Parameters
input_file: 20101125_LUjt8_3_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: 19889
[x-link sites] used in any map: 5834 (29.33%)
[single hits in whole-genome, cDNA counts] total: 19889
[single hits in whole-genome, cDNA counts] used in any map: 7149 (31.35%)

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	991	4.98%	16.99%	1032	4.53%	14.44%
intron-exon	-300; 300	1279	6.43%	21.92%	1390	6.10%	19.44%
5-ncRNA	-1000; 300	451	2.27%	7.73%	894	3.92%	12.51%
ncRNA-3	-300; 1000	421	2.12%	7.22%	642	2.82%	8.98%
ORF-3UTR	-300; 300	1073	5.39%	18.39%	1328	5.82%	18.58%
5UTR-ORF	-300; 300	42	0.21%	0.72%	42	0.18%	0.59%
inter-5UTR	-1000; 300	103	0.52%	1.77%	106	0.46%	1.48%
3UTR-inter	-300; 1000	1298	6.53%	22.25%	1532	6.72%	21.43%
inter-5	-1000; 300	427	2.15%	7.32%	689	3.02%	9.64%
3-inter	-300; 1000	1695	8.52%	29.05%	2143	9.40%	29.98%
BP best in intron	-300; 100	425	2.14%	7.28%	445	1.95%	6.22%

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	946	4.76%	16.22%	95.46%	831	1.08486
anti	45	0.23%	0.77%	4.54%	41	0.0516055
both	991	4.98%	16.99%	100.00%	872	1.13647
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	986	4.32%	13.79%	95.54%	831	1.13073
anti	46	0.20%	0.64%	4.46%	41	0.0527523
both	1032	4.53%	14.44%	100.00%	872	1.18349

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)
chr22:38687371@-	-285; 177	CSNK1E	9; 0	12; 0
chr7:135613418@-	-300; 300	MTPN	6; 0	7; 0
chr10:54077417@+	-300; 133	DKK1	5; 0	6; 0
chrX:39910497@-	-300; 300	BCOR	4; 0	4; 0
chr9:114306712@+	-300; 300	ZNF483	4; 0	4; 0
chr8:99057169@-	-73; 300	RPL30	4; 0	4; 0
chr3:197400831@-	-267; 300	KIAA0226	4; 0	4; 0
chr21:34949840@-	-194; 300	DONSON	4; 0	4; 0
chr21:27425550@-	-134; 300	APP	4; 0	5; 0
chr2:10931919@-	-66; 300	PDIA6	4; 0	4; 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)
chr10:105174908@+	-74; 300	PDCD11	2; 0	14; 0
chr22:38687371@-	-285; 177	CSNK1E	9; 0	12; 0
chr7:135613418@-	-300; 300	MTPN	6; 0	7; 0
chr10:54077417@+	-300; 133	DKK1	5; 0	6; 0
chr21:27425550@-	-134; 300	APP	4; 0	5; 0
chrX:39910497@-	-300; 300	BCOR	4; 0	4; 0
chr9:114306712@+	-300; 300	ZNF483	4; 0	4; 0
chr8:99057169@-	-73; 300	RPL30	4; 0	4; 0
chr3:197400831@-	-267; 300	KIAA0226	4; 0	4; 0
chr21:34949840@-	-194; 300	DONSON	4; 0	4; 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	1221	6.14%	20.93%	95.47%	1025	1.1337
anti	58	0.29%	0.99%	4.53%	52	0.0538533
both	1279	6.43%	21.92%	100.00%	1077	1.18756
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	1330	5.83%	18.60%	95.68%	1025	1.23491
anti	60	0.26%	0.84%	4.32%	52	0.0557103
both	1390	6.10%	19.44%	100.00%	1077	1.29062

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)
chr3:64502796@-	-300; 300	ADAMTS9	50; 0	91; 0
chr4:174253388@-	-291; 267	HMGB2	15; 0	31; 0
chr2:242291357@+	-300; 300	SEPT2	7; 0	8; 0
chr10:33200597@-	-108; 111	ITGB1	7; 0	7; 0
chr10:73048324@+	-300; 82	UNC5B	7; 0	8; 0
chr5:179041959@-	-293; 300	HNRNPH1	5; 0	7; 0
chr20:57485737@+	-141; 255	GNAS	5; 0	5; 0
chr2:47387942@-	-300; 300	CALM2	5; 0	5; 0
chr1:26227577@-	-160; 260	STMN1	5; 0	5; 0
chr9:139247508@+	-300; 49	GPSM1	4; 0	4; 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)
chr3:64502796@-	-300; 300	ADAMTS9	50; 0	91; 0
chr4:174253388@-	-291; 267	HMGB2	15; 0	31; 0
chr8:15480586@+	-300; 86	TUSC3	3; 0	10; 0
chr2:242291357@+	-300; 300	SEPT2	7; 0	8; 0
chr10:73048324@+	-300; 82	UNC5B	7; 0	8; 0
chr5:179041959@-	-293; 300	HNRNPH1	5; 0	7; 0
chr12:104709554@+	-300; 60	TXNRD1	2; 0	7; 0
chr10:33200597@-	-108; 111	ITGB1	7; 0	7; 0
chr20:57485737@+	-141; 255	GNAS	5; 0	5; 0
chr2:47387942@-	-300; 300	CALM2	5; 0	5; 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	264	1.33%	4.53%	58.54%	103	1.26316
anti	187	0.94%	3.21%	41.46%	108	0.894737
both	451	2.27%	7.73%	100.00%	209	2.15789
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	661	2.90%	9.25%	73.94%	103	3.16268
anti	233	1.02%	3.26%	26.06%	108	1.11483
both	894	3.92%	12.51%	100.00%	209	4.27751

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	70; 0	263; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	50; 0	221; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 32	0; 73
chr12:74934899@+	-1000; 108	ATXN7L3B	12; 0	12; 0
chrM:16022@-	-274; 34	J01415.14	9; 0	18; 0
chrM:576@+	-288; 35	J01415.1	3; 5	4; 6
chr19:54379302@-	-1000; 120	AC008440.5	0; 6	0; 7
chr11:65269806@+	-1000; 29	MALAT1	6; 0	7; 0
chr5:82877138@-	-1000; 114	CTC-348L14.1	0; 5	0; 5
chr1:205685227@+	-1000; 300	AC119673.2	0; 4	0; 5

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	70; 0	263; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	50; 0	221; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 32	0; 73
chrM:16022@-	-274; 34	J01415.14	9; 0	18; 0
chr19:58024440@-	-1000; 33	hsa-mir-1274b	1; 0	13; 0
chr12:74934899@+	-1000; 108	ATXN7L3B	12; 0	12; 0
chrM:576@+	-288; 35	J01415.1	3; 5	4; 6
chr19:54379302@-	-1000; 120	AC008440.5	0; 6	0; 7
chr11:65269806@+	-1000; 29	MALAT1	6; 0	7; 0
chr5:82877138@-	-1000; 114	CTC-348L14.1	0; 5	0; 5

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	285	1.43%	4.89%	67.70%	112	1.31944
anti	136	0.68%	2.33%	32.30%	104	0.62963
both	421	2.12%	7.22%	100.00%	216	1.94907
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	488	2.14%	6.83%	76.01%	112	2.25926
anti	154	0.68%	2.15%	23.99%	104	0.712963
both	642	2.82%	8.98%	100.00%	216	2.97222

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	117; 0	291; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	18; 0	24; 0
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	27; 0
chrM:15953@+	-33; 309	J01415.6	0; 9	0; 18
chr7:131812561@+	-122; 1000	AC093106.4	0; 7	0; 8
chr7:149018954@-	-114; 1000	AC004941.5	6; 0	9; 0
chr5:149408910@-	-52; 1000	snoU13-ENSG00000238369	0; 6	0; 6
chr8:99056338@+	-185; 1000	SNORA72-ENSG00000245970	0; 4	0; 4
chr2:120979498@-	-300; 1000	TMEM185B	4; 0	4; 0
chr1:109643234@+	-210; 1000	snoU2-25	4; 0	5; 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	117; 0	291; 0
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	27; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	18; 0	24; 0
chrM:15953@+	-33; 309	J01415.6	0; 9	0; 18
chr7:149018954@-	-114; 1000	AC004941.5	6; 0	9; 0
chr7:131812561@+	-122; 1000	AC093106.4	0; 7	0; 8
chr19:781001@-	-300; 1000	AC006273.2	2; 0	8; 0
chr5:149408910@-	-52; 1000	snoU13-ENSG00000238369	0; 6	0; 6
chr7:19853306@-	-20; 1000	AC004543.2	0; 1	0; 5
chr1:109643234@+	-210; 1000	snoU2-25	4; 0	5; 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	1058	5.32%	18.14%	98.60%	563	1.84642
anti	15	0.08%	0.26%	1.40%	10	0.026178
both	1073	5.39%	18.39%	100.00%	573	1.8726
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	1304	5.72%	18.24%	98.19%	563	2.27574
anti	24	0.11%	0.34%	1.81%	10	0.0418848
both	1328	5.82%	18.58%	100.00%	573	2.31763

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	48; 0	66; 0
chr7:100806072@-	-56; 142	VGF	33; 0	181; 0
chr16:67472427@-	-82; 253	ATP6V0D1	21; 0	25; 0
chr7:26252043@+	-171; 300	CBX3	14; 0	16; 0
chr5:122359566@-	-66; 300	PPIC	13; 0	14; 0
chrX:40465007@+	-98; 300	ATP6AP2	12; 0	13; 0
chr4:174448424@-	-51; 300	HAND2	11; 0	16; 0
chr1:149876562@-	-93; 300	SV2A	11; 0	14; 0
chr4:148465132@+	-300; 300	EDNRA	9; 0	11; 0
chr1:36181229@-	-300; 300	C1orf216	9; 0	10; 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	33; 0	181; 0
chr7:92244026@-	-287; 300	CDK6	48; 0	66; 0
chr16:67472427@-	-82; 253	ATP6V0D1	21; 0	25; 0
chr7:26252043@+	-171; 300	CBX3	14; 0	16; 0
chr4:174448424@-	-51; 300	HAND2	11; 0	16; 0
chr5:122359566@-	-66; 300	PPIC	13; 0	14; 0
chr1:149876562@-	-93; 300	SV2A	11; 0	14; 0
chrX:40465007@+	-98; 300	ATP6AP2	12; 0	13; 0
chr4:148465132@+	-300; 300	EDNRA	9; 0	11; 0
chr3:160219888@-	-51; 300	KPNA4	8; 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 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	37	0.19%	0.63%	88.10%	30	1.05714
anti	5	0.03%	0.09%	11.90%	5	0.142857
both	42	0.21%	0.72%	100.00%	35	1.2
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	37	0.16%	0.52%	88.10%	30	1.05714
anti	5	0.02%	0.07%	11.90%	5	0.142857
both	42	0.18%	0.59%	100.00%	35	1.2

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)
chr2:72374990@-	-88; 116	CYP26B1	4; 0	4; 0
chr2:61764828@-	-277; 66	XPO1	3; 0	3; 0
chr4:71588290@+	-290; 89	RUFY3	2; 0	2; 0
chr17:46128423@+	-228; 283	NFE2L1	2; 0	2; 0
chrX:40594663@-	-60; 107	MED14	1; 0	1; 0
chr8:101733810@-	-252; 96	PABPC1	1; 0	1; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr7:100200025@+	-113; 74	PCOLCE	1; 0	1; 0
chr3:48964894@+	-300; 176	ARIH2	1; 0	1; 0
chr22:37098620@-	-300; 105	CACNG2	1; 0	1; 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)
chr2:72374990@-	-88; 116	CYP26B1	4; 0	4; 0
chr2:61764828@-	-277; 66	XPO1	3; 0	3; 0
chr4:71588290@+	-290; 89	RUFY3	2; 0	2; 0
chr17:46128423@+	-228; 283	NFE2L1	2; 0	2; 0
chrX:40594663@-	-60; 107	MED14	1; 0	1; 0
chr8:101733810@-	-252; 96	PABPC1	1; 0	1; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr7:100200025@+	-113; 74	PCOLCE	1; 0	1; 0
chr3:48964894@+	-300; 176	ARIH2	1; 0	1; 0
chr22:37098620@-	-300; 105	CACNG2	1; 0	1; 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	40	0.20%	0.69%	38.83%	29	0.481928
anti	63	0.32%	1.08%	61.17%	55	0.759036
both	103	0.52%	1.77%	100.00%	83	1.24096
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	40	0.18%	0.56%	37.74%	29	0.481928
anti	66	0.29%	0.92%	62.26%	55	0.795181
both	106	0.46%	1.48%	100.00%	83	1.27711

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)
chr2:72375166@-	-1000; 88	CYP26B1	7; 0	7; 0
chr17:68165675@+	-1000; 83	KCNJ2	0; 5	0; 6
chr20:51588945@+	-1000; 300	TSHZ2	3; 0	3; 0
chr18:29523090@-	-1000; 182	KIAA1012	0; 3	0; 3
chr15:93443418@+	-1000; 300	CHD2	3; 0	3; 0
chr5:55290771@-	-1000; 80	IL6ST	1; 1	1; 1
chr19:40502942@+	-1000; 61	ZNF546	0; 2	0; 2
chr19:37569336@+	-1000; 68	ZNF420	0; 2	0; 2
chr16:89980524@+	-1000; 52	AC092143.1	2; 0	2; 0
chr9:131084814@+	-1000; 161	COQ4	0; 1	0; 1

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)
chr2:72375166@-	-1000; 88	CYP26B1	7; 0	7; 0
chr17:68165675@+	-1000; 83	KCNJ2	0; 5	0; 6
chr20:51588945@+	-1000; 300	TSHZ2	3; 0	3; 0
chr18:29523090@-	-1000; 182	KIAA1012	0; 3	0; 3
chr15:93443418@+	-1000; 300	CHD2	3; 0	3; 0
chr5:55290771@-	-1000; 80	IL6ST	1; 1	1; 1
chr19:40502942@+	-1000; 61	ZNF546	0; 2	0; 2
chr19:37569336@+	-1000; 68	ZNF420	0; 2	0; 2
chr17:70117160@+	-1000; 186	SOX9	0; 1	0; 2
chr16:89980524@+	-1000; 52	AC092143.1	2; 0	2; 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	1160	5.83%	19.88%	89.37%	633	1.65714
anti	138	0.69%	2.37%	10.63%	69	0.197143
both	1298	6.53%	22.25%	100.00%	700	1.85429
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	1374	6.03%	19.22%	89.69%	633	1.96286
anti	158	0.69%	2.21%	10.31%	69	0.225714
both	1532	6.72%	21.43%	100.00%	700	2.18857

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	41; 0	75; 0
chr7:100805788@-	-142; 1000	VGF	21; 0	58; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 25
chr3:128338815@-	-218; 1000	RPN1	18; 0	24; 0
chr1:192781403@+	-300; 1000	RGS2	17; 0	20; 0
chr19:47278138@-	-300; 1000	SLC1A5	14; 0	14; 0
chr2:9628613@-	-300; 1000	ADAM17	13; 0	28; 0
chr12:89741837@-	-300; 1000	DUSP6	12; 0	26; 0
chr12:48176534@+	-267; 1000	SLC48A1	0; 12	0; 13
chr6:122764494@-	-300; 1000	SERINC1	11; 0	22; 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	41; 0	75; 0
chr7:100805788@-	-142; 1000	VGF	21; 0	58; 0
chr2:9628613@-	-300; 1000	ADAM17	13; 0	28; 0
chr12:89741837@-	-300; 1000	DUSP6	12; 0	26; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 25
chr3:128338815@-	-218; 1000	RPN1	18; 0	24; 0
chr6:122764494@-	-300; 1000	SERINC1	11; 0	22; 0
chr1:192781403@+	-300; 1000	RGS2	17; 0	20; 0
chr18:40847857@-	-300; 1000	SYT4	11; 0	18; 0
chr12:56555634@-	-300; 1000	SMARCC2	0; 11	0; 18

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	165	0.83%	2.83%	38.64%	72	0.743243
anti	262	1.32%	4.49%	61.36%	151	1.18018
both	427	2.15%	7.32%	100.00%	222	1.92342
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	362	1.59%	5.06%	52.54%	72	1.63063
anti	327	1.43%	4.57%	47.46%	151	1.47297
both	689	3.02%	9.64%	100.00%	222	3.1036

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	70; 0	263; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 32	0; 73
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 28	0; 42
chr12:74934899@+	-1000; 108	ATXN7L3B	12; 0	12; 0
chr2:72375166@-	-1000; 88	CYP26B1	7; 0	7; 0
chrM:5903@+	-162; 300	J01415.8	0; 6	0; 7
chr19:54379302@-	-1000; 120	AC008440.5	0; 6	0; 7
chr5:82877138@-	-1000; 114	CTC-348L14.1	0; 5	0; 5
chr17:68165675@+	-1000; 83	KCNJ2	0; 5	0; 6
chr1:205685227@+	-1000; 300	AC119673.2	0; 4	0; 5

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	70; 0	263; 0
chr4:174448420@+	-1000; 300	RP11-471J12.1	0; 32	0; 73
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 28	0; 42
chr12:74934899@+	-1000; 108	ATXN7L3B	12; 0	12; 0
chrM:5903@+	-162; 300	J01415.8	0; 6	0; 7
chr2:72375166@-	-1000; 88	CYP26B1	7; 0	7; 0
chr19:54379302@-	-1000; 120	AC008440.5	0; 6	0; 7
chr17:68165675@+	-1000; 83	KCNJ2	0; 5	0; 6
chr5:82877138@-	-1000; 114	CTC-348L14.1	0; 5	0; 5
chr1:205685227@+	-1000; 300	AC119673.2	0; 4	0; 5

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	1447	7.28%	24.80%	85.37%	732	1.66513
anti	248	1.25%	4.25%	14.63%	140	0.285386
both	1695	8.52%	29.05%	100.00%	869	1.95052
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	1865	8.18%	26.09%	87.03%	732	2.14614
anti	278	1.22%	3.89%	12.97%	140	0.319908
both	2143	9.40%	29.98%	100.00%	869	2.46605

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	117; 0	291; 0
chr2:72356365@-	-300; 1000	CYP26B1	41; 0	75; 0
chr17:26880403@-	-300; 372	PIGS	22; 0	26; 0
chr7:100805788@-	-142; 1000	VGF	21; 0	58; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 25
chr3:128338815@-	-218; 1000	RPN1	18; 0	24; 0
chr1:192781403@+	-300; 1000	RGS2	17; 0	20; 0
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	27; 0
chr19:47278138@-	-300; 1000	SLC1A5	14; 0	14; 0
chr1:169101767@-	-127; 1000	NME7	0; 14	0; 21

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	117; 0	291; 0
chr2:72356365@-	-300; 1000	CYP26B1	41; 0	75; 0
chr7:100805788@-	-142; 1000	VGF	21; 0	58; 0
chr2:9628613@-	-300; 1000	ADAM17	13; 0	28; 0
chrUn_gl000220:118417@+	-300; 1000	28S	14; 0	27; 0
chr17:26880403@-	-300; 372	PIGS	22; 0	26; 0
chr12:89741837@-	-300; 1000	DUSP6	12; 0	26; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 25
chr3:128338815@-	-218; 1000	RPN1	18; 0	24; 0
chr6:122764494@-	-300; 1000	SERINC1	11; 0	22; 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	390	1.96%	6.68%	91.76%	325	1.09859
anti	35	0.18%	0.60%	8.24%	31	0.0985915
both	425	2.14%	7.28%	100.00%	355	1.19718
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	408	1.79%	5.71%	91.69%	325	1.1493
anti	37	0.16%	0.52%	8.31%	31	0.104225
both	445	1.95%	6.22%	100.00%	355	1.25352

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	24; 0	36; 0
chr10:73048078@+	-157; 100	UNC5B	10; 0	11; 0
chr7:90041856@+	-300; 99	CLDN12	4; 0	4; 0
chr9:130698280@-	-164; 100	DPM2	3; 0	3; 0
chr6:35715009@+	-300; 26	C6orf81	0; 3	0; 3
chr2:170668525@-	-141; 100	METTL5	0; 3	0; 3
chr19:42409887@+	-227; 22	ARHGEF1	3; 0	3; 0
chr19:37342559@+	-300; 68	AC008733.3	3; 0	3; 0
chr15:75308869@+	-300; 62	SCAMP5	3; 0	4; 0
chrX:118754079@-	-300; 66	SEPT6	2; 0	2; 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	24; 0	36; 0
chr10:73048078@+	-157; 100	UNC5B	10; 0	11; 0
chr7:90041856@+	-300; 99	CLDN12	4; 0	4; 0
chr15:75308869@+	-300; 62	SCAMP5	3; 0	4; 0
chr9:130698280@-	-164; 100	DPM2	3; 0	3; 0
chr6:35715009@+	-300; 26	C6orf81	0; 3	0; 3
chr2:170668525@-	-141; 100	METTL5	0; 3	0; 3
chr19:42409887@+	-227; 22	ARHGEF1	3; 0	3; 0
chr19:37342559@+	-300; 68	AC008733.3	3; 0	3; 0
chr1:165175377@-	-300; 100	LMX1A	0; 1	0; 3

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