Parameters
input_file: 20091102_LUjt5_8_hg19_ensembl59_G_iCLIP_TDP-43_SHSY5Y_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: 163131
[x-link sites] used in any map: 24414 (14.97%)
[single hits in whole-genome, cDNA counts] total: 163131
[single hits in whole-genome, cDNA counts] used in any map: 30213 (16.62%)

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	7250	4.44%	29.70%	7844	4.31%	25.96%
intron-exon	-300; 300	6892	4.22%	28.23%	7501	4.13%	24.83%
5-ncRNA	-1000; 300	2057	1.26%	8.43%	3661	2.01%	12.12%
ncRNA-3	-300; 1000	2370	1.45%	9.71%	4785	2.63%	15.84%
ORF-3UTR	-300; 300	1043	0.64%	4.27%	1140	0.63%	3.77%
5UTR-ORF	-300; 300	153	0.09%	0.63%	191	0.11%	0.63%
inter-5UTR	-1000; 300	565	0.35%	2.31%	681	0.37%	2.25%
3UTR-inter	-300; 1000	1807	1.11%	7.40%	1957	1.08%	6.48%
inter-5	-1000; 300	1703	1.04%	6.98%	3055	1.68%	10.11%
3-inter	-300; 1000	3211	1.97%	13.15%	5355	2.95%	17.72%
BP best in intron	-300; 100	5627	3.45%	23.05%	6139	3.38%	20.32%

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	6834	4.19%	27.99%	94.26%	5027	1.27357
anti	416	0.26%	1.70%	5.74%	352	0.0775252
both	7250	4.44%	29.70%	100.00%	5366	1.3511
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	7364	4.05%	24.37%	93.88%	5027	1.37234
anti	480	0.26%	1.59%	6.12%	352	0.0894521
both	7844	4.31%	25.96%	100.00%	5366	1.4618

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)
chr11:12886447@+	-32; 300	TEAD1	21; 0	24; 0
chr15:37391100@-	-248; 299	MEIS2	19; 0	29; 0
chr3:128206552@-	-106; 300	GATA2	18; 0	23; 0
chr2:242608275@+	-300; 300	ATG4B	17; 0	21; 0
chr1:156845458@+	-74; 206	NTRK1	17; 0	24; 0
chr3:50407749@-	-31; 300	CACNA2D2	16; 0	17; 0
chr1:1158622@-	-57; 300	SDF4	15; 0	18; 0
chr7:128001358@-	-190; 300	PRRT4	14; 0	17; 0
chr17:38506177@+	-71; 300	RARA	14; 0	14; 0
chr1:50575636@+	-75; 300	ELAVL4	13; 0	14; 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)
chr15:37391100@-	-248; 299	MEIS2	19; 0	29; 0
chr11:12886447@+	-32; 300	TEAD1	21; 0	24; 0
chr1:156845458@+	-74; 206	NTRK1	17; 0	24; 0
chr3:128206552@-	-106; 300	GATA2	18; 0	23; 0
chr2:242608275@+	-300; 300	ATG4B	17; 0	21; 0
chr22:50661414@-	-300; 197	TUBGCP6	12; 0	18; 0
chr1:1158622@-	-57; 300	SDF4	15; 0	18; 0
chr7:128001358@-	-190; 300	PRRT4	14; 0	17; 0
chr3:50407749@-	-31; 300	CACNA2D2	16; 0	17; 0
chr15:37390166@-	-117; 300	MEIS2	12; 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 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	6520	4.00%	26.71%	94.60%	5008	1.22556
anti	372	0.23%	1.52%	5.40%	323	0.0699248
both	6892	4.22%	28.23%	100.00%	5320	1.29549
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	7027	3.87%	23.26%	93.68%	5008	1.32086
anti	474	0.26%	1.57%	6.32%	323	0.0890977
both	7501	4.13%	24.83%	100.00%	5320	1.40996

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	39; 0	76; 0
chr3:64502796@-	-300; 300	ADAMTS9	25; 0	36; 0
chr10:43595906@+	-300; 132	RET	24; 0	29; 0
chr15:37388630@-	-300; 71	MEIS2	17; 0	22; 0
chr8:11640711@+	-300; 98	NEIL2	16; 0	18; 0
chr20:60912041@-	-300; 41	LAMA5	16; 0	22; 0
chr15:75308933@+	-300; 78	SCAMP5	15; 0	16; 0
chr12:124915332@-	-300; 86	NCOR2	13; 0	14; 0
chr1:156834145@+	-300; 37	NTRK1	13; 0	13; 0
chrX:118754013@-	-300; 300	SEPT6	12; 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	39; 0	76; 0
chr1:162330326@+	-300; 194	NOS1AP	0; 5	0; 41
chr3:64502796@-	-300; 300	ADAMTS9	25; 0	36; 0
chr10:43595906@+	-300; 132	RET	24; 0	29; 0
chrX:107408267@-	-166; 81	COL4A6	0; 4	0; 25
chr20:60912041@-	-300; 41	LAMA5	16; 0	22; 0
chr15:37388630@-	-300; 71	MEIS2	17; 0	22; 0
chr8:11640711@+	-300; 98	NEIL2	16; 0	18; 0
chr5:3600722@+	-174; 36	IRX1	0; 5	0; 17
chrX:118754013@-	-300; 300	SEPT6	12; 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	1122	0.69%	4.60%	54.55%	526	0.981627
anti	935	0.57%	3.83%	45.45%	625	0.818023
both	2057	1.26%	8.43%	100.00%	1143	1.79965
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	2657	1.46%	8.79%	72.58%	526	2.32458
anti	1004	0.55%	3.32%	27.42%	625	0.87839
both	3661	2.01%	12.12%	100.00%	1143	3.20297

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	115; 0	1153; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	77; 0	262; 0
chr11:65269806@+	-1000; 29	MALAT1	67; 0	89; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 32
chr14:104150351@-	-1000; 300	AL139300.3	0; 17	0; 20
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 17	0; 22
chr22:50295450@+	-1000; 30	AL671710.1	13; 1	13; 1
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	13; 0	70; 0
chr10:72977968@-	-1000; 81	RP11-790G19.2	0; 12	0; 12
chr20:47895476@+	-101; 44	C20orf199, SNORD12-ENSG00000209042	11; 0	19; 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)
chr1:109642814@+	-1000; 210	snoU2-25	115; 0	1153; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	77; 0	262; 0
chrM:5890@-	-777; 32	J01415.32	5; 4	99; 5
chr11:65269806@+	-1000; 29	MALAT1	67; 0	89; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	13; 0	70; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 32
chr17:62223442@+	-1000; 35	SNORND104	11; 0	24; 0
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 17	0; 22
chr14:104150351@-	-1000; 300	AL139300.3	0; 17	0; 20
chr20:47895476@+	-101; 44	C20orf199, SNORD12-ENSG00000209042	11; 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 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	1405	0.86%	5.75%	59.28%	584	1.18967
anti	965	0.59%	3.95%	40.72%	608	0.817104
both	2370	1.45%	9.71%	100.00%	1181	2.00677
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	3680	2.02%	12.18%	76.91%	584	3.116
anti	1105	0.61%	3.66%	23.09%	608	0.935648
both	4785	2.63%	15.84%	100.00%	1181	4.05165

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	414; 0	2219; 0
chr1:109643234@+	-210; 1000	snoU2-25	28; 0	64; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	23; 0	54; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 18	0; 27
chr7:19153894@+	-300; 1000	AC003986.6	0; 16	0; 17
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	29; 0
chr11:10823012@-	-71; 189	EIF4G2, snoU97	14; 0	30; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 14	0; 39
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	13; 0	189; 0
chr3:186504641@+	-89; 137	EIF4A2, SNORA81-ENSG00000221420	13; 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	414; 0	2219; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	13; 0	189; 0
chr1:109643234@+	-210; 1000	snoU2-25	28; 0	64; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	23; 0	54; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 14	0; 39
chr3:186504641@+	-89; 137	EIF4A2, SNORA81-ENSG00000221420	13; 0	35; 0
chr11:10823012@-	-71; 189	EIF4G2, snoU97	14; 0	30; 0
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	29; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 18	0; 27
chr1:28975245@+	-67; 1000	U11-ENSG00000209804	8; 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 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	955	0.59%	3.91%	91.56%	590	1.43825
anti	88	0.05%	0.36%	8.44%	75	0.13253
both	1043	0.64%	4.27%	100.00%	664	1.57078
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	1047	0.58%	3.47%	91.84%	590	1.57681
anti	93	0.05%	0.31%	8.16%	75	0.14006
both	1140	0.63%	3.77%	100.00%	664	1.71687

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)
chr7:92244026@-	-287; 300	CDK6	28; 0	38; 0
chr16:29831075@+	-100; 300	C16orf53	27; 0	29; 0
chr7:100806072@-	-56; 142	VGF	16; 0	37; 0
chr17:45016126@+	-81; 300	GOSR2	13; 0	14; 0
chr7:26252043@+	-171; 300	CBX3	11; 0	12; 0
chr1:11083386@+	-69; 300	TARDBP	11; 0	12; 0
chr4:174448424@-	-51; 300	HAND2	10; 0	11; 0
chr10:94837061@+	-171; 293	CYP26A1	8; 0	8; 0
chr22:19025348@-	-300; 300	DGCR2	7; 0	7; 0
chr6:7289914@-	-84; 300	SSR1	6; 0	7; 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)
chr7:92244026@-	-287; 300	CDK6	28; 0	38; 0
chr7:100806072@-	-56; 142	VGF	16; 0	37; 0
chr16:29831075@+	-100; 300	C16orf53	27; 0	29; 0
chr17:45016126@+	-81; 300	GOSR2	13; 0	14; 0
chr7:26252043@+	-171; 300	CBX3	11; 0	12; 0
chr4:71655313@+	-51; 243	RUFY3	6; 0	12; 0
chr1:11083386@+	-69; 300	TARDBP	11; 0	12; 0
chr4:174448424@-	-51; 300	HAND2	10; 0	11; 0
chr16:67472427@-	-82; 253	ATP6V0D1	6; 0	8; 0
chr10:94837061@+	-171; 293	CYP26A1	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	130	0.08%	0.53%	84.97%	84	1.28713
anti	23	0.01%	0.09%	15.03%	17	0.227723
both	153	0.09%	0.63%	100.00%	101	1.51485
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	139	0.08%	0.46%	72.77%	84	1.37624
anti	52	0.03%	0.17%	27.23%	17	0.514851
both	191	0.11%	0.63%	100.00%	101	1.89109

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	10; 0	11; 0
chr6:31508971@-	-66; 265	BAT1	9; 0	13; 0
chr22:24033492@+	-266; 300	RGL4	0; 5	0; 5
chr17:47755471@-	-62; 89	SPOP	5; 0	7; 0
chr16:89980628@+	-52; 300	AC092143.1	5; 0	5; 0
chr4:71588290@+	-290; 89	RUFY3	4; 0	4; 0
chr1:50575487@+	-95; 74	ELAVL4	4; 0	4; 0
chr7:69064639@+	-300; 154	AUTS2	3; 0	3; 0
chr6:7542148@+	-171; 85	DSP	0; 3	0; 32
chr5:86564268@+	-282; 269	RASA1	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)
chr6:7542148@+	-171; 85	DSP	0; 3	0; 32
chr6:31508971@-	-66; 265	BAT1	9; 0	13; 0
chr2:61764828@-	-277; 66	XPO1	10; 0	11; 0
chr17:47755471@-	-62; 89	SPOP	5; 0	7; 0
chr22:24033492@+	-266; 300	RGL4	0; 5	0; 5
chr16:89980628@+	-52; 300	AC092143.1	5; 0	5; 0
chr4:71588290@+	-290; 89	RUFY3	4; 0	4; 0
chr1:50575487@+	-95; 74	ELAVL4	4; 0	4; 0
chr7:69064639@+	-300; 154	AUTS2	3; 0	3; 0
chr5:86564268@+	-282; 269	RASA1	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	216	0.13%	0.88%	38.23%	141	0.629738
anti	349	0.21%	1.43%	61.77%	206	1.01749
both	565	0.35%	2.31%	100.00%	343	1.64723
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	234	0.13%	0.77%	34.36%	141	0.682216
anti	447	0.25%	1.48%	65.64%	206	1.30321
both	681	0.37%	2.25%	100.00%	343	1.98542

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)
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 22
chr6:166401114@+	-1000; 249	AL132661.1	0; 13	0; 15
chr20:51588945@+	-1000; 300	TSHZ2	11; 0	11; 0
chr2:72375166@-	-1000; 88	CYP26B1	11; 0	13; 0
chr1:151030233@+	-1000; 300	MLLT11	0; 11	0; 14
chr21:38445469@-	-1000; 90	PIGP	0; 10	0; 10
chr11:62623517@+	-1000; 112	SLC3A2	0; 9	0; 9
chr16:89980524@+	-1000; 52	AC092143.1	8; 0	8; 0
chr6:127664753@-	-1000; 137	ECHDC1	0; 7	0; 7
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)
chr15:89878025@-	-1000; 61	POLG	0; 6	0; 48
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 22
chr11:66115160@-	-1000; 72	AP001107.2	0; 5	0; 19
chr6:166401114@+	-1000; 249	AL132661.1	0; 13	0; 15
chr1:151030233@+	-1000; 300	MLLT11	0; 11	0; 14
chr2:72375166@-	-1000; 88	CYP26B1	11; 0	13; 0
chr20:51588945@+	-1000; 300	TSHZ2	11; 0	11; 0
chr17:37026255@+	-1000; 93	LASP1	0; 2	0; 11
chr21:38445469@-	-1000; 90	PIGP	0; 10	0; 10
chr11:62623517@+	-1000; 112	SLC3A2	0; 9	0; 9

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	1461	0.90%	5.98%	80.85%	900	1.29292
anti	346	0.21%	1.42%	19.15%	239	0.306195
both	1807	1.11%	7.40%	100.00%	1130	1.59912
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	1592	0.88%	5.27%	81.35%	900	1.40885
anti	365	0.20%	1.21%	18.65%	239	0.323009
both	1957	1.08%	6.48%	100.00%	1130	1.73186

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	24; 0	29; 0
chr7:100813772@-	-300; 1000	C7orf52	20; 0	24; 0
chr12:48176534@+	-267; 1000	SLC48A1	0; 16	0; 20
chr2:69686412@-	-300; 1000	AC114772.2	13; 0	15; 0
chr10:43625799@+	-300; 1000	RET	12; 0	12; 0
chr1:179785333@+	-300; 1000	FAM163A	12; 0	13; 0
chr7:47314750@-	-300; 1000	TNS3	11; 0	11; 0
chr7:100805788@-	-142; 1000	VGF	10; 0	18; 0
chr3:115528639@-	-241; 1000	LSAMP	10; 0	11; 0
chr10:102309763@+	-300; 1000	HIF1AN	10; 0	12; 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	24; 0	29; 0
chr7:100813772@-	-300; 1000	C7orf52	20; 0	24; 0
chr12:48176534@+	-267; 1000	SLC48A1	0; 16	0; 20
chr7:100805788@-	-142; 1000	VGF	10; 0	18; 0
chr19:18390561@-	-300; 1000	JUND	8; 0	18; 0
chr2:69686412@-	-300; 1000	AC114772.2	13; 0	15; 0
chr1:180859387@+	-300; 1000	XPR1	10; 0	14; 0
chr1:179785333@+	-300; 1000	FAM163A	12; 0	13; 0
chr10:102309763@+	-300; 1000	HIF1AN	10; 0	12; 0
chr10:43625799@+	-300; 1000	RET	12; 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 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	567	0.35%	2.32%	33.29%	323	0.553171
anti	1136	0.70%	4.65%	66.71%	711	1.10829
both	1703	1.04%	6.98%	100.00%	1025	1.66146
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	1658	0.91%	5.49%	54.27%	323	1.61756
anti	1397	0.77%	4.62%	45.73%	711	1.36293
both	3055	1.68%	10.11%	100.00%	1025	2.98049

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	115; 0	1153; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 29	0; 49
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 32
chr14:104150351@-	-1000; 300	AL139300.3	0; 17	0; 20
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 17	0; 22
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 22
chr6:166401114@+	-1000; 249	AL132661.1	0; 13	0; 15
chr10:72977968@-	-1000; 81	RP11-790G19.2	0; 12	0; 12
chr20:51588945@+	-1000; 300	TSHZ2	11; 0	11; 0
chr2:72375166@-	-1000; 88	CYP26B1	11; 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)
chr1:109642814@+	-1000; 210	snoU2-25	115; 0	1153; 0
chrM:5903@+	-162; 300	J01415.8	1; 7	1; 101
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 29	0; 49
chr15:89878025@-	-1000; 61	POLG	0; 6	0; 48
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 32
chr20:47894962@-	-1000; 248	ZNFX1	0; 14	0; 22
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 17	0; 22
chr14:104150351@-	-1000; 300	AL139300.3	0; 17	0; 20
chr11:66115160@-	-1000; 72	AP001107.2	0; 5	0; 19
chr6:166401114@+	-1000; 249	AL132661.1	0; 13	0; 15

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	2228	1.37%	9.13%	69.39%	1120	1.28637
anti	983	0.60%	4.03%	30.61%	625	0.567552
both	3211	1.97%	13.15%	100.00%	1732	1.85393
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	4260	2.34%	14.10%	79.55%	1120	2.45958
anti	1095	0.60%	3.62%	20.45%	625	0.632217
both	5355	2.95%	17.72%	100.00%	1732	3.0918

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	414; 0	2219; 0
chr1:109643234@+	-210; 1000	snoU2-25	28; 0	64; 0
chr2:72356365@-	-300; 1000	CYP26B1	24; 0	29; 0
chr7:100813772@-	-300; 1000	C7orf52	20; 0	24; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 18	0; 27
chr7:19153894@+	-300; 1000	AC003986.6	0; 16	0; 17
chr12:48176534@+	-267; 1000	SLC48A1	0; 16	0; 20
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	29; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 14	0; 39
chr2:69686412@-	-300; 1000	AC114772.2	13; 0	15; 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	414; 0	2219; 0
chr1:109643234@+	-210; 1000	snoU2-25	28; 0	64; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 14	0; 39
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	29; 0
chr2:72356365@-	-300; 1000	CYP26B1	24; 0	29; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 18	0; 27
chr7:100813772@-	-300; 1000	C7orf52	20; 0	24; 0
chr2:158155317@-	-176; 1000	7SK-ENSG00000222404	0; 3	0; 21
chr12:48176534@+	-267; 1000	SLC48A1	0; 16	0; 20
chr20:32500127@-	-217; 1000	TPM5P	3; 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 "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	5372	3.29%	22.00%	95.47%	3925	1.29477
anti	255	0.16%	1.04%	4.53%	232	0.0614606
both	5627	3.45%	23.05%	100.00%	4149	1.35623
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	5838	3.21%	19.32%	95.10%	3925	1.40709
anti	301	0.17%	1.00%	4.90%	232	0.0725476
both	6139	3.38%	20.32%	100.00%	4149	1.47963

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	36; 0	68; 0
chr10:43595881@+	-300; 23	RET	24; 0	29; 0
chr15:37388702@-	-300; 95	MEIS2	19; 0	24; 0
chr20:62364539@+	-300; 29	ZGPAT	15; 0	15; 0
chr15:75308869@+	-300; 62	SCAMP5	15; 0	16; 0
chr1:156834120@+	-300; 23	NTRK1	15; 0	15; 0
chr20:32661328@+	-300; 38	RALY	14; 0	16; 0
chr1:28835317@+	-300; 22	SNHG3	14; 0	39; 0
chr15:37390646@-	-300; 100	MEIS2	13; 0	19; 0
chr12:124915763@-	-300; 100	NCOR2	13; 0	14; 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	36; 0	68; 0
chr1:28835317@+	-300; 22	SNHG3	14; 0	39; 0
chr10:43595881@+	-300; 23	RET	24; 0	29; 0
chrX:107408303@-	-130; 36	COL4A6	0; 4	0; 25
chr15:37388702@-	-300; 95	MEIS2	19; 0	24; 0
chr15:37390646@-	-300; 100	MEIS2	13; 0	19; 0
chrX:118754079@-	-300; 66	SEPT6	12; 0	16; 0
chr20:32661328@+	-300; 38	RALY	14; 0	16; 0
chr15:75308869@+	-300; 62	SCAMP5	15; 0	16; 0
chr20:62364539@+	-300; 29	ZGPAT	15; 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.