Parameters
input_file: 20101125_LUjt8_1_hg19_ensembl59_S_iCLIP_TDP-43_SH-SY5Y_bedGraph-cDNA.bed.gz
input_res_type: single hits (=G+T), 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: 181733
[x-link sites] used in any map: 24666 (13.57%)
[single hits (=G+T), cDNA counts] total: 181733
[single hits (=G+T), cDNA counts] used in any map: 30718 (15.39%)

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 (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map
exon-intron	-300; 300	7591	4.18%	30.78%	8132	4.07%	26.47%
intron-exon	-300; 300	6634	3.65%	26.90%	7133	3.57%	23.22%
5-ncRNA	-1000; 300	2278	1.25%	9.24%	4283	2.15%	13.94%
ncRNA-3	-300; 1000	2300	1.27%	9.32%	4795	2.40%	15.61%
ORF-3UTR	-300; 300	947	0.52%	3.84%	1071	0.54%	3.49%
5UTR-ORF	-300; 300	181	0.10%	0.73%	196	0.10%	0.64%
inter-5UTR	-1000; 300	681	0.37%	2.76%	729	0.37%	2.37%
3UTR-inter	-300; 1000	1706	0.94%	6.92%	1852	0.93%	6.03%
inter-5	-1000; 300	2062	1.13%	8.36%	3849	1.93%	12.53%
3-inter	-300; 1000	3158	1.74%	12.80%	5733	2.87%	18.66%
BP best in intron	-300; 100	5555	3.06%	22.52%	6004	3.01%	19.55%

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	7004	3.85%	28.40%	92.27%	4788	1.32326
anti	587	0.32%	2.38%	7.73%	520	0.110901
both	7591	4.18%	30.78%	100.00%	5293	1.43416
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	7515	3.77%	24.46%	92.41%	4788	1.4198
anti	617	0.31%	2.01%	7.59%	520	0.116569
both	8132	4.07%	26.47%	100.00%	5293	1.53637

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 (=G+T), 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
chr3:116163722@-	-78; 300	LSAMP	18; 0	23; 0
chr17:38506177@+	-71; 300	RARA	18; 0	19; 0
chr15:37390166@-	-117; 300	MEIS2	18; 0	24; 0
chr4:71655799@+	-243; 300	RUFY3	17; 0	23; 0
chr15:37391100@-	-248; 299	MEIS2	17; 0	18; 0
chr1:33478643@-	-42; 300	AK2	17; 0	19; 0
chr7:128001358@-	-190; 300	PRRT4	16; 0	20; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr5:59188993@-	-228; 300	PDE4D	24; 0	33; 0
chr11:71944788@+	-45; 268	INPPL1	13; 0	32; 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
chr3:116163722@-	-78; 300	LSAMP	18; 0	23; 0
chr1:1158622@-	-57; 300	SDF4	20; 0	23; 0
chr1:21101941@-	-278; 222	HP1BP3	9; 0	22; 0
chr3:128206552@-	-106; 300	GATA2	16; 0	21; 0
chr7:128001358@-	-190; 300	PRRT4	16; 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.

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	6016	3.31%	24.39%	90.68%	4353	1.2343
anti	618	0.34%	2.51%	9.32%	539	0.126795
both	6634	3.65%	26.90%	100.00%	4874	1.3611
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	6491	3.25%	21.13%	91.00%	4353	1.33176
anti	642	0.32%	2.09%	9.00%	539	0.131719
both	7133	3.57%	23.22%	100.00%	4874	1.46348

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 (=G+T), cDNA counts] (same; anti)
chr3:64502796@-	-300; 300	ADAMTS9	41; 0	66; 0
chr10:43604478@+	-300; 100	RET	41; 0	84; 0
chr20:60912041@-	-300; 41	LAMA5	23; 0	30; 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
chr1:156834145@+	-300; 37	NTRK1	17; 0	23; 0
chr15:75308933@+	-300; 78	SCAMP5	16; 0	20; 0
chr10:43595906@+	-300; 132	RET	15; 0	20; 0
chr8:11640711@+	-300; 98	NEIL2	14; 0	16; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr10:43604478@+	-300; 100	RET	41; 0	84; 0
chr3:64502796@-	-300; 300	ADAMTS9	41; 0	66; 0
chr15:37388630@-	-300; 71	MEIS2	20; 0	36; 0
chr20:60912041@-	-300; 41	LAMA5	23; 0	30; 0
chr4:863744@-	-300; 300	GAK	21; 0	23; 0
chr20:32661368@+	-300; 36	RALY	18; 0	23; 0
chr1:156834145@+	-300; 37	NTRK1	17; 0	23; 0
chr15:75308933@+	-300; 78	SCAMP5	16; 0	20; 0
chr10:43595906@+	-300; 132	RET	15; 0	20; 0
chrX:47067960@+	-300; 300	UBA1	11; 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	1112	0.61%	4.51%	48.81%	562	0.857363
anti	1166	0.64%	4.73%	51.19%	748	0.898998
both	2278	1.25%	9.24%	100.00%	1297	1.75636
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	3011	1.51%	9.80%	70.30%	562	2.32151
anti	1272	0.64%	4.14%	29.70%	748	0.980725
both	4283	2.15%	13.94%	100.00%	1297	3.30224

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 (=G+T), cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	1754; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	64; 0	267; 0
chr11:65269806@+	-1000; 29	MALAT1	43; 0	50; 0
chr14:104150351@-	-1000; 300	AL139300.3	0; 25	0; 30
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 49
chr22:50295450@+	-1000; 30	AL671710.1	19; 0	20; 0
chr10:72975556@+	-1000; 36	AL359832.1, UNC5B	19; 0	29; 0
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 19	0; 24
chr3:37903270@-	-1000; 40	AC093415.2	0; 16	0; 18
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	16; 0	17; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	1754; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	64; 0	267; 0
chr11:65269806@+	-1000; 29	MALAT1	43; 0	50; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 49
chr14:104150351@-	-1000; 300	AL139300.3	0; 25	0; 30
chr10:72975556@+	-1000; 36	AL359832.1, UNC5B	19; 0	29; 0
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 19	0; 24
chr22:50295450@+	-1000; 30	AL671710.1	19; 0	20; 0
chr3:37903270@-	-1000; 40	AC093415.2	0; 16	0; 18
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	1200	0.66%	4.86%	52.17%	559	0.967742
anti	1100	0.61%	4.46%	47.83%	690	0.887097
both	2300	1.27%	9.32%	100.00%	1240	1.85484
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	3612	1.81%	11.76%	75.33%	559	2.9129
anti	1183	0.59%	3.85%	24.67%	690	0.954032
both	4795	2.40%	15.61%	100.00%	1240	3.86694

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 (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	375; 0	2714; 0
chr9:70646409@+	-300; 1000	RP11-154P18.1	0; 25	0; 26
chr4:71655925@-	-300; 1000	AC009570.3	0; 23	0; 31
chr7:19153894@+	-300; 1000	AC003986.6	0; 18	0; 19
chr19:35491390@+	-73; 1000	AC020907.6, GRAMD1A-ENSG00000248852	17; 0	20; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	25; 0
chr9:66456495@+	-205; 394	RP11-262H14.10	0; 14	0; 26
chr3:129112992@+	-55; 1000	RP11-529F4.1	0; 14	0; 15
chr3:160232693@-	-165; 362	KPNA4, snoU90	13; 0	16; 0
chr10:43474463@-	-42; 1000	RP11-124O11.2	12; 0	13; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	375; 0	2714; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 23	0; 31
chr9:70646409@+	-300; 1000	RP11-154P18.1	0; 25	0; 26
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	20; 0
chr7:19153894@+	-300; 1000	AC003986.6	0; 18	0; 19
chr3:160232693@-	-165; 362	KPNA4, snoU90	13; 0	16; 0
chr3:129112992@+	-55; 1000	RP11-529F4.1	0; 14	0; 15
chr15:37343027@-	-52; 1000	MEIS2, Y_RNA-ENSG00000206676	10; 0	15; 0

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

RNAmap 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	845	0.46%	3.43%	89.23%	523	1.38072
anti	102	0.06%	0.41%	10.77%	93	0.166667
both	947	0.52%	3.84%	100.00%	612	1.54739
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	958	0.48%	3.12%	89.45%	523	1.56536
anti	113	0.06%	0.37%	10.55%	93	0.184641
both	1071	0.54%	3.49%	100.00%	612	1.75

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 (=G+T), cDNA counts] (same; anti)
chr16:29831075@+	-100; 300	C16orf53	18; 0	20; 0
chr7:100806072@-	-56; 142	VGF	15; 0	51; 0
chr7:92244026@-	-287; 300	CDK6	14; 0	18; 0
chr7:26252043@+	-171; 300	CBX3	13; 0	15; 0
chr1:36181229@-	-300; 300	C1orf216	11; 0	12; 0
chr17:45016126@+	-81; 300	GOSR2	10; 0	11; 0
chr1:11083386@+	-69; 300	TARDBP	10; 0	12; 0
chr12:58217348@-	-81; 300	CTDSP2	8; 0	9; 0
chr10:32094640@-	-300; 138	ARHGAP12	8; 0	8; 0
chr1:149876562@-	-93; 300	SV2A	8; 0	9; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr7:100806072@-	-56; 142	VGF	15; 0	51; 0
chr16:29831075@+	-100; 300	C16orf53	18; 0	20; 0
chr7:92244026@-	-287; 300	CDK6	14; 0	18; 0
chr7:26252043@+	-171; 300	CBX3	13; 0	15; 0
chr1:36181229@-	-300; 300	C1orf216	11; 0	12; 0
chr1:11083386@+	-69; 300	TARDBP	10; 0	12; 0
chr17:45016126@+	-81; 300	GOSR2	10; 0	11; 0
chr12:58217348@-	-81; 300	CTDSP2	8; 0	9; 0
chr1:149876562@-	-93; 300	SV2A	8; 0	9; 0
chr4:174448424@-	-51; 300	HAND2	7; 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	155	0.09%	0.63%	85.64%	98	1.30252
anti	26	0.01%	0.11%	14.36%	21	0.218487
both	181	0.10%	0.73%	100.00%	119	1.52101
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	168	0.08%	0.55%	85.71%	98	1.41176
anti	28	0.01%	0.09%	14.29%	21	0.235294
both	196	0.10%	0.64%	100.00%	119	1.64706

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 (=G+T), 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 (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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
chr17:47755471@-	-62; 89	SPOP	3; 0	5; 0
chr6:31619552@-	-191; 60	BAT3	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	280	0.15%	1.14%	41.12%	192	0.625
anti	401	0.22%	1.63%	58.88%	259	0.895089
both	681	0.37%	2.76%	100.00%	448	1.52009
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	299	0.15%	0.97%	41.02%	192	0.667411
anti	430	0.22%	1.40%	58.98%	259	0.959821
both	729	0.37%	2.37%	100.00%	448	1.62723

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 (=G+T), 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; 12
chr20:51588945@+	-1000; 300	TSHZ2	10; 0	12; 0
chr16:89980524@+	-1000; 52	AC092143.1	10; 0	11; 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 (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr21:38445469@-	-1000; 90	PIGP	0; 13	0; 19
chr4:175205414@-	-1000; 300	FBXO8	0; 13	0; 16
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 12
chr20:51588945@+	-1000; 300	TSHZ2	10; 0	12; 0
chr19:36705503@+	-1000; 297	ZNF146	0; 8	0; 11
chr16:89980524@+	-1000; 52	AC092143.1	10; 0	11; 0
chr7:99717235@+	-1000; 66	CNPY4	0; 8	0; 10
chr19:36705985@-	-1000; 98	ZNF565	0; 8	0; 9
chr15:70390255@-	-1000; 300	TLE3	8; 0	9; 0
chr13:26828275@+	-1000; 251	CDK8	7; 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.

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	1365	0.75%	5.53%	80.01%	861	1.26623
anti	341	0.19%	1.38%	19.99%	232	0.316327
both	1706	0.94%	6.92%	100.00%	1078	1.58256
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	1486	0.74%	4.84%	80.24%	861	1.37848
anti	366	0.18%	1.19%	19.76%	232	0.339518
both	1852	0.93%	6.03%	100.00%	1078	1.718

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 (=G+T), cDNA counts] (same; anti)
chr2:72356365@-	-300; 1000	CYP26B1	19; 0	29; 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	20; 0
chr1:179785333@+	-300; 1000	FAM163A	11; 0	13; 0
chr7:100805788@-	-142; 1000	VGF	10; 0	26; 0
chr8:38132558@-	-299; 1000	WHSC1L1	9; 0	10; 0
chr18:40847857@-	-300; 1000	SYT4	9; 0	12; 0
chr12:48176534@+	-267; 1000	SLC48A1	0; 9	0; 16

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr2:72356365@-	-300; 1000	CYP26B1	19; 0	29; 0
chr7:100805788@-	-142; 1000	VGF	10; 0	26; 0
chr7:100813772@-	-300; 1000	C7orf52	17; 0	24; 0
chr6:122764494@-	-300; 1000	SERINC1	11; 0	20; 0
chr16:31000473@+	-300; 1000	HSD3B7	0; 16	0; 19
chr12:48176534@+	-267; 1000	SLC48A1	0; 9	0; 16
chr5:167975498@-	-300; 1000	PANK3	12; 0	13; 0
chr1:179785333@+	-300; 1000	FAM163A	11; 0	13; 0
chr18:40847857@-	-300; 1000	SYT4	9; 0	12; 0
chr10:43625799@+	-300; 1000	RET	8; 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	723	0.40%	2.93%	35.06%	413	0.575179
anti	1339	0.74%	5.43%	64.94%	855	1.06523
both	2062	1.13%	8.36%	100.00%	1257	1.64041
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	2391	1.20%	7.78%	62.12%	413	1.90215
anti	1458	0.73%	4.75%	37.88%	855	1.1599
both	3849	1.93%	12.53%	100.00%	1257	3.06205

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 (=G+T), cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	1754; 0
chr14:104150351@-	-1000; 300	AL139300.3	0; 25	0; 30
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 49
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 19	0; 24
chrUn_gl000220:109077@+	-758; 300	18S	14; 0	14; 0
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; 12	0; 13

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	1754; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 22	0; 49
chr14:104150351@-	-1000; 300	AL139300.3	0; 25	0; 30
chr1:204246132@+	-1000; 50	RP11-203F10.5	0; 19	0; 24
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_gl000220:109077@+	-758; 300	18S	14; 0	14; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 12	0; 13

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	2077	1.14%	8.42%	65.77%	1090	1.18618
anti	1081	0.59%	4.38%	34.23%	679	0.617362
both	3158	1.74%	12.80%	100.00%	1751	1.80354
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	4569	2.29%	14.87%	79.70%	1090	2.60937
anti	1164	0.58%	3.79%	20.30%	679	0.664763
both	5733	2.87%	18.66%	100.00%	1751	3.27413

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 (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	375; 0	2714; 0
chr9:70646409@+	-300; 1000	RP11-154P18.1	0; 25	0; 26
chr4:71655925@-	-300; 1000	AC009570.3	0; 23	0; 31
chr2:72356365@-	-300; 1000	CYP26B1	19; 0	29; 0
chr7:19153894@+	-300; 1000	AC003986.6	0; 18	0; 19
chr7:100813772@-	-300; 1000	C7orf52	17; 0	24; 0
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

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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	19; 0	29; 0
chr9:70646409@+	-300; 1000	RP11-154P18.1	0; 25	0; 26
chr9:66456495@+	-205; 394	RP11-262H14.10	0; 14	0; 26
chr7:100805788@-	-142; 1000	VGF	10; 0	26; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	25; 0
chr7:100813772@-	-300; 1000	C7orf52	17; 0	24; 0
chr6:122764494@-	-300; 1000	SERINC1	11; 0	20; 0
chr7:19153894@+	-300; 1000	AC003986.6	0; 18	0; 19

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	5147	2.83%	20.87%	92.66%	3576	1.31368
anti	408	0.22%	1.65%	7.34%	352	0.104135
both	5555	3.06%	22.52%	100.00%	3918	1.41782
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [BPs] in map	[single hits (=G+T), cDNA counts] per unique [BP]
same	5574	2.79%	18.15%	92.84%	3576	1.42266
anti	430	0.22%	1.40%	7.16%	352	0.10975
both	6004	3.01%	19.55%	100.00%	3918	1.53241

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 (=G+T), 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
chr1:156834120@+	-300; 23	NTRK1	17; 0	23; 0
chr20:62364539@+	-300; 29	ZGPAT	16; 0	21; 0
chr16:1509362@-	-300; 100	CLCN7	15; 0	15; 0
chr15:75308869@+	-300; 62	SCAMP5	15; 0	19; 0
chr3:48686751@-	-300; 100	CELSR3	14; 0	17; 0
chr10:43595881@+	-300; 23	RET	14; 0	19; 0

Top 10 BPs with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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
chr1:156834120@+	-300; 23	NTRK1	17; 0	23; 0
chr20:62364539@+	-300; 29	ZGPAT	16; 0	21; 0
chr15:75308869@+	-300; 62	SCAMP5	15; 0	19; 0
chr10:43595881@+	-300; 23	RET	14; 0	19; 0
chr7:157174488@+	-300; 100	DNAJB6	13; 0	18; 0
chr8:38279639@-	-300; 100	FGFR1	10; 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.