Parameters
input_file: 20101125_LUjt8_1_hg19_ensembl59_G_iCLIP_TDP-43_SH-SY5Y_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: 165524
[x-link sites] used in any map: 22756 (13.75%)
[single hits in whole-genome, cDNA counts] total: 165524
[single hits in whole-genome, cDNA counts] used in any map: 28623 (15.73%)

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	7046	4.26%	30.96%	7550	4.15%	26.38%
intron-exon	-300; 300	6109	3.69%	26.85%	6566	3.61%	22.94%
5-ncRNA	-1000; 300	2071	1.25%	9.10%	4022	2.21%	14.05%
ncRNA-3	-300; 1000	2093	1.26%	9.20%	4573	2.51%	15.98%
ORF-3UTR	-300; 300	876	0.53%	3.85%	990	0.54%	3.46%
5UTR-ORF	-300; 300	165	0.10%	0.73%	176	0.10%	0.61%
inter-5UTR	-1000; 300	638	0.39%	2.80%	684	0.38%	2.39%
3UTR-inter	-300; 1000	1618	0.98%	7.11%	1755	0.96%	6.13%
inter-5	-1000; 300	1873	1.13%	8.23%	3628	1.99%	12.68%
3-inter	-300; 1000	2956	1.79%	12.99%	5515	3.03%	19.27%
BP best in intron	-300; 100	5115	3.09%	22.48%	5530	3.04%	19.32%

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	6568	3.97%	28.86%	93.22%	4500	1.3385
anti	478	0.29%	2.10%	6.78%	417	0.0974119
both	7046	4.26%	30.96%	100.00%	4907	1.43591
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	7048	3.87%	24.62%	93.35%	4500	1.43632
anti	502	0.28%	1.75%	6.65%	417	0.102303
both	7550	4.15%	26.38%	100.00%	4907	1.53862

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)
chr5:59188993@-	-228; 300	PDE4D	24; 0	33; 0
chr1:1158622@-	-57; 300	SDF4	20; 0	23; 0
chr11:12886447@+	-32; 300	TEAD1	19; 0	24; 0
chr15:37390166@-	-117; 300	MEIS2	18; 0	24; 0
chr4:71655799@+	-243; 300	RUFY3	17; 0	23; 0
chr17:38506177@+	-71; 300	RARA	17; 0	18; 0
chr15:37391100@-	-248; 299	MEIS2	17; 0	18; 0
chr1:33478643@-	-42; 300	AK2	17; 0	18; 0
chr7:128001358@-	-190; 300	PRRT4	16; 0	19; 0
chr5:883069@-	-226; 300	BRD9	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)
chr5:59188993@-	-228; 300	PDE4D	24; 0	33; 0
chr11:71944788@+	-45; 268	INPPL1	12; 0	29; 0
chr15:37390166@-	-117; 300	MEIS2	18; 0	24; 0
chr11:12886447@+	-32; 300	TEAD1	19; 0	24; 0
chr4:71655799@+	-243; 300	RUFY3	17; 0	23; 0
chr1:1158622@-	-57; 300	SDF4	20; 0	23; 0
chr3:128206552@-	-106; 300	GATA2	15; 0	20; 0
chr7:128001358@-	-190; 300	PRRT4	16; 0	19; 0
chr3:116163722@-	-78; 300	LSAMP	16; 0	19; 0
chr20:60912644@-	-69; 300	LAMA5	16; 0	19; 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	5625	3.40%	24.72%	92.08%	4074	1.25614
anti	484	0.29%	2.13%	7.92%	416	0.108084
both	6109	3.69%	26.85%	100.00%	4478	1.36423
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	6068	3.33%	21.20%	92.42%	4074	1.35507
anti	498	0.27%	1.74%	7.58%	416	0.11121
both	6566	3.61%	22.94%	100.00%	4478	1.46628

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)
chr10:43604478@+	-300; 100	RET	41; 0	84; 0
chr3:64502796@-	-300; 300	ADAMTS9	38; 0	62; 0
chr20:60912041@-	-300; 41	LAMA5	23; 0	28; 0
chr4:863744@-	-300; 300	GAK	21; 0	23; 0
chr15:37388630@-	-300; 71	MEIS2	20; 0	36; 0
chr20:32661368@+	-300; 36	RALY	18; 0	23; 0
chr15:75308933@+	-300; 78	SCAMP5	16; 0	20; 0
chr10:43595906@+	-300; 132	RET	15; 0	20; 0
chr1:156834145@+	-300; 37	NTRK1	15; 0	19; 0
chr6:170059613@-	-300; 34	WDR27	14; 0	16; 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)
chr10:43604478@+	-300; 100	RET	41; 0	84; 0
chr3:64502796@-	-300; 300	ADAMTS9	38; 0	62; 0
chr15:37388630@-	-300; 71	MEIS2	20; 0	36; 0
chr20:60912041@-	-300; 41	LAMA5	23; 0	28; 0
chr4:863744@-	-300; 300	GAK	21; 0	23; 0
chr20:32661368@+	-300; 36	RALY	18; 0	23; 0
chr15:75308933@+	-300; 78	SCAMP5	16; 0	20; 0
chr10:43595906@+	-300; 132	RET	15; 0	20; 0
chr1:156834145@+	-300; 37	NTRK1	15; 0	19; 0
chr6:170059613@-	-300; 34	WDR27	14; 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 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	1005	0.61%	4.42%	48.53%	507	0.851695
anti	1066	0.64%	4.68%	51.47%	681	0.90339
both	2071	1.25%	9.10%	100.00%	1180	1.75508
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	2857	1.57%	9.98%	71.03%	507	2.42119
anti	1165	0.64%	4.07%	28.97%	681	0.987288
both	4022	2.21%	14.05%	100.00%	1180	3.40847

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)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	1728; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	59; 0	250; 0
chr11:65269806@+	-1000; 29	MALAT1	43; 0	50; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 21	0; 48
chr14:104150351@-	-1000; 300	AL139300.3	0; 21	0; 25
chr22:50295450@+	-1000; 30	AL671710.1	19; 0	20; 0
chr10:72975556@+	-1000; 36	AL359832.1, UNC5B	18; 0	24; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	16; 0	17; 0
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 16	0; 21
chr3:37903270@-	-1000; 40	AC093415.2	0; 15	0; 17

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)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	1728; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	59; 0	250; 0
chr11:65269806@+	-1000; 29	MALAT1	43; 0	50; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 21	0; 48
chr14:104150351@-	-1000; 300	AL139300.3	0; 21	0; 25
chr10:72975556@+	-1000; 36	AL359832.1, UNC5B	18; 0	24; 0
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 16	0; 21
chr22:50295450@+	-1000; 30	AL671710.1	19; 0	20; 0
chr3:37903270@-	-1000; 40	AC093415.2	0; 15	0; 17
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	16; 0	17; 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	1115	0.67%	4.90%	53.27%	500	1.0018
anti	978	0.59%	4.30%	46.73%	621	0.878706
both	2093	1.26%	9.20%	100.00%	1113	1.8805
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	3519	1.93%	12.29%	76.95%	500	3.16173
anti	1054	0.58%	3.68%	23.05%	621	0.94699
both	4573	2.51%	15.98%	100.00%	1113	4.10872

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	375; 0	2714; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 23	0; 31
chr7:19153894@+	-300; 1000	AC003986.6	0; 17	0; 18
chr19:35491390@+	-73; 1000	AC020907.6, GRAMD1A-ENSG00000248852	17; 0	19; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	25; 0
chr9:66456495@+	-205; 394	RP11-262H14.10	0; 14	0; 26
chr3:160232693@-	-165; 362	KPNA4, snoU90	13; 0	16; 0
chr3:129112992@+	-55; 1000	RP11-529F4.1	0; 12	0; 13
chr10:43474463@-	-42; 1000	RP11-124O11.2	12; 0	13; 0
chr3:73643089@-	-32; 1000	PDZRN3, U7-ENSG00000239119	10; 0	13; 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	375; 0	2714; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 23	0; 31
chr9:66456495@+	-205; 394	RP11-262H14.10	0; 14	0; 26
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	25; 0
chr19:35491390@+	-73; 1000	AC020907.6, GRAMD1A-ENSG00000248852	17; 0	19; 0
chr7:19153894@+	-300; 1000	AC003986.6	0; 17	0; 18
chr3:160232693@-	-165; 362	KPNA4, snoU90	13; 0	16; 0
chr15:37343027@-	-52; 1000	MEIS2, Y_RNA-ENSG00000206676	10; 0	15; 0
chr10:72975628@+	-36; 1000	AL359832.1, UNC5B	7; 0	14; 0
chr3:73643089@-	-32; 1000	PDZRN3, U7-ENSG00000239119	10; 0	13; 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	790	0.48%	3.47%	90.18%	493	1.3884
anti	86	0.05%	0.38%	9.82%	79	0.151142
both	876	0.53%	3.85%	100.00%	569	1.53954
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	894	0.49%	3.12%	90.30%	493	1.57118
anti	96	0.05%	0.34%	9.70%	79	0.168717
both	990	0.54%	3.46%	100.00%	569	1.73989

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)
chr16:29831075@+	-100; 300	C16orf53	17; 0	19; 0
chr7:100806072@-	-56; 142	VGF	15; 0	51; 0
chr7:92244026@-	-287; 300	CDK6	14; 0	18; 0
chr1:36181229@-	-300; 300	C1orf216	11; 0	12; 0
chr17:45016126@+	-81; 300	GOSR2	10; 0	11; 0
chr1:11083386@+	-69; 300	TARDBP	9; 0	10; 0
chr7:26252043@+	-171; 300	CBX3	8; 0	10; 0
chr10:32094640@-	-300; 138	ARHGAP12	8; 0	8; 0
chr1:149876562@-	-93; 300	SV2A	8; 0	9; 0
chr4:174448424@-	-51; 300	HAND2	7; 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)
chr7:100806072@-	-56; 142	VGF	15; 0	51; 0
chr16:29831075@+	-100; 300	C16orf53	17; 0	19; 0
chr7:92244026@-	-287; 300	CDK6	14; 0	18; 0
chr1:36181229@-	-300; 300	C1orf216	11; 0	12; 0
chr17:45016126@+	-81; 300	GOSR2	10; 0	11; 0
chr7:26252043@+	-171; 300	CBX3	8; 0	10; 0
chr1:11083386@+	-69; 300	TARDBP	9; 0	10; 0
chr1:149876562@-	-93; 300	SV2A	8; 0	9; 0
chr4:174448424@-	-51; 300	HAND2	7; 0	8; 0
chr10:32094640@-	-300; 138	ARHGAP12	8; 0	8; 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	142	0.09%	0.62%	86.06%	88	1.33962
anti	23	0.01%	0.10%	13.94%	18	0.216981
both	165	0.10%	0.73%	100.00%	106	1.5566
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	152	0.08%	0.53%	86.36%	88	1.43396
anti	24	0.01%	0.08%	13.64%	18	0.226415
both	176	0.10%	0.61%	100.00%	106	1.66038

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)
chr2:61764828@-	-277; 66	XPO1	13; 0	14; 0
chr4:71588290@+	-290; 89	RUFY3	9; 0	11; 0
chr16:89980628@+	-52; 300	AC092143.1	6; 0	6; 0
chr22:24033492@+	-266; 300	RGL4	0; 5	0; 5
chr1:153610770@+	-300; 77	C1orf77	5; 0	9; 0
chr1:1551887@+	-117; 300	MIB2	5; 0	6; 0
chr11:64073917@+	-110; 200	ESRRA	4; 0	6; 0
chr6:31619552@-	-191; 60	BAT3	3; 0	3; 0
chr5:86564268@+	-282; 269	RASA1	3; 0	3; 0
chr4:140005491@-	-79; 103	ELF2	3; 0	3; 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)
chr2:61764828@-	-277; 66	XPO1	13; 0	14; 0
chr4:71588290@+	-290; 89	RUFY3	9; 0	11; 0
chr1:153610770@+	-300; 77	C1orf77	5; 0	9; 0
chr16:89980628@+	-52; 300	AC092143.1	6; 0	6; 0
chr11:64073917@+	-110; 200	ESRRA	4; 0	6; 0
chr1:1551887@+	-117; 300	MIB2	5; 0	6; 0
chr22:24033492@+	-266; 300	RGL4	0; 5	0; 5
chr6:31619552@-	-191; 60	BAT3	3; 0	3; 0
chr5:86564268@+	-282; 269	RASA1	3; 0	3; 0
chr4:140005491@-	-79; 103	ELF2	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.

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	260	0.16%	1.14%	40.75%	179	0.625
anti	378	0.23%	1.66%	59.25%	240	0.908654
both	638	0.39%	2.80%	100.00%	416	1.53365
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	278	0.15%	0.97%	40.64%	179	0.668269
anti	406	0.22%	1.42%	59.36%	240	0.975962
both	684	0.38%	2.39%	100.00%	416	1.64423

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)
chr4:175205414@-	-1000; 300	FBXO8	0; 13	0; 16
chr21:38445469@-	-1000; 90	PIGP	0; 13	0; 19
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 11
chr20:51588945@+	-1000; 300	TSHZ2	10; 0	12; 0
chr16:89980524@+	-1000; 52	AC092143.1	9; 0	9; 0
chr7:99717235@+	-1000; 66	CNPY4	0; 8	0; 10
chr19:36705985@-	-1000; 98	ZNF565	0; 8	0; 9
chr19:36705503@+	-1000; 297	ZNF146	0; 8	0; 11
chr15:70390255@-	-1000; 300	TLE3	8; 0	9; 0
chr5:36152062@-	-1000; 203	LMBRD2	0; 7	0; 8

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)
chr21:38445469@-	-1000; 90	PIGP	0; 13	0; 19
chr4:175205414@-	-1000; 300	FBXO8	0; 13	0; 16
chr20:51588945@+	-1000; 300	TSHZ2	10; 0	12; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 11
chr19:36705503@+	-1000; 297	ZNF146	0; 8	0; 11
chr7:99717235@+	-1000; 66	CNPY4	0; 8	0; 10
chr19:36705985@-	-1000; 98	ZNF565	0; 8	0; 9
chr16:89980524@+	-1000; 52	AC092143.1	9; 0	9; 0
chr15:70390255@-	-1000; 300	TLE3	8; 0	9; 0
chr5:36152062@-	-1000; 203	LMBRD2	0; 7	0; 8

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	1304	0.79%	5.73%	80.59%	824	1.27468
anti	314	0.19%	1.38%	19.41%	213	0.30694
both	1618	0.98%	7.11%	100.00%	1023	1.58162
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	1417	0.78%	4.95%	80.74%	824	1.38514
anti	338	0.19%	1.18%	19.26%	213	0.330401
both	1755	0.96%	6.13%	100.00%	1023	1.71554

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)
chr2:72356365@-	-300; 1000	CYP26B1	18; 0	28; 0
chr7:100813772@-	-300; 1000	C7orf52	17; 0	24; 0
chr16:31000473@+	-300; 1000	HSD3B7	0; 16	0; 19
chr5:167975498@-	-300; 1000	PANK3	12; 0	13; 0
chr6:122764494@-	-300; 1000	SERINC1	11; 0	18; 0
chr7:100805788@-	-142; 1000	VGF	10; 0	25; 0
chr8:38132558@-	-299; 1000	WHSC1L1	9; 0	10; 0
chr18:40847857@-	-300; 1000	SYT4	9; 0	12; 0
chr1:180859387@+	-300; 1000	XPR1	9; 0	9; 0
chr1:179785333@+	-300; 1000	FAM163A	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)
chr2:72356365@-	-300; 1000	CYP26B1	18; 0	28; 0
chr7:100805788@-	-142; 1000	VGF	10; 0	25; 0
chr7:100813772@-	-300; 1000	C7orf52	17; 0	24; 0
chr16:31000473@+	-300; 1000	HSD3B7	0; 16	0; 19
chr6:122764494@-	-300; 1000	SERINC1	11; 0	18; 0
chr12:48176534@+	-267; 1000	SLC48A1	0; 8	0; 15
chr5:167975498@-	-300; 1000	PANK3	12; 0	13; 0
chr18:40847857@-	-300; 1000	SYT4	9; 0	12; 0
chr10:43625799@+	-300; 1000	RET	8; 0	11; 0
chr1:179785333@+	-300; 1000	FAM163A	9; 0	11; 0

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

RNAmap 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	637	0.38%	2.80%	34.01%	367	0.557305
anti	1236	0.75%	5.43%	65.99%	784	1.08136
both	1873	1.13%	8.23%	100.00%	1143	1.63867
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	2276	1.25%	7.95%	62.73%	367	1.99125
anti	1352	0.74%	4.72%	37.27%	784	1.18285
both	3628	1.99%	12.68%	100.00%	1143	3.1741

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)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	1728; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 21	0; 48
chr14:104150351@-	-1000; 300	AL139300.3	0; 21	0; 25
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 16	0; 21
chr4:175205414@-	-1000; 300	FBXO8	0; 13	0; 16
chr21:38445469@-	-1000; 90	PIGP	0; 13	0; 19
chr21:38739235@+	-1000; 300	DYRK1A	13; 0	15; 0
chr10:72977968@-	-1000; 81	RP11-790G19.2	0; 13	0; 15
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 11	0; 12
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 11

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)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	1728; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 21	0; 48
chr14:104150351@-	-1000; 300	AL139300.3	0; 21	0; 25
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 16	0; 21
chr21:38445469@-	-1000; 90	PIGP	0; 13	0; 19
chr4:175205414@-	-1000; 300	FBXO8	0; 13	0; 16
chr21:38739235@+	-1000; 300	DYRK1A	13; 0	15; 0
chr10:72977968@-	-1000; 81	RP11-790G19.2	0; 13	0; 15
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 11	0; 12
chr20:51588945@+	-1000; 300	TSHZ2	10; 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 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	1978	1.19%	8.69%	66.91%	1025	1.21053
anti	978	0.59%	4.30%	33.09%	625	0.598531
both	2956	1.79%	12.99%	100.00%	1634	1.80906
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	4460	2.45%	15.58%	80.87%	1025	2.7295
anti	1055	0.58%	3.69%	19.13%	625	0.645655
both	5515	3.03%	19.27%	100.00%	1634	3.37515

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	375; 0	2714; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 23	0; 31
chr2:72356365@-	-300; 1000	CYP26B1	18; 0	28; 0
chr7:100813772@-	-300; 1000	C7orf52	17; 0	24; 0
chr7:19153894@+	-300; 1000	AC003986.6	0; 17	0; 18
chr16:31000473@+	-300; 1000	HSD3B7	0; 16	0; 19
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	25; 0
chr9:66456495@+	-205; 394	RP11-262H14.10	0; 14	0; 26
chr5:167975498@-	-300; 1000	PANK3	12; 0	13; 0
chr6:122764494@-	-300; 1000	SERINC1	11; 0	18; 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	375; 0	2714; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 23	0; 31
chr2:72356365@-	-300; 1000	CYP26B1	18; 0	28; 0
chr9:66456495@+	-205; 394	RP11-262H14.10	0; 14	0; 26
chr7:100805788@-	-142; 1000	VGF	10; 0	25; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	25; 0
chr7:100813772@-	-300; 1000	C7orf52	17; 0	24; 0
chr16:31000473@+	-300; 1000	HSD3B7	0; 16	0; 19
chr7:19153894@+	-300; 1000	AC003986.6	0; 17	0; 18
chr6:122764494@-	-300; 1000	SERINC1	11; 0	18; 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	4815	2.91%	21.16%	94.13%	3353	1.33639
anti	300	0.18%	1.32%	5.87%	255	0.0832639
both	5115	3.09%	22.48%	100.00%	3603	1.41965
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	5217	2.87%	18.23%	94.34%	3353	1.44796
anti	313	0.17%	1.09%	5.66%	255	0.0868721
both	5530	3.04%	19.32%	100.00%	3603	1.53483

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)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	30; 0	90; 0
chr15:37388702@-	-300; 95	MEIS2	22; 0	38; 0
chr20:32661328@+	-300; 38	RALY	21; 0	27; 0
chr3:128205938@-	-300; 20	GATA2	18; 0	27; 0
chr20:62364539@+	-300; 29	ZGPAT	15; 0	20; 0
chr16:1509362@-	-300; 100	CLCN7	15; 0	15; 0
chr15:75308869@+	-300; 62	SCAMP5	15; 0	19; 0
chr1:156834120@+	-300; 23	NTRK1	15; 0	19; 0
chr10:43595881@+	-300; 23	RET	14; 0	19; 0
chr6:170059676@-	-300; 63	WDR27	13; 0	15; 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)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	30; 0	90; 0
chr15:37388702@-	-300; 95	MEIS2	22; 0	38; 0
chr3:128205938@-	-300; 20	GATA2	18; 0	27; 0
chr20:32661328@+	-300; 38	RALY	21; 0	27; 0
chr20:62364539@+	-300; 29	ZGPAT	15; 0	20; 0
chr15:75308869@+	-300; 62	SCAMP5	15; 0	19; 0
chr10:43595881@+	-300; 23	RET	14; 0	19; 0
chr1:156834120@+	-300; 23	NTRK1	15; 0	19; 0
chr8:38279639@-	-300; 100	FGFR1	10; 0	17; 0
chr7:107642327@-	-300; 100	LAMB1	12; 0	17; 0

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