Parameters
input_file: 20100222_LUjt3_4_hg19_ensembl59_S_iCLIP_TDP-43_Embrionic-Stem-Cells_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: 2.47844e+06
[x-link sites] used in any map: 321615 (12.98%)
[single hits (=G+T), cDNA counts] total: 2.47844e+06
[single hits (=G+T), cDNA counts] used in any map: 395005 (13.92%)

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	91302	3.68%	28.39%	103069	3.63%	26.09%
intron-exon	-300; 300	92810	3.74%	28.86%	104167	3.67%	26.37%
5-ncRNA	-1000; 300	27991	1.13%	8.70%	42057	1.48%	10.65%
ncRNA-3	-300; 1000	29518	1.19%	9.18%	51671	1.82%	13.08%
ORF-3UTR	-300; 300	15393	0.62%	4.79%	18312	0.65%	4.64%
5UTR-ORF	-300; 300	2128	0.09%	0.66%	2534	0.09%	0.64%
inter-5UTR	-1000; 300	6771	0.27%	2.11%	8418	0.30%	2.13%
3UTR-inter	-300; 1000	24568	0.99%	7.64%	27782	0.98%	7.03%
inter-5	-1000; 300	22663	0.91%	7.05%	34627	1.22%	8.77%
3-inter	-300; 1000	40342	1.63%	12.54%	59692	2.10%	15.11%
BP best in intron	-300; 100	72812	2.94%	22.64%	84183	2.97%	21.31%

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	87129	3.52%	27.09%	95.43%	37045	2.22614
anti	4173	0.17%	1.30%	4.57%	2512	0.10662
both	91302	3.68%	28.39%	100.00%	39139	2.33276
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	98546	3.47%	24.95%	95.61%	37045	2.51785
anti	4523	0.16%	1.15%	4.39%	2512	0.115562
both	103069	3.63%	26.09%	100.00%	39139	2.63341

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)
chr3:116163722@-	-78; 300	LSAMP	135; 0	350; 0
chr6:161575179@-	-81; 300	AGPAT4	125; 0	342; 0
chr11:12886447@+	-32; 300	TEAD1	118; 0	337; 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	161; 0
chr19:46815910@+	-247; 300	HIF3A	96; 0	169; 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)
chr3:116163722@-	-78; 300	LSAMP	135; 0	350; 0
chr6:161575179@-	-81; 300	AGPAT4	125; 0	342; 0
chr11:12886447@+	-32; 300	TEAD1	118; 0	337; 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	161; 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	88196	3.56%	27.42%	95.03%	38278	2.16922
anti	4614	0.19%	1.43%	4.97%	2918	0.113483
both	92810	3.74%	28.86%	100.00%	40658	2.2827
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	99134	3.49%	25.10%	95.17%	38278	2.43824
anti	5033	0.18%	1.27%	4.83%	2918	0.123789
both	104167	3.67%	26.37%	100.00%	40658	2.56203

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)
chr12:124915332@-	-300; 86	NCOR2	176; 0	491; 0
chr1:156643318@-	-300; 37	NES	149; 0	471; 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	100; 0	191; 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	75; 0	104; 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)
chr12:124915332@-	-300; 86	NCOR2	176; 0	491; 0
chr1:156643318@-	-300; 37	NES	149; 0	471; 0
chr6:161574530@-	-300; 77	AGPAT4	137; 0	381; 0
chr3:9291368@-	-300; 300	SRGAP3	57; 0	242; 0
chr20:62364570@+	-300; 67	ZGPAT	113; 0	217; 0
chr4:863744@-	-300; 300	GAK	131; 0	206; 0
chrX:47067960@+	-300; 300	UBA1	100; 0	191; 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	13733	0.55%	4.27%	49.06%	3234	2.03001
anti	14258	0.58%	4.43%	50.94%	3807	2.10761
both	27991	1.13%	8.70%	100.00%	6765	4.13762
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	25751	0.91%	6.52%	61.23%	3234	3.8065
anti	16306	0.57%	4.13%	38.77%	3807	2.41035
both	42057	1.48%	10.65%	100.00%	6765	6.21685

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)
chr11:65269806@+	-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
chrUn_gl000220:109077@+	-758; 300	18S	168; 0	749; 0
chr15:25232071@+	-879; 35	SNORD108	156; 0	231; 0
chr22:50295450@+	-1000; 30	AL671710.1	150; 0	308; 0
chrUn_gl000220:113347@+	-585; 300	28S	140; 0	398; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 140	0; 292

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	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
chrUn_gl000220:109077@+	-758; 300	18S	168; 0	749; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	86; 0	665; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	278; 0	596; 0
chrUn_gl000220:113347@+	-585; 300	28S	140; 0	398; 0
chr12:97885686@+	-1000; 35	hsa-mir-1251	220; 0	372; 0
chr22:50295450@+	-1000; 30	AL671710.1	150; 0	308; 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	14763	0.60%	4.59%	50.01%	3519	2.11232
anti	14755	0.60%	4.59%	49.99%	3758	2.11117
both	29518	1.19%	9.18%	100.00%	6989	4.22349
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	34510	1.22%	8.74%	66.79%	3519	4.93776
anti	17161	0.60%	4.34%	33.21%	3758	2.45543
both	51671	1.82%	13.08%	100.00%	6989	7.39319

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	1069; 0	9829; 0
chr10:712562@+	-203; 1000	RP11-809C18.1	0; 232	0; 482
chrUn_gl000220:110946@+	-300; 539	18S	218; 0	1445; 0
chr1:109643234@+	-210; 1000	snoU2-25	210; 0	2221; 0
chr1:142653799@+	-41; 1000	AL583842.1-ENSG00000239012, AL583842.3-ENSG00000230880	0; 186	0; 433
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
chr3:160232693@-	-165; 362	KPNA4, snoU90	136; 0	1478; 0
chr4:17629790@+	-177; 1000	AC006160.1	126; 0	189; 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	1069; 0	9829; 0
chr1:109643234@+	-210; 1000	snoU2-25	210; 0	2221; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	136; 0	1478; 0
chrUn_gl000220:110946@+	-300; 539	18S	218; 0	1445; 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; 232	0; 482
chr1:142653799@+	-41; 1000	AL583842.1-ENSG00000239012, AL583842.3-ENSG00000230880	0; 186	0; 433
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	17; 0	348; 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	14425	0.58%	4.49%	93.71%	4239	3.13315
anti	968	0.04%	0.30%	6.29%	499	0.210252
both	15393	0.62%	4.79%	100.00%	4604	3.3434
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	17247	0.61%	4.37%	94.18%	4239	3.74609
anti	1065	0.04%	0.27%	5.82%	499	0.231321
both	18312	0.65%	4.64%	100.00%	4604	3.97741

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)
chr1:11083386@+	-69; 300	TARDBP	116; 0	206; 0
chr9:126139954@+	-300; 300	CRB2	115; 0	289; 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	92; 0	244; 0
chr7:26252043@+	-171; 300	CBX3	83; 0	142; 0
chr6:47200497@-	-116; 300	TNFRSF21	83; 0	136; 0
chr2:189876774@+	-211; 300	COL3A1	83; 0	122; 0
chr14:59835577@+	-105; 300	DAAM1	81; 0	131; 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)
chr9:126139954@+	-300; 300	CRB2	115; 0	289; 0
chr16:67472427@-	-82; 253	ATP6V0D1	92; 0	244; 0
chr16:29831075@+	-100; 300	C16orf53	105; 0	229; 0
chr1:11083386@+	-69; 300	TARDBP	116; 0	206; 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	151; 0
chr7:26252043@+	-171; 300	CBX3	83; 0	142; 0
chr12:58217348@-	-81; 300	CTDSP2	61; 0	137; 0
chr6:47200497@-	-116; 300	TNFRSF21	83; 0	136; 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	1883	0.08%	0.59%	88.49%	771	2.1972
anti	245	0.01%	0.08%	11.51%	95	0.285881
both	2128	0.09%	0.66%	100.00%	857	2.48308
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	2254	0.08%	0.57%	88.95%	771	2.63011
anti	280	0.01%	0.07%	11.05%	95	0.326721
both	2534	0.09%	0.64%	100.00%	857	2.95683

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)
chr16:89980628@+	-52; 300	AC092143.1	115; 0	190; 0
chr2:61764828@-	-277; 66	XPO1	87; 0	166; 0
chr4:71588290@+	-290; 89	RUFY3	64; 0	115; 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	24; 0	33; 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 (=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)
chr16:89980628@+	-52; 300	AC092143.1	115; 0	190; 0
chr2:61764828@-	-277; 66	XPO1	87; 0	166; 0
chr4:71588290@+	-290; 89	RUFY3	64; 0	115; 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	24; 0	33; 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	2717	0.11%	0.84%	40.13%	894	1.32537
anti	4054	0.16%	1.26%	59.87%	1292	1.97756
both	6771	0.27%	2.11%	100.00%	2050	3.30293
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	3407	0.12%	0.86%	40.47%	894	1.66195
anti	5011	0.18%	1.27%	59.53%	1292	2.44439
both	8418	0.30%	2.13%	100.00%	2050	4.10634

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)
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	242; 1
chr9:95709732@+	-1000; 139	FGD3	0; 90	0; 144
chr22:42526907@-	-1000; 57	CYP2D6	87; 0	177; 0
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

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; 155	0; 319
chr16:89980524@+	-1000; 52	AC092143.1	148; 0	256; 0
chr20:51588945@+	-1000; 300	TSHZ2	91; 1	242; 1
chr22:42526907@-	-1000; 57	CYP2D6	87; 0	177; 0
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

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	19674	0.79%	6.12%	80.08%	5057	3.2519
anti	4894	0.20%	1.52%	19.92%	1551	0.808926
both	24568	0.99%	7.64%	100.00%	6050	4.06083
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	22088	0.78%	5.59%	79.50%	5057	3.65091
anti	5694	0.20%	1.44%	20.50%	1551	0.941157
both	27782	0.98%	7.03%	100.00%	6050	4.59207

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)
chr12:56989980@+	-300; 1000	RBMS2	0; 199	0; 285
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
chr7:47314750@-	-300; 1000	TNS3	92; 0	121; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 91	0; 243
chr12:48176534@+	-267; 1000	SLC48A1	1; 83	1; 175
chr17:37078023@+	-300; 1000	LASP1	81; 0	113; 0
chr3:128338815@-	-218; 1000	RPN1	73; 0	168; 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)
chr19:47278138@-	-300; 1000	SLC1A5	102; 0	313; 0
chr12:56989980@+	-300; 1000	RBMS2	0; 199	0; 285
chr16:67471456@+	-275; 1000	HSD11B2	0; 91	0; 243
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	165; 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	7099	0.29%	2.21%	31.32%	2242	1.12736
anti	15564	0.63%	4.84%	68.68%	4388	2.47165
both	22663	0.91%	7.05%	100.00%	6297	3.59902
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	15511	0.55%	3.93%	44.79%	2242	2.46324
anti	19116	0.67%	4.84%	55.21%	4388	3.03573
both	34627	1.22%	8.77%	100.00%	6297	5.49897

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)
chr12:97957589@+	-1000; 50	hsa-mir-135a-2	361; 0	1403; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 277	0; 1401
chr1:109642814@+	-1000; 210	snoU2-25	205; 0	3728; 0
chrUn_gl000220:109077@+	-758; 300	18S	168; 0	749; 0
chr21:38445469@-	-1000; 90	PIGP	0; 155	0; 319
chr16:89980524@+	-1000; 52	AC092143.1	148; 0	256; 0
chrUn_gl000220:113347@+	-585; 300	28S	140; 0	398; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 140	0; 292
chr14:104150351@-	-1000; 300	AL139300.3	0; 129	0; 260
chr19:36705503@+	-1000; 297	ZNF146	1; 118	1; 147

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	205; 0	3728; 0
chr12:97957589@+	-1000; 50	hsa-mir-135a-2	361; 0	1403; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 277	0; 1401
chrUn_gl000220:109077@+	-758; 300	18S	168; 0	749; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	86; 0	665; 0
chrUn_gl000220:113347@+	-585; 300	28S	140; 0	398; 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; 140	0; 292
chr14:104150351@-	-1000; 300	AL139300.3	0; 129	0; 260

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	26259	1.06%	8.16%	65.09%	6699	2.66076
anti	14083	0.57%	4.38%	34.91%	3935	1.42699
both	40342	1.63%	12.54%	100.00%	9869	4.08775
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	43620	1.54%	11.04%	73.08%	6699	4.4199
anti	16072	0.57%	4.07%	26.92%	3935	1.62853
both	59692	2.10%	15.11%	100.00%	9869	6.04843

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	1069; 0	9829; 0
chr10:712562@+	-203; 1000	RP11-809C18.1	0; 232	0; 482
chrUn_gl000220:110946@+	-300; 539	18S	218; 0	1445; 0
chr1:109643234@+	-210; 1000	snoU2-25	210; 0	2221; 0
chr12:56989980@+	-300; 1000	RBMS2	0; 199	0; 285
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	45; 75	54; 82
chr4:17629790@+	-177; 1000	AC006160.1	117; 0	180; 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	1069; 0	9829; 0
chr1:109643234@+	-210; 1000	snoU2-25	210; 0	2221; 0
chrUn_gl000220:110946@+	-300; 539	18S	218; 0	1445; 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; 232	0; 482
chr19:47278138@-	-300; 1000	SLC1A5	102; 0	313; 0
chr12:56989980@+	-300; 1000	RBMS2	0; 199	0; 285
chr4:71655925@-	-300; 1000	AC009570.3	0; 161	0; 258
chr16:67471456@+	-275; 1000	HSD11B2	0; 91	0; 243

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	69360	2.80%	21.57%	95.26%	29081	2.23728
anti	3452	0.14%	1.07%	4.74%	2284	0.111348
both	72812	2.94%	22.64%	100.00%	31002	2.34862
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	80503	2.84%	20.38%	95.63%	29081	2.5967
anti	3680	0.13%	0.93%	4.37%	2284	0.118702
both	84183	2.97%	21.31%	100.00%	31002	2.71541

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)
chr12:124915763@-	-300; 100	NCOR2	180; 0	509; 0
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	149; 0	1470; 0
chr1:156643345@-	-300; 27	NES	145; 0	467; 0
chr6:161574570@-	-285; 40	AGPAT4	144; 0	447; 0
chr17:2583081@+	-300; 100	PAFAH1B1	132; 0	362; 0
chr20:62364539@+	-300; 29	ZGPAT	121; 0	242; 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	221; 0
chr4:5827485@-	-300; 100	CRMP1	101; 1	147; 1

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	149; 0	1470; 0
chr12:124915763@-	-300; 100	NCOR2	180; 0	509; 0
chr1:156643345@-	-300; 27	NES	145; 0	467; 0
chr6:161574570@-	-285; 40	AGPAT4	144; 0	447; 0
chr17:2583081@+	-300; 100	PAFAH1B1	132; 0	362; 0
chr20:62364539@+	-300; 29	ZGPAT	121; 0	242; 0
chr19:2337060@+	-300; 100	AC004410.1	120; 0	221; 0
chr17:3727411@-	-300; 26	C17orf85	104; 0	221; 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.