	2.52%	53.79%	1583	1.24215
both	6399	1.48%	4.69%	100.00%	2771	2.30927
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	5500	1.16%	3.54%	58.69%	1244	1.98484
anti	3872	0.82%	2.49%	41.31%	1583	1.39733
both	9372	1.97%	6.03%	100.00%	2771	3.38217

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	479; 0	1596; 0
chr8:128231332@-	-1000; 139	AC020688.1	150; 1	206; 1
chr3:49571651@-	-1000; 300	AC104452.1	0; 53	0; 67
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 52	0; 60
chr17:57918626@+	-338; 36	hsa-mir-21	49; 0	103; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 43	0; 51
chr1:205685227@+	-1000; 300	AC119673.2	0; 38	0; 48
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 36	0; 41
chr2:70315685@-	-1000; 62	AC136007.2	0; 30	0; 35
chr6:72113323@-	-1000; 35	C6orf155, hsa-mir-30a	26; 0	27; 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	479; 0	1596; 0
chr8:128231332@-	-1000; 139	AC020688.1	150; 1	206; 1
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	20; 0	182; 0
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	21; 0	163; 0
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 10	0; 148
chr5:135416285@-	-1000; 50	Vault-ENSG00000202030	11; 0	124; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	15; 0	122; 0
chr17:57918626@+	-338; 36	hsa-mir-21	49; 0	103; 0
chr14:74055600@-	-1000; 36	AC005225.1	4; 0	96; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	16; 2	79; 2

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	3585	0.83%	2.63%	54.36%	1487	1.26634
anti	3010	0.70%	2.20%	45.64%	1386	1.06323
both	6595	1.53%	4.83%	100.00%	2831	2.32957
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	6326	1.33%	4.07%	65.71%	1487	2.23455
anti	3301	0.70%	2.12%	34.29%	1386	1.16602
both	9627	2.03%	6.20%	100.00%	2831	3.40057

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	627; 0	1995; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 55	0; 72
chr11:62609089@-	-96; 978	U2-ENSG00000222328	51; 0	264; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 47	0; 69
chr3:14530617@-	-300; 1000	GRIP2	0; 45	0; 60
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 41	0; 54
chrUn_gl000220:118417@+	-300; 1000	28S	40; 0	92; 0
chr8:144939422@+	-300; 1000	AC105049.1	0; 36	0; 44
chr10:112658486@-	-300; 1000	NCRNA00081	0; 34	0; 65
chr11:62620380@-	-63; 1000	SNORD22-ENSG00000207487	33; 0	35; 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	627; 0	1995; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	51; 0	264; 0
chr1:17216097@+	-254; 1000	RP11-108M9.5	10; 0	148; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	26; 0	133; 0
chrUn_gl000220:118417@+	-300; 1000	28S	40; 0	92; 0
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	16; 0	84; 0
chr5:135416184@-	-51; 1000	Vault-ENSG00000202030	14; 0	79; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 55	0; 72
chr1:28835512@-	-182; 1000	AL513497.3	0; 47	0; 69
chr10:112658486@-	-300; 1000	NCRNA00081	0; 34	0; 65

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	16626	3.85%	12.18%	98.26%	4109	3.91938
anti	295	0.07%	0.22%	1.74%	194	0.0695427
both	16921	3.91%	12.40%	100.00%	4242	3.98892
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	20263	4.27%	13.04%	98.48%	4109	4.77676
anti	313	0.07%	0.20%	1.52%	194	0.073786
both	20576	4.33%	13.25%	100.00%	4242	4.85054

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	104; 0	210; 0
chr14:62213803@+	-76; 300	HIF1A	70; 0	165; 0
chr5:179156650@+	-145; 300	CANX	68; 0	142; 0
chr21:27253823@-	-129; 300	APP	67; 0	97; 0
chr3:149087560@-	-53; 300	TM4SF1	63; 0	162; 0
chr1:35650053@-	-70; 300	SFPQ	54; 0	89; 0
chr1:156109094@+	-112; 233	LMNA	50; 0	98; 0
chr7:148700882@-	-209; 300	PDIA4	48; 0	63; 0
chr17:4849191@-	-50; 123	PFN1	47; 0	244; 0
chrX:114884310@+	-165; 300	PLS3	45; 0	62; 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)
chr17:4849191@-	-50; 123	PFN1	47; 0	244; 0
chr19:13054727@+	-101; 288	CALR	104; 0	210; 0
chr14:62213803@+	-76; 300	HIF1A	70; 0	165; 0
chr3:149087560@-	-53; 300	TM4SF1	63; 0	162; 0
chr5:179156650@+	-145; 300	CANX	68; 0	142; 0
chr1:156109094@+	-112; 233	LMNA	50; 0	98; 0
chr21:27253823@-	-129; 300	APP	67; 0	97; 0
chr1:35650053@-	-70; 300	SFPQ	54; 0	89; 0
chr7:128409221@+	-53; 300	CALU	38; 0	83; 0
chr2:189876774@+	-211; 300	COL3A1	37; 0	72; 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	877	0.20%	0.64%	90.13%	546	1.50429
anti	96	0.02%	0.07%	9.87%	41	0.164666
both	973	0.23%	0.71%	100.00%	583	1.66895
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	929	0.20%	0.60%	89.85%	546	1.59348
anti	105	0.02%	0.07%	10.15%	41	0.180103
both	1034	0.22%	0.67%	100.00%	583	1.77358

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)
chr17:4851688@-	-300; 66	PFN1	33; 0	43; 0
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 22	0; 25
chr6:64286785@+	-92; 52	PTP4A1	13; 0	15; 0
chr8:101733810@-	-252; 96	PABPC1	12; 0	13; 0
chr6:24718895@-	-300; 64	C6orf62	10; 0	11; 0
chr11:3012265@+	-300; 90	AC131971.1	0; 10	0; 12
chr7:135612307@+	-300; 127	AC015987.2	0; 9	0; 10
chr6:166401613@+	-250; 300	AL132661.1	0; 9	0; 11
chr2:211421442@+	-91; 70	CPS1	8; 0	13; 0
chr1:12677352@-	-192; 97	DHRS3	8; 0	9; 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)
chr17:4851688@-	-300; 66	PFN1	33; 0	43; 0
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 22	0; 25
chr6:64286785@+	-92; 52	PTP4A1	13; 0	15; 0
chr8:101733810@-	-252; 96	PABPC1	12; 0	13; 0
chr2:211421442@+	-91; 70	CPS1	8; 0	13; 0
chr11:3012265@+	-300; 90	AC131971.1	0; 10	0; 12
chr6:24718895@-	-300; 64	C6orf62	10; 0	11; 0
chr6:166401613@+	-250; 300	AL132661.1	0; 9	0; 11
chr6:33168574@+	-177; 300	SLC39A7	7; 0	11; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 9	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-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	641	0.15%	0.47%	34.89%	468	0.591328
anti	1196	0.28%	0.88%	65.11%	674	1.10332
both	1837	0.42%	1.35%	100.00%	1084	1.69465
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	663	0.14%	0.43%	31.23%	468	0.611624
anti	1460	0.31%	0.94%	68.77%	674	1.34686
both	2123	0.45%	1.37%	100.00%	1084	1.95849

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; 58	0; 110
chr5:32788944@+	-844; 281	C5orf23	23; 0	26; 0
chr11:62623517@+	-1000; 112	SLC3A2	0; 21	0; 28
chr8:71485680@+	-1000; 300	AC120194.1	0; 19	0; 21
chr20:47894962@-	-1000; 248	ZNFX1	0; 15	0; 23
chr17:7387865@+	-741; 109	POLR2A	13; 1	13; 1
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 14	0; 16
chr8:33370702@-	-1000; 286	C8orf41	0; 12	0; 21
chr11:66115160@-	-1000; 72	AP001107.2	0; 12	0; 90
chr8:101734314@-	-1000; 252	PABPC1	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)
chr6:166401114@+	-1000; 249	AL132661.1	0; 58	0; 110
chr11:66115160@-	-1000; 72	AP001107.2	0; 12	0; 90
chr19:39903224@+	-1000; 300	PLEKHG2	0; 6	0; 39
chr11:62623517@+	-1000; 112	SLC3A2	0; 21	0; 28
chr5:32788944@+	-844; 281	C5orf23	23; 0	26; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 15	0; 23
chr8:33370702@-	-1000; 286	C8orf41	0; 12	0; 21
chr8:71485680@+	-1000; 300	AC120194.1	0; 19	0; 21
chr8:101734314@-	-1000; 252	PABPC1	11; 0	20; 0
chr1:173837219@+	-1000; 87	ZBTB37	0; 11	0; 17

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	13452	3.11%	9.85%	83.34%	3907	3.00469
anti	2689	0.62%	1.97%	16.66%	855	0.600625
both	16141	3.73%	11.82%	100.00%	4477	3.60532
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	15813	3.33%	10.18%	82.63%	3907	3.53205
anti	3323	0.70%	2.14%	17.37%	855	0.742238
both	19136	4.03%	12.32%	100.00%	4477	4.27429

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)
chr19:39220830@-	-300; 1000	CAPN12	0; 86	0; 152
chr8:128753674@+	-235; 1000	MYC	68; 0	151; 0
chr15:45010359@+	-278; 1000	B2M	65; 0	151; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 52	0; 60
chr17:4848518@+	-104; 1000	RNF167	0; 47	0; 244
chr12:53874278@-	-300; 1000	MAP3K12	1; 46	1; 76
chr16:18802989@-	-300; 667	ARL6IP1	46; 0	66; 0
chr16:87863620@-	-300; 1000	SLC7A5	43; 0	96; 0
chr21:44834393@-	-300; 1000	SIK1	41; 0	66; 0
chr19:57805436@+	-300; 1000	ZNF460	40; 0	43; 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)
chr17:4848518@+	-104; 1000	RNF167	0; 47	0; 244
chr19:39220830@-	-300; 1000	CAPN12	0; 86	0; 152
chr8:128753674@+	-235; 1000	MYC	68; 0	151; 0
chr15:45010359@+	-278; 1000	B2M	65; 0	151; 0
chr17:79476997@-	-300; 1000	ACTG1	37; 0	107; 0
chr16:87863620@-	-300; 1000	SLC7A5	43; 0	96; 0
chr17:38613983@+	-300; 1000	IGFBP4	26; 0	92; 0
chr2:1635657@-	-300; 1000	PXDN	28; 0	87; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 46	1; 76
chr12:104744062@+	-300; 1000	TXNRD1	40; 0	67; 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	1671	0.39%	1.22%	28.55%	995	0.572653
anti	4181	0.97%	3.06%	71.45%	2032	1.43283
both	5852	1.35%	4.29%	100.00%	2918	2.00548
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	2304	0.49%	1.48%	31.85%	995	0.789582
anti	4930	1.04%	3.17%	68.15%	2032	1.68951
both	7234	1.52%	4.66%	100.00%	2918	2.4791

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)
chr8:128231332@-	-1000; 139	AC020688.1	150; 1	206; 1
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 73	0; 155
chr6:166401114@+	-1000; 249	AL132661.1	0; 57	0; 109
chr3:49571651@-	-1000; 300	AC104452.1	0; 53	0; 67
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 52	0; 60
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 43	0; 51
chr1:205685227@+	-1000; 300	AC119673.2	0; 38	0; 48
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 36	0; 41
chr2:70315685@-	-1000; 62	AC136007.2	0; 30	0; 35
chr6:26199470@-	-1000; 196	HIST1H2AD	3; 20	4; 36

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)
chr8:128231332@-	-1000; 139	AC020688.1	150; 1	206; 1
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	20; 0	182; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 73	0; 155
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 10	0; 148
chr5:135416285@-	-1000; 50	Vault-ENSG00000202030	11; 0	124; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 57	0; 109
chr11:66115160@-	-1000; 72	AP001107.2	0; 12	0; 90
chr6:89773408@-	-1000; 95	U2-ENSG00000223001	4; 0	75; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 53	0; 67
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 52	0; 60

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	16413	3.80%	12.02%	75.83%	4815	2.60938
anti	5232	1.21%	3.83%	24.17%	1822	0.831797
both	21645	5.01%	15.86%	100.00%	6290	3.44118
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	21267	4.48%	13.69%	77.37%	4815	3.38108
anti	6221	1.31%	4.00%	22.63%	1822	0.98903
both	27488	5.79%	17.70%	100.00%	6290	4.37011

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	627; 0	1995; 0
chr1:169101767@-	-127; 1000	NME7	0; 131	0; 202
chr19:39220830@-	-300; 1000	CAPN12	0; 86	0; 152
chr8:128753674@+	-235; 1000	MYC	68; 0	151; 0
chr15:45010359@+	-278; 1000	B2M	65; 0	151; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 55	0; 72
chr22:38879452@+	-263; 1000	KDELR3	0; 52	0; 60
chr4:57897324@+	-130; 1000	POLR2B	5; 46	6; 93
chr17:4848518@+	-104; 1000	RNF167	0; 47	0; 244
chr12:53874278@-	-300; 1000	MAP3K12	1; 46	1; 76

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	627; 0	1995; 0
chr17:4848518@+	-104; 1000	RNF167	0; 47	0; 244
chr1:169101767@-	-127; 1000	NME7	0; 131	0; 202
chr7:5566780@-	-300; 1000	ACTB	42; 0	152; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 86	0; 152
chr8:128753674@+	-235; 1000	MYC	68; 0	151; 0
chr15:45010359@+	-278; 1000	B2M	65; 0	151; 0
chr1:17216097@+	-254; 1000	RP11-108M9.5	10; 0	148; 0
chr1:153516087@-	-156; 923	S100A4	26; 0	141; 0
chr6:26031876@-	-206; 1000	HIST1H3B	18; 0	140; 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	17516	4.05%	12.83%	96.74%	12928	1.30971
anti	590	0.14%	0.43%	3.26%	474	0.0441154
both	18106	4.19%	13.26%	100.00%	13374	1.35382
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	18236	3.84%	11.74%	96.71%	12928	1.36354
anti	621	0.13%	0.40%	3.29%	474	0.0464334
both	18857	3.97%	12.14%	100.00%	13374	1.40997

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)
chr3:186506588@+	-298; 100	EIF4A2	26; 0	28; 0
chr5:179046653@-	-300; 100	HNRNPH1	22; 0	27; 0
chr5:179048854@-	-300; 100	HNRNPH1	21; 0	23; 0
chr1:1326494@-	-300; 100	CCNL2	21; 0	31; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	20; 0	20; 0
chr5:10401919@+	-300; 100	MARCH6	20; 0	34; 0
chr2:61413393@+	-229; 100	AHSA2	18; 0	27; 0
chr14:70237083@+	-300; 98	SFRS5	18; 0	20; 0
chr20:34326966@-	-300; 28	RBM39	17; 0	20; 0
chr1:70697488@+	-300; 100	SFRS11	17; 0	22; 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)
chr9:86584384@-	-300; 90	HNRNPK	14; 0	86; 0
chr5:10401919@+	-300; 100	MARCH6	20; 0	34; 0
chr1:1326494@-	-300; 100	CCNL2	21; 0	31; 0
chr3:186506588@+	-298; 100	EIF4A2	26; 0	28; 0
chr5:179046653@-	-300; 100	HNRNPH1	22; 0	27; 0
chr2:61413393@+	-229; 100	AHSA2	18; 0	27; 0
chr1:28835317@+	-300; 22	SNHG3	14; 0	27; 0
chr5:179048854@-	-300; 100	HNRNPH1	21; 0	23; 0
chr1:70697488@+	-300; 100	SFRS11	17; 0	22; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	20; 0	20; 0

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