Parameters
input_file: 20090724_LUd3_1_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: 208288
[x-link sites] used in any map: 67420 (32.37%)
[single hits in whole-genome, cDNA counts] total: 208288
[single hits in whole-genome, cDNA counts] used in any map: 76292 (33.47%)

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	21258	10.21%	31.53%	22377	9.82%	29.33%
intron-exon	-300; 300	15322	7.36%	22.73%	16230	7.12%	21.27%
5-ncRNA	-1000; 300	3367	1.62%	4.99%	4959	2.18%	6.50%
ncRNA-3	-300; 1000	3458	1.66%	5.13%	4757	2.09%	6.24%
ORF-3UTR	-300; 300	10275	4.93%	15.24%	12366	5.42%	16.21%
5UTR-ORF	-300; 300	517	0.25%	0.77%	546	0.24%	0.72%
inter-5UTR	-1000; 300	979	0.47%	1.45%	1147	0.50%	1.50%
3UTR-inter	-300; 1000	9552	4.59%	14.17%	11105	4.87%	14.56%
inter-5	-1000; 300	3174	1.52%	4.71%	3940	1.73%	5.16%
3-inter	-300; 1000	12599	6.05%	18.69%	15378	6.75%	20.16%
BP best in intron	-300; 100	8287	3.98%	12.29%	8581	3.76%	11.25%

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	20754	9.96%	30.78%	97.63%	15559	1.30528
anti	504	0.24%	0.75%	2.37%	366	0.0316981
both	21258	10.21%	31.53%	100.00%	15900	1.33698
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	21757	9.54%	28.52%	97.23%	15559	1.36836
anti	620	0.27%	0.81%	2.77%	366	0.0389937
both	22377	9.82%	29.33%	100.00%	15900	1.40736

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; 45	0; 137
chr7:128411528@+	-300; 107	CALU	33; 0	49; 0
chr3:41281934@+	-300; 300	CTNNB1	33; 0	51; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 30	0; 42
chr1:165624857@+	-127; 300	MGST3	28; 0	42; 0
chr12:50158717@+	-300; 300	TMBIM6	24; 0	42; 0
chr5:10401598@+	-300; 185	MARCH6	20; 0	28; 0
chr2:191800015@+	-300; 300	GLS	19; 0	21; 0
chr6:160527583@+	-300; 300	IGF2R	16; 0	21; 0
chr4:108534820@-	-291; 300	PAPSS1	16; 0	17; 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; 45	0; 137
chr3:41281934@+	-300; 300	CTNNB1	33; 0	51; 0
chr7:128411528@+	-300; 107	CALU	33; 0	49; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 30	0; 42
chr12:50158717@+	-300; 300	TMBIM6	24; 0	42; 0
chr1:165624857@+	-127; 300	MGST3	28; 0	42; 0
chr5:10401598@+	-300; 185	MARCH6	20; 0	28; 0
chr5:179048241@-	-78; 103	HNRNPH1	13; 0	24; 0
chr7:139025365@+	-85; 256	C7orf55	6; 0	21; 0
chr6:160527583@+	-300; 300	IGF2R	16; 0	21; 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	14822	7.12%	21.98%	96.74%	11215	1.27864
anti	500	0.24%	0.74%	3.26%	405	0.0431332
both	15322	7.36%	22.73%	100.00%	11592	1.32177
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	15714	6.89%	20.60%	96.82%	11215	1.35559
anti	516	0.23%	0.68%	3.18%	405	0.0445135
both	16230	7.12%	21.27%	100.00%	11592	1.4001

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	49; 0	100; 0
chr5:179041959@-	-293; 300	HNRNPH1	30; 0	46; 0
chr2:211542610@+	-300; 300	CPS1	26; 0	36; 0
chr9:131456919@+	-292; 300	SET	25; 0	80; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	21; 0	30; 0
chr10:112657785@+	-300; 300	PDCD4	21; 0	28; 0
chr8:128753204@+	-241; 235	MYC	20; 0	32; 0
chr17:57915655@+	-300; 51	TMEM49	19; 0	21; 0
chr1:26227577@-	-160; 260	STMN1	19; 0	33; 0
chr2:47387942@-	-300; 300	CALM2	18; 0	24; 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	49; 0	100; 0
chr9:131456919@+	-292; 300	SET	25; 0	80; 0
chr5:179041959@-	-293; 300	HNRNPH1	30; 0	46; 0
chr2:211542610@+	-300; 300	CPS1	26; 0	36; 0
chr1:26227577@-	-160; 260	STMN1	19; 0	33; 0
chr8:128753204@+	-241; 235	MYC	20; 0	32; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	21; 0	30; 0
chr2:189876353@+	-300; 210	COL3A1	16; 0	29; 0
chr10:112657785@+	-300; 300	PDCD4	21; 0	28; 0
chr7:6502805@-	-300; 300	KDELR2	13; 0	25; 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	1579	0.76%	2.34%	46.90%	781	0.931563
anti	1788	0.86%	2.65%	53.10%	940	1.05487
both	3367	1.62%	4.99%	100.00%	1695	1.98643
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	2931	1.29%	3.84%	59.10%	781	1.7292
anti	2028	0.89%	2.66%	40.90%	940	1.19646
both	4959	2.18%	6.50%	100.00%	1695	2.92566

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	244; 0	682; 0
chr8:128231332@-	-1000; 139	AC020688.1	61; 1	78; 1
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 40	0; 46
chr1:205685227@+	-1000; 300	AC119673.2	0; 37	0; 42
chr3:49571651@-	-1000; 300	AC104452.1	0; 29	0; 37
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 28	0; 35
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 26	0; 38
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 26
chr2:70315685@-	-1000; 62	AC136007.2	0; 21	0; 22
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	20; 0	111; 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	244; 0	682; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	141; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	13; 0	140; 0
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	20; 0	111; 0
chr14:74055600@-	-1000; 36	AC005225.1	5; 0	105; 0
chr5:140105742@+	-1000; 44	Vault-ENSG00000202515	17; 0	89; 0
chr8:128231332@-	-1000; 139	AC020688.1	61; 1	78; 1
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	16; 0	79; 0
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 6	0; 66
chr5:140098509@+	-1000; 44	Vault-ENSG00000202111	16; 0	48; 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	1973	0.95%	2.93%	57.06%	936	1.14178
anti	1485	0.71%	2.20%	42.94%	807	0.859375
both	3458	1.66%	5.13%	100.00%	1728	2.00116
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	3165	1.39%	4.15%	66.53%	936	1.8316
anti	1592	0.70%	2.09%	33.47%	807	0.921296
both	4757	2.09%	6.24%	100.00%	1728	2.75289

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	349; 0	821; 0
chrUn_gl000220:118417@+	-300; 1000	28S	42; 0	81; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 36	0; 46
chr11:62609089@-	-96; 978	U2-ENSG00000222328	35; 0	112; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 33	0; 41
chr1:21070455@+	-63; 1000	RP5-930J4.4	0; 29	0; 29
chr10:112658486@-	-300; 1000	NCRNA00081	0; 28	0; 37
chr8:144939422@+	-300; 1000	AC105049.1	0; 25	0; 29
chrY:21154137@-	-229; 1000	CD24L4, NCRNA00185	20; 0	20; 0
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 20	0; 24

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	349; 0	821; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	35; 0	112; 0
chrUn_gl000220:118417@+	-300; 1000	28S	42; 0	81; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	18; 0	71; 0
chr1:17216097@+	-254; 1000	RP11-108M9.5	6; 0	66; 0
chr14:74055527@-	-37; 1000	AC005225.1	2; 0	62; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	13; 0	47; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 36	0; 46
chr2:191798136@-	-300; 1000	AC067945.1	0; 33	0; 41
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	11; 0	40; 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	10139	4.87%	15.04%	98.68%	3180	3.12836
anti	136	0.07%	0.20%	1.32%	85	0.0419624
both	10275	4.93%	15.24%	100.00%	3241	3.17032
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	12210	5.36%	16.00%	98.74%	3180	3.76736
anti	156	0.07%	0.20%	1.26%	85	0.0481333
both	12366	5.42%	16.21%	100.00%	3241	3.81549

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	97; 0	203; 0
chr14:62213803@+	-76; 300	HIF1A	62; 0	99; 0
chr5:179156650@+	-145; 300	CANX	50; 0	97; 0
chr3:149087560@-	-53; 300	TM4SF1	45; 0	104; 0
chr1:35650053@-	-70; 300	SFPQ	42; 0	58; 0
chr1:156109094@+	-112; 233	LMNA	42; 0	65; 0
chr21:27253823@-	-129; 300	APP	38; 0	56; 0
chr2:136872205@-	-300; 144	CXCR4	37; 0	45; 0
chr17:4849191@-	-50; 123	PFN1	35; 0	192; 0
chrX:77381764@+	-239; 300	PGK1	34; 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)
chr19:13054727@+	-101; 288	CALR	97; 0	203; 0
chr17:4849191@-	-50; 123	PFN1	35; 0	192; 0
chr3:149087560@-	-53; 300	TM4SF1	45; 0	104; 0
chr14:62213803@+	-76; 300	HIF1A	62; 0	99; 0
chr5:179156650@+	-145; 300	CANX	50; 0	97; 0
chr1:156109094@+	-112; 233	LMNA	42; 0	65; 0
chr2:189876774@+	-211; 300	COL3A1	32; 0	60; 0
chr1:54497690@-	-144; 172	TMEM59	34; 0	60; 0
chr1:35650053@-	-70; 300	SFPQ	42; 0	58; 0
chr7:128409221@+	-53; 300	CALU	25; 0	56; 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	464	0.22%	0.69%	89.75%	318	1.34493
anti	53	0.03%	0.08%	10.25%	28	0.153623
both	517	0.25%	0.77%	100.00%	345	1.49855
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	490	0.21%	0.64%	89.74%	318	1.42029
anti	56	0.02%	0.07%	10.26%	28	0.162319
both	546	0.24%	0.72%	100.00%	345	1.58261

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	13; 0	16; 0
chr6:64286785@+	-92; 52	PTP4A1	11; 0	13; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 9	0; 10
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 8	0; 9
chr8:101733810@-	-252; 96	PABPC1	7; 0	8; 0
chr6:24718895@-	-300; 64	C6orf62	7; 0	7; 0
chr6:33168574@+	-177; 300	SLC39A7	7; 0	7; 0
chr5:180670946@-	-131; 134	GNB2L1	6; 0	7; 0
chr7:1608974@-	-300; 108	PSMG3	5; 0	5; 0
chr6:31508971@-	-66; 265	BAT1	5; 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)
chr17:4851688@-	-300; 66	PFN1	13; 0	16; 0
chr6:64286785@+	-92; 52	PTP4A1	11; 0	13; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 9	0; 10
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 8	0; 9
chr8:101733810@-	-252; 96	PABPC1	7; 0	8; 0
chr6:24718895@-	-300; 64	C6orf62	7; 0	7; 0
chr6:33168574@+	-177; 300	SLC39A7	7; 0	7; 0
chr5:180670946@-	-131; 134	GNB2L1	6; 0	7; 0
chr2:211421442@+	-91; 70	CPS1	5; 0	7; 0
chr6:31508971@-	-66; 265	BAT1	5; 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 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	316	0.15%	0.47%	32.28%	243	0.466765
anti	663	0.32%	0.98%	67.72%	447	0.979321
both	979	0.47%	1.45%	100.00%	677	1.44609
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	335	0.15%	0.44%	29.21%	243	0.49483
anti	812	0.36%	1.06%	70.79%	447	1.19941
both	1147	0.50%	1.50%	100.00%	677	1.69424

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; 28	0; 45
chr20:47894962@-	-1000; 248	ZNFX1	0; 12	0; 12
chr11:62623517@+	-1000; 112	SLC3A2	0; 12	0; 17
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 11	0; 11
chr5:32788944@+	-844; 281	C5orf23	10; 0	10; 0
chr8:33370702@-	-1000; 286	C8orf41	0; 9	0; 10
chr1:173837219@+	-1000; 87	ZBTB37	0; 9	0; 11
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 76
chr5:93954051@+	-1000; 151	ANKRD32	0; 6	0; 7
chr12:54673914@-	-1000; 62	CBX5	0; 6	0; 6

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)
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 76
chr6:166401114@+	-1000; 249	AL132661.1	0; 28	0; 45
chr11:62623517@+	-1000; 112	SLC3A2	0; 12	0; 17
chr15:89878025@-	-1000; 61	POLG	0; 4	0; 14
chr19:39903224@+	-1000; 300	PLEKHG2	0; 5	0; 13
chr20:47894962@-	-1000; 248	ZNFX1	0; 12	0; 12
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 11	0; 11
chr1:173837219@+	-1000; 87	ZBTB37	0; 9	0; 11
chr8:33370702@-	-1000; 286	C8orf41	0; 9	0; 10
chr5:32788944@+	-844; 281	C5orf23	10; 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 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	8111	3.89%	12.03%	84.91%	2946	2.4104
anti	1441	0.69%	2.14%	15.09%	563	0.428232
both	9552	4.59%	14.17%	100.00%	3365	2.83863
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	9270	4.07%	12.15%	83.48%	2946	2.75483
anti	1835	0.80%	2.41%	16.52%	563	0.545319
both	11105	4.87%	14.56%	100.00%	3365	3.30015

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; 72	0; 116
chr8:128753674@+	-235; 1000	MYC	51; 0	87; 0
chr15:45010359@+	-278; 1000	B2M	47; 0	79; 0
chr17:79476997@-	-300; 1000	ACTG1	38; 0	92; 0
chr16:18802989@-	-300; 667	ARL6IP1	38; 0	57; 0
chr21:44834393@-	-300; 1000	SIK1	37; 0	50; 0
chr14:62214976@+	-300; 1000	HIF1A	36; 0	54; 0
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 192
chr12:104744062@+	-300; 1000	TXNRD1	31; 0	49; 0
chr12:20833881@+	-300; 1000	PDE3A	31; 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)
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 192
chr19:39220830@-	-300; 1000	CAPN12	0; 72	0; 116
chr17:79476997@-	-300; 1000	ACTG1	38; 0	92; 0
chr8:128753674@+	-235; 1000	MYC	51; 0	87; 0
chr15:45010359@+	-278; 1000	B2M	47; 0	79; 0
chr11:65622306@-	-249; 1000	CFL1	30; 0	64; 0
chr2:1635657@-	-300; 1000	PXDN	22; 0	63; 0
chr16:18802989@-	-300; 667	ARL6IP1	38; 0	57; 0
chr14:62214976@+	-300; 1000	HIF1A	36; 0	54; 0
chr21:44834393@-	-300; 1000	SIK1	37; 0	50; 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	893	0.43%	1.32%	28.13%	582	0.499441
anti	2281	1.10%	3.38%	71.87%	1244	1.27573
both	3174	1.52%	4.71%	100.00%	1788	1.77517
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	1190	0.52%	1.56%	30.20%	582	0.665548
anti	2750	1.21%	3.60%	69.80%	1244	1.53803
both	3940	1.73%	5.16%	100.00%	1788	2.20358

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; 84	0; 163
chr8:128231332@-	-1000; 139	AC020688.1	61; 1	78; 1
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 40	0; 46
chr1:205685227@+	-1000; 300	AC119673.2	0; 37	0; 42
chr3:49571651@-	-1000; 300	AC104452.1	0; 29	0; 37
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 28	0; 35
chr6:166401114@+	-1000; 249	AL132661.1	0; 27	0; 44
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 26	0; 38
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 26
chr2:70315685@-	-1000; 62	AC136007.2	0; 21	0; 22

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; 84	0; 163
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	141; 0
chr8:128231332@-	-1000; 139	AC020688.1	61; 1	78; 1
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 76
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 6	0; 66
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 40	0; 46
chr5:135416285@-	-1000; 50	Vault-ENSG00000202030	10; 0	45; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 27	0; 44
chr1:205685227@+	-1000; 300	AC119673.2	0; 37	0; 42
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 26	0; 38

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	9897	4.75%	14.68%	78.55%	3595	2.17182
anti	2702	1.30%	4.01%	21.45%	1133	0.592934
both	12599	6.05%	18.69%	100.00%	4557	2.76476
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	12119	5.32%	15.89%	78.81%	3595	2.65943
anti	3259	1.43%	4.27%	21.19%	1133	0.715163
both	15378	6.75%	20.16%	100.00%	4557	3.37459

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	349; 0	821; 0
chr1:169101767@-	-127; 1000	NME7	0; 84	0; 141
chr19:39220830@-	-300; 1000	CAPN12	0; 72	0; 116
chr8:128753674@+	-235; 1000	MYC	51; 0	87; 0
chr15:45010359@+	-278; 1000	B2M	47; 0	79; 0
chrUn_gl000220:118417@+	-300; 1000	28S	42; 0	81; 0
chr17:79476997@-	-300; 1000	ACTG1	38; 0	92; 0
chr16:18802989@-	-300; 667	ARL6IP1	38; 0	57; 0
chr21:44834393@-	-300; 1000	SIK1	37; 0	50; 0
chr14:62214976@+	-300; 1000	HIF1A	36; 0	54; 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	349; 0	821; 0
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 192
chr1:169101767@-	-127; 1000	NME7	0; 84	0; 141
chr1:153516087@-	-156; 923	S100A4	24; 0	126; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 72	0; 116
chr7:5566780@-	-300; 1000	ACTB	31; 0	112; 0
chr17:79476997@-	-300; 1000	ACTG1	38; 0	92; 0
chr8:128753674@+	-235; 1000	MYC	51; 0	87; 0
chrUn_gl000220:118417@+	-300; 1000	28S	42; 0	81; 0
chr15:45010359@+	-278; 1000	B2M	47; 0	79; 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	7989	3.84%	11.85%	96.40%	6674	1.15582
anti	298	0.14%	0.44%	3.60%	245	0.0431134
both	8287	3.98%	12.29%	100.00%	6912	1.19893
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	8271	3.63%	10.84%	96.39%	6674	1.19661
anti	310	0.14%	0.41%	3.61%	245	0.0448495
both	8581	3.76%	11.25%	100.00%	6912	1.24146

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)
chr5:179046653@-	-300; 100	HNRNPH1	17; 0	19; 0
chr1:1326494@-	-300; 100	CCNL2	17; 0	20; 0
chr5:10401919@+	-300; 100	MARCH6	14; 0	19; 0
chr1:70697488@+	-300; 100	SFRS11	10; 0	10; 0
chr1:28835317@+	-300; 22	SNHG3	10; 0	15; 0
chr15:66783435@-	-300; 100	SNAPC5	0; 9	0; 10
chr14:70237083@+	-300; 98	SFRS5	9; 0	9; 0
chr5:14290650@+	-300; 100	TRIO	8; 0	8; 0
chr3:186506588@+	-298; 100	EIF4A2	7; 1	7; 1
chr20:34326966@-	-300; 28	RBM39	8; 0	10; 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	7; 0	29; 0
chr1:1326494@-	-300; 100	CCNL2	17; 0	20; 0
chr5:179046653@-	-300; 100	HNRNPH1	17; 0	19; 0
chr5:10401919@+	-300; 100	MARCH6	14; 0	19; 0
chr1:28835317@+	-300; 22	SNHG3	10; 0	15; 0
chr20:34326966@-	-300; 28	RBM39	8; 0	10; 0
chr15:66783435@-	-300; 100	SNAPC5	0; 9	0; 10
chr1:70697488@+	-300; 100	SFRS11	10; 0	10; 0
chr7:26237431@-	-300; 80	HNRNPA2B1	6; 0	9; 0
chr14:70237083@+	-300; 98	SFRS5	9; 0	9; 0

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