Parameters
input_file: 20100222_LUjt3_4_hg19_ensembl59_G_iCLIP_TDP-43_Embrionic-Stem-Cells_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: 2.42556e+06
[x-link sites] used in any map: 315962 (13.03%)
[single hits in whole-genome, cDNA counts] total: 2.42556e+06
[single hits in whole-genome, cDNA counts] used in any map: 386030 (13.95%)

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	90265	3.72%	28.57%	101856	3.68%	26.39%
intron-exon	-300; 300	91862	3.79%	29.07%	103071	3.72%	26.70%
5-ncRNA	-1000; 300	26906	1.11%	8.52%	39790	1.44%	10.31%
ncRNA-3	-300; 1000	28422	1.17%	9.00%	49060	1.77%	12.71%
ORF-3UTR	-300; 300	15067	0.62%	4.77%	17926	0.65%	4.64%
5UTR-ORF	-300; 300	2112	0.09%	0.67%	2514	0.09%	0.65%
inter-5UTR	-1000; 300	6612	0.27%	2.09%	8099	0.29%	2.10%
3UTR-inter	-300; 1000	24095	0.99%	7.63%	27248	0.98%	7.06%
inter-5	-1000; 300	21819	0.90%	6.91%	32731	1.18%	8.48%
3-inter	-300; 1000	39235	1.62%	12.42%	57170	2.07%	14.81%
BP best in intron	-300; 100	71944	2.97%	22.77%	83220	3.01%	21.56%

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	86281	3.56%	27.31%	95.59%	36725	2.22868
anti	3984	0.16%	1.26%	4.41%	2379	0.102909
both	90265	3.72%	28.57%	100.00%	38714	2.33159
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	97537	3.52%	25.27%	95.76%	36725	2.51942
anti	4319	0.16%	1.12%	4.24%	2379	0.111562
both	101856	3.68%	26.39%	100.00%	38714	2.63099

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)
chr3:116163722@-	-78; 300	LSAMP	135; 0	345; 0
chr6:161575179@-	-81; 300	AGPAT4	124; 0	341; 0
chr11:12886447@+	-32; 300	TEAD1	118; 0	336; 0
chr3:9290567@-	-300; 300	SRGAP3	110; 0	153; 0
chr21:44269334@-	-300; 300	WDR4	109; 0	246; 0
chr5:883069@-	-226; 300	BRD9	108; 0	163; 0
chrX:28606164@+	-300; 300	IL1RAPL1	107; 0	186; 0
chr1:1158622@-	-57; 300	SDF4	101; 0	210; 0
chr8:38280260@-	-216; 300	FGFR1	97; 0	158; 0
chr19:46815910@+	-247; 300	HIF3A	96; 0	169; 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)
chr3:116163722@-	-78; 300	LSAMP	135; 0	345; 0
chr6:161575179@-	-81; 300	AGPAT4	124; 0	341; 0
chr11:12886447@+	-32; 300	TEAD1	118; 0	336; 0
chr21:44269334@-	-300; 300	WDR4	109; 0	246; 0
chr1:1158622@-	-57; 300	SDF4	101; 0	210; 0
chrX:28606164@+	-300; 300	IL1RAPL1	107; 0	186; 0
chr19:46815910@+	-247; 300	HIF3A	96; 0	169; 0
chr1:39812882@+	-117; 300	MACF1	70; 0	165; 0
chr5:883069@-	-226; 300	BRD9	108; 0	163; 0
chr8:38280260@-	-216; 300	FGFR1	97; 0	158; 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	87480	3.61%	27.69%	95.23%	38035	2.17196
anti	4382	0.18%	1.39%	4.77%	2738	0.108797
both	91862	3.79%	29.07%	100.00%	40277	2.28076
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	98282	3.55%	25.46%	95.35%	38035	2.44015
anti	4789	0.17%	1.24%	4.65%	2738	0.118902
both	103071	3.72%	26.70%	100.00%	40277	2.55905

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)
chr12:124915332@-	-300; 86	NCOR2	176; 0	491; 0
chr1:156643318@-	-300; 37	NES	149; 0	470; 0
chr6:161574530@-	-300; 77	AGPAT4	137; 0	381; 0
chr4:863744@-	-300; 300	GAK	131; 0	206; 0
chr20:62364570@+	-300; 67	ZGPAT	113; 0	217; 0
chrX:47067960@+	-300; 300	UBA1	99; 0	188; 0
chr17:2583457@+	-300; 78	PAFAH1B1	92; 0	154; 0
chrX:48677853@+	-300; 300	HDAC6	91; 0	124; 0
chr16:31199172@+	-300; 253	FUS	79; 0	102; 0
chrX:110346386@+	-300; 74	PAK3	73; 0	102; 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)
chr12:124915332@-	-300; 86	NCOR2	176; 0	491; 0
chr1:156643318@-	-300; 37	NES	149; 0	470; 0
chr6:161574530@-	-300; 77	AGPAT4	137; 0	381; 0
chr3:9291368@-	-300; 300	SRGAP3	57; 0	239; 0
chr20:62364570@+	-300; 67	ZGPAT	113; 0	217; 0
chr4:863744@-	-300; 300	GAK	131; 0	206; 0
chrX:47067960@+	-300; 300	UBA1	99; 0	188; 0
chr19:49607890@+	-300; 51	SNRNP70	73; 0	178; 0
chr17:2583457@+	-300; 78	PAFAH1B1	92; 0	154; 0
chr1:31406188@-	-300; 249	PUM1	66; 0	152; 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	13053	0.54%	4.13%	48.51%	3101	1.99161
anti	13853	0.57%	4.38%	51.49%	3696	2.11367
both	26906	1.11%	8.52%	100.00%	6554	4.10528
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	24046	0.87%	6.23%	60.43%	3101	3.6689
anti	15744	0.57%	4.08%	39.57%	3696	2.4022
both	39790	1.44%	10.31%	100.00%	6554	6.0711

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	548; 0	1466; 0
chr12:97957589@+	-1000; 50	hsa-mir-135a-2	361; 0	1403; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	278; 0	596; 0
chr12:97885686@+	-1000; 35	hsa-mir-1251	220; 0	372; 0
chr1:109642814@+	-1000; 210	snoU2-25	205; 0	3728; 0
chr15:25232071@+	-879; 35	SNORD108	156; 0	231; 0
chr22:50295450@+	-1000; 30	AL671710.1	150; 0	307; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 137	0; 289
chr3:160233023@-	-108; 165	KPNA4, snoU90	129; 0	887; 0
chr14:104150351@-	-1000; 300	AL139300.3	0; 129	0; 260

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	205; 0	3728; 0
chr11:65269806@+	-1000; 29	MALAT1	548; 0	1466; 0
chr12:97957589@+	-1000; 50	hsa-mir-135a-2	361; 0	1403; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	129; 0	887; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	86; 0	665; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	278; 0	596; 0
chr12:97885686@+	-1000; 35	hsa-mir-1251	220; 0	372; 0
chr22:50295450@+	-1000; 30	AL671710.1	150; 0	307; 0
chr7:148684339@-	-1000; 56	Y_RNA-ENSG00000201098	40; 0	302; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 137	0; 289

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	14119	0.58%	4.47%	49.68%	3407	2.08091
anti	14303	0.59%	4.53%	50.32%	3635	2.10803
both	28422	1.17%	9.00%	100.00%	6785	4.18895
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	32491	1.17%	8.42%	66.23%	3407	4.78865
anti	16569	0.60%	4.29%	33.77%	3635	2.442
both	49060	1.77%	12.71%	100.00%	6785	7.23066

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	1069; 0	9829; 0
chr10:712562@+	-203; 1000	RP11-809C18.1	0; 230	0; 479
chr1:109643234@+	-210; 1000	snoU2-25	210; 0	2218; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	166; 0	733; 0
chrUn_gl000220:118417@+	-300; 1000	28S	164; 0	1067; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 161	0; 258
chr1:142653799@+	-41; 1000	AL583842.1-ENSG00000239012, AL583842.3-ENSG00000230880	0; 161	0; 345
chr3:160232693@-	-165; 362	KPNA4, snoU90	136; 0	1478; 0
chr4:17629790@+	-177; 1000	AC006160.1	126; 0	189; 0
chr12:97957689@+	-50; 1000	hsa-mir-135a-2	124; 0	208; 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	1069; 0	9829; 0
chr1:109643234@+	-210; 1000	snoU2-25	210; 0	2218; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	136; 0	1478; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	93; 0	1143; 0
chrUn_gl000220:118417@+	-300; 1000	28S	164; 0	1067; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	166; 0	733; 0
chr10:712562@+	-203; 1000	RP11-809C18.1	0; 230	0; 479
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	17; 0	348; 0
chr1:142653799@+	-41; 1000	AL583842.1-ENSG00000239012, AL583842.3-ENSG00000230880	0; 161	0; 345
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	30; 4	310; 4

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	14119	0.58%	4.47%	93.71%	4190	3.10581
anti	948	0.04%	0.30%	6.29%	484	0.208535
both	15067	0.62%	4.77%	100.00%	4546	3.31434
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	16881	0.61%	4.37%	94.17%	4190	3.71337
anti	1045	0.04%	0.27%	5.83%	484	0.229872
both	17926	0.65%	4.64%	100.00%	4546	3.94325

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)
chr9:126139954@+	-300; 300	CRB2	115; 0	289; 0
chr1:11083386@+	-69; 300	TARDBP	115; 0	199; 0
chr7:92244026@-	-287; 300	CDK6	111; 0	191; 0
chr16:89981552@+	-300; 300	AC092143.1	111; 0	174; 0
chr16:29831075@+	-100; 300	C16orf53	105; 0	229; 0
chr16:67472427@-	-82; 253	ATP6V0D1	91; 0	238; 0
chr2:189876774@+	-211; 300	COL3A1	83; 0	122; 0
chr6:47200497@-	-116; 300	TNFRSF21	82; 0	135; 0
chr14:59835577@+	-105; 300	DAAM1	81; 0	130; 0
chr7:26252043@+	-171; 300	CBX3	80; 0	137; 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)
chr9:126139954@+	-300; 300	CRB2	115; 0	289; 0
chr16:67472427@-	-82; 253	ATP6V0D1	91; 0	238; 0
chr16:29831075@+	-100; 300	C16orf53	105; 0	229; 0
chr1:11083386@+	-69; 300	TARDBP	115; 0	199; 0
chr7:92244026@-	-287; 300	CDK6	111; 0	191; 0
chr16:89981552@+	-300; 300	AC092143.1	111; 0	174; 0
chr1:39469934@+	-90; 300	AKIRIN1	70; 0	150; 0
chr7:26252043@+	-171; 300	CBX3	80; 0	137; 0
chr12:58217348@-	-81; 300	CTDSP2	61; 0	137; 0
chr6:47200497@-	-116; 300	TNFRSF21	82; 0	135; 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	1873	0.08%	0.59%	88.68%	768	2.20612
anti	239	0.01%	0.08%	11.32%	90	0.281508
both	2112	0.09%	0.67%	100.00%	849	2.48763
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	2240	0.08%	0.58%	89.10%	768	2.6384
anti	274	0.01%	0.07%	10.90%	90	0.322733
both	2514	0.09%	0.65%	100.00%	849	2.96113

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)
chr16:89980628@+	-52; 300	AC092143.1	115; 0	190; 0
chr2:61764828@-	-277; 66	XPO1	87; 0	166; 0
chr4:71588290@+	-290; 89	RUFY3	62; 0	112; 0
chrX:139866530@-	-96; 300	CDR1	0; 58	0; 72
chr22:24033492@+	-266; 300	RGL4	0; 35	0; 45
chr21:38455925@+	-300; 300	TTC3	35; 0	39; 0
chr11:64073917@+	-110; 200	ESRRA	29; 0	42; 0
chrX:47068739@+	-300; 173	UBA1	23; 0	31; 0
chr6:31619552@-	-191; 60	BAT3	22; 0	31; 0
chr5:86564268@+	-282; 269	RASA1	22; 0	30; 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)
chr16:89980628@+	-52; 300	AC092143.1	115; 0	190; 0
chr2:61764828@-	-277; 66	XPO1	87; 0	166; 0
chr4:71588290@+	-290; 89	RUFY3	62; 0	112; 0
chrX:139866530@-	-96; 300	CDR1	0; 58	0; 72
chr22:24033492@+	-266; 300	RGL4	0; 35	0; 45
chr11:64073917@+	-110; 200	ESRRA	29; 0	42; 0
chr21:38455925@+	-300; 300	TTC3	35; 0	39; 0
chrX:47068739@+	-300; 173	UBA1	23; 0	31; 0
chr6:31619552@-	-191; 60	BAT3	22; 0	31; 0
chr6:31508971@-	-66; 265	BAT1	16; 0	30; 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	2616	0.11%	0.83%	39.56%	874	1.29249
anti	3996	0.16%	1.26%	60.44%	1279	1.97431
both	6612	0.27%	2.09%	100.00%	2024	3.2668
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	3221	0.12%	0.83%	39.77%	874	1.5914
anti	4878	0.18%	1.26%	60.23%	1279	2.41008
both	8099	0.29%	2.10%	100.00%	2024	4.00148

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)
chr21:38445469@-	-1000; 90	PIGP	0; 155	0; 319
chr16:89980524@+	-1000; 52	AC092143.1	148; 0	256; 0
chr19:36705503@+	-1000; 297	ZNF146	1; 118	1; 147
chr20:51588945@+	-1000; 300	TSHZ2	91; 1	239; 1
chr9:95709732@+	-1000; 139	FGD3	0; 90	0; 144
chr12:24103864@-	-1000; 269	SOX5	78; 0	112; 0
chr6:31620192@+	-1000; 68	APOM	0; 71	0; 87
chr19:36705985@-	-1000; 98	ZNF565	0; 58	0; 73
chr8:33370702@-	-1000; 286	C8orf41	0; 53	0; 122
chr5:140027369@-	-1000; 101	NDUFA2	0; 52	0; 72

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; 155	0; 319
chr16:89980524@+	-1000; 52	AC092143.1	148; 0	256; 0
chr20:51588945@+	-1000; 300	TSHZ2	91; 1	239; 1
chr15:89878025@-	-1000; 61	POLG	0; 12	0; 155
chr19:36705503@+	-1000; 297	ZNF146	1; 118	1; 147
chr9:95709732@+	-1000; 139	FGD3	0; 90	0; 144
chr8:33370702@-	-1000; 286	C8orf41	0; 53	0; 122
chr12:24103864@-	-1000; 269	SOX5	78; 0	112; 0
chr6:31620192@+	-1000; 68	APOM	0; 71	0; 87
chr19:36705985@-	-1000; 98	ZNF565	0; 58	0; 73

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	19335	0.80%	6.12%	80.24%	4999	3.23652
anti	4760	0.20%	1.51%	19.76%	1512	0.796786
both	24095	0.99%	7.63%	100.00%	5974	4.03331
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	21708	0.78%	5.62%	79.67%	4999	3.63375
anti	5540	0.20%	1.44%	20.33%	1512	0.927352
both	27248	0.98%	7.06%	100.00%	5974	4.5611

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)
chr12:56989980@+	-300; 1000	RBMS2	0; 197	0; 283
chr15:93586635@-	-300; 1000	RGMA	124; 0	204; 0
chr10:102309763@+	-300; 1000	HIF1AN	112; 0	155; 0
chr19:47278138@-	-300; 1000	SLC1A5	102; 0	313; 0
chr4:17630927@-	-300; 1000	FAM184B	0; 101	0; 148
chr16:67471456@+	-275; 1000	HSD11B2	0; 90	0; 237
chr7:47314750@-	-300; 1000	TNS3	86; 0	114; 0
chr12:48176534@+	-267; 1000	SLC48A1	1; 83	1; 175
chr17:37078023@+	-300; 1000	LASP1	80; 0	112; 0
chr3:128338815@-	-218; 1000	RPN1	73; 0	168; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr19:47278138@-	-300; 1000	SLC1A5	102; 0	313; 0
chr12:56989980@+	-300; 1000	RBMS2	0; 197	0; 283
chr16:67471456@+	-275; 1000	HSD11B2	0; 90	0; 237
chr15:93586635@-	-300; 1000	RGMA	124; 0	204; 0
chr12:48176534@+	-267; 1000	SLC48A1	1; 83	1; 175
chr3:128338815@-	-218; 1000	RPN1	73; 0	168; 0
chr2:169983617@-	-300; 1000	LRP2	70; 0	164; 0
chr6:43149243@+	-300; 334	SRF	72; 0	159; 0
chr10:102309763@+	-300; 1000	HIF1AN	112; 0	155; 0
chr4:17630927@-	-300; 1000	FAM184B	0; 101	0; 148

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	6516	0.27%	2.06%	29.86%	2150	1.06037
anti	15303	0.63%	4.84%	70.14%	4301	2.49032
both	21819	0.90%	6.91%	100.00%	6145	3.55069
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	13979	0.51%	3.62%	42.71%	2150	2.27486
anti	18752	0.68%	4.86%	57.29%	4301	3.05159
both	32731	1.18%	8.48%	100.00%	6145	5.32644

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)
chr12:97957589@+	-1000; 50	hsa-mir-135a-2	361; 0	1403; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 274	0; 1390
chr1:109642814@+	-1000; 210	snoU2-25	205; 0	3728; 0
chr21:38445469@-	-1000; 90	PIGP	0; 155	0; 319
chr16:89980524@+	-1000; 52	AC092143.1	148; 0	256; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 137	0; 289
chr14:104150351@-	-1000; 300	AL139300.3	0; 129	0; 260
chr19:36705503@+	-1000; 297	ZNF146	1; 118	1; 147
chr20:51588945@+	-1000; 300	TSHZ2	91; 1	239; 1
chr9:95709732@+	-1000; 139	FGD3	0; 90	0; 144

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	205; 0	3728; 0
chr12:97957589@+	-1000; 50	hsa-mir-135a-2	361; 0	1403; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 274	0; 1390
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	86; 0	665; 0
chr21:38445469@-	-1000; 90	PIGP	0; 155	0; 319
chr7:148684339@-	-1000; 56	Y_RNA-ENSG00000201098	40; 0	302; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 137	0; 289
chr14:104150351@-	-1000; 300	AL139300.3	0; 129	0; 260
chr16:89980524@+	-1000; 52	AC092143.1	148; 0	256; 0
chr10:103124791@-	-1000; 95	U2-ENSG00000222414	22; 0	247; 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	25533	1.05%	8.08%	65.08%	6587	2.63444
anti	13702	0.56%	4.34%	34.92%	3840	1.41374
both	39235	1.62%	12.42%	100.00%	9692	4.04818
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	41552	1.50%	10.76%	72.68%	6587	4.28725
anti	15618	0.56%	4.05%	27.32%	3840	1.61143
both	57170	2.07%	14.81%	100.00%	9692	5.89868

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	1069; 0	9829; 0
chr10:712562@+	-203; 1000	RP11-809C18.1	0; 230	0; 479
chr1:109643234@+	-210; 1000	snoU2-25	210; 0	2218; 0
chr12:56989980@+	-300; 1000	RBMS2	0; 197	0; 283
chrUn_gl000220:118417@+	-300; 1000	28S	164; 0	1067; 0
chr4:71655925@-	-300; 1000	AC009570.3	0; 161	0; 258
chr15:93586635@-	-300; 1000	RGMA	124; 0	204; 0
chrM:14147@-	-263; 1000	J01415.15	44; 75	53; 82
chr4:17629790@+	-177; 1000	AC006160.1	117; 0	180; 0
chr10:102309763@+	-300; 1000	HIF1AN	112; 0	155; 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	1069; 0	9829; 0
chr1:109643234@+	-210; 1000	snoU2-25	210; 0	2218; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	93; 0	1143; 0
chrUn_gl000220:118417@+	-300; 1000	28S	164; 0	1067; 0
chr10:712562@+	-203; 1000	RP11-809C18.1	0; 230	0; 479
chr19:47278138@-	-300; 1000	SLC1A5	102; 0	313; 0
chr12:56989980@+	-300; 1000	RBMS2	0; 197	0; 283
chr4:71655925@-	-300; 1000	AC009570.3	0; 161	0; 258
chr16:67471456@+	-275; 1000	HSD11B2	0; 90	0; 237
chr15:93586635@-	-300; 1000	RGMA	124; 0	204; 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	68740	2.83%	21.76%	95.55%	28839	2.24692
anti	3204	0.13%	1.01%	4.45%	2090	0.10473
both	71944	2.97%	22.77%	100.00%	30593	2.35165
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	79808	2.88%	20.67%	95.90%	28839	2.6087
anti	3412	0.12%	0.88%	4.10%	2090	0.111529
both	83220	3.01%	21.56%	100.00%	30593	2.72023

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)
chr12:124915763@-	-300; 100	NCOR2	179; 0	508; 0
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	149; 0	1470; 0
chr1:156643345@-	-300; 27	NES	145; 0	466; 0
chr6:161574570@-	-285; 40	AGPAT4	144; 0	447; 0
chr17:2583081@+	-300; 100	PAFAH1B1	131; 0	361; 0
chr20:62364539@+	-300; 29	ZGPAT	120; 0	241; 0
chr19:2337060@+	-300; 100	AC004410.1	120; 0	221; 0
chr14:23519384@-	-300; 100	AL132780.1	118; 0	183; 0
chr17:3727411@-	-300; 26	C17orf85	104; 0	219; 0
chr4:5827485@-	-300; 100	CRMP1	101; 1	147; 1

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	149; 0	1470; 0
chr12:124915763@-	-300; 100	NCOR2	179; 0	508; 0
chr1:156643345@-	-300; 27	NES	145; 0	466; 0
chr6:161574570@-	-285; 40	AGPAT4	144; 0	447; 0
chr17:2583081@+	-300; 100	PAFAH1B1	131; 0	361; 0
chr20:62364539@+	-300; 29	ZGPAT	120; 0	241; 0
chr19:2337060@+	-300; 100	AC004410.1	120; 0	221; 0
chr17:3727411@-	-300; 26	C17orf85	104; 0	219; 0
chr17:46633205@-	-300; 100	HOXB3	82; 0	199; 0
chr14:23519384@-	-300; 100	AL132780.1	118; 0	183; 0

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