Parameters
input_file: 20090724_LUjt1_1_hg19_ensembl59_G_iCLIP_TDP-43_Brain-C30_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: 87940
[x-link sites] used in any map: 17442 (19.83%)
[single hits in whole-genome, cDNA counts] total: 87940
[single hits in whole-genome, cDNA counts] used in any map: 21278 (21.49%)

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	4445	5.05%	25.48%	4868	4.92%	22.88%
intron-exon	-300; 300	5007	5.69%	28.71%	5421	5.48%	25.48%
5-ncRNA	-1000; 300	1854	2.11%	10.63%	3328	3.36%	15.64%
ncRNA-3	-300; 1000	1681	1.91%	9.64%	2639	2.67%	12.40%
ORF-3UTR	-300; 300	1336	1.52%	7.66%	1507	1.52%	7.08%
5UTR-ORF	-300; 300	346	0.39%	1.98%	402	0.41%	1.89%
inter-5UTR	-1000; 300	684	0.78%	3.92%	940	0.95%	4.42%
3UTR-inter	-300; 1000	1294	1.47%	7.42%	1430	1.44%	6.72%
inter-5	-1000; 300	1864	2.12%	10.69%	3411	3.45%	16.03%
3-inter	-300; 1000	2176	2.47%	12.48%	2649	2.68%	12.45%
BP best in intron	-300; 100	2125	2.42%	12.18%	2323	2.35%	10.92%

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	4184	4.76%	23.99%	94.13%	3273	1.20611
anti	261	0.30%	1.50%	5.87%	198	0.0752378
both	4445	5.05%	25.48%	100.00%	3469	1.28135
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	4577	4.62%	21.51%	94.02%	3273	1.3194
anti	291	0.29%	1.37%	5.98%	198	0.0838858
both	4868	4.92%	22.88%	100.00%	3469	1.40329

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr10:103590823@-	-50; 300	KCNIP2	45; 0	76; 0
chr10:135150336@-	-69; 300	CALY	22; 0	36; 0
chr11:1023507@-	-72; 300	MUC6	0; 21	0; 26
chr1:1158622@-	-57; 300	SDF4	20; 0	22; 0
chr6:167368981@-	-67; 300	RNASET2	19; 0	24; 0
chr17:982568@-	-31; 300	ABR	18; 0	32; 0
chr1:156387702@-	-62; 300	C1orf61	18; 0	21; 0
chr7:139025365@+	-85; 256	C7orf55	15; 0	52; 0
chr21:44269334@-	-300; 300	WDR4	15; 0	17; 0
chr17:7111392@-	-83; 300	DLG4	15; 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)
chr10:103590823@-	-50; 300	KCNIP2	45; 0	76; 0
chr7:139025365@+	-85; 256	C7orf55	15; 0	52; 0
chr10:135150336@-	-69; 300	CALY	22; 0	36; 0
chr17:982568@-	-31; 300	ABR	18; 0	32; 0
chr11:1023507@-	-72; 300	MUC6	0; 21	0; 26
chr6:167368981@-	-67; 300	RNASET2	19; 0	24; 0
chr17:7111392@-	-83; 300	DLG4	15; 0	22; 0
chr1:1158622@-	-57; 300	SDF4	20; 0	22; 0
chr1:156387702@-	-62; 300	C1orf61	18; 0	21; 0
chr7:158055898@+	-72; 300	AC019043.2	0; 13	0; 20

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	4766	5.42%	27.32%	95.19%	3851	1.18087
anti	241	0.27%	1.38%	4.81%	192	0.0597126
both	5007	5.69%	28.71%	100.00%	4036	1.24058
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	5144	5.20%	24.18%	94.89%	3851	1.27453
anti	277	0.28%	1.30%	5.11%	192	0.0686323
both	5421	5.48%	25.48%	100.00%	4036	1.34316

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)
chr19:4198136@+	-300; 196	ANKRD24	33; 0	46; 0
chr3:9291368@-	-300; 300	SRGAP3	25; 0	42; 0
chr2:127811587@-	-300; 54	BIN1	20; 0	26; 0
chr19:11467477@+	-300; 87	AC024575.1	15; 0	16; 0
chr10:103874722@-	-300; 280	LDB1	14; 0	20; 0
chr7:31117605@+	-300; 54	ADCYAP1R1	12; 0	12; 0
chr20:1165318@-	-231; 300	C20orf46	12; 0	13; 0
chr4:31018439@-	-300; 44	AC110766.1	0; 11	0; 12
chr20:10286776@+	-300; 300	SNAP25	11; 0	11; 0
chr16:75269883@-	-300; 300	BCAR1	11; 0	13; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr19:4198136@+	-300; 196	ANKRD24	33; 0	46; 0
chr3:9291368@-	-300; 300	SRGAP3	25; 0	42; 0
chr2:127811587@-	-300; 54	BIN1	20; 0	26; 0
chr10:103874722@-	-300; 280	LDB1	14; 0	20; 0
chr11:18425240@+	-300; 59	LDHA	3; 0	17; 0
chr19:11467477@+	-300; 87	AC024575.1	15; 0	16; 0
chr10:103589698@-	-241; 49	KCNIP2	11; 0	15; 0
chr1:182356426@-	-300; 259	GLUL	1; 1	1; 14
chr22:39715115@-	-130; 42	RPL3	7; 0	14; 0
chr20:1165318@-	-231; 300	C20orf46	12; 0	13; 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	1192	1.36%	6.83%	64.29%	541	1.24296
anti	662	0.75%	3.80%	35.71%	426	0.690302
both	1854	2.11%	10.63%	100.00%	959	1.93326
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	2575	2.60%	12.10%	77.37%	541	2.68509
anti	753	0.76%	3.54%	22.63%	426	0.785193
both	3328	3.36%	15.64%	100.00%	959	3.47028

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	124; 0	879; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 53	0; 89
chr11:65269806@+	-1000; 29	MALAT1	52; 0	66; 0
chr14:101318726@+	-1000; 49	MEG3, hsa-mir-770	49; 0	59; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	42; 0	125; 0
chr1:241469181@-	-1000; 152	RGS7, RP11-306K13.1	40; 0	58; 0
chrM:16022@-	-274; 34	J01415.14	19; 2	137; 2
chr1:159172176@-	-1000; 69	CTA-134P22.2	0; 20	0; 24
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	18; 0	21; 0
chr14:101315644@+	-1000; 36	MEG3, SNORD112-ENSG00000252701	14; 0	18; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	879; 0
chrM:16022@-	-274; 34	J01415.14	19; 2	137; 2
chr3:160233023@-	-108; 165	KPNA4, snoU90	42; 0	125; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 53	0; 89
chr11:65269806@+	-1000; 29	MALAT1	52; 0	66; 0
chr14:101318726@+	-1000; 49	MEG3, hsa-mir-770	49; 0	59; 0
chr1:241469181@-	-1000; 152	RGS7, RP11-306K13.1	40; 0	58; 0
chrM:5890@-	-777; 32	J01415.32	5; 8	42; 9
chr6:36607448@-	-1000; 64	U1-ENSG00000238554	9; 0	36; 0
chr22:43011249@+	-1000; 75	U12-ENSG00000199382	9; 0	33; 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	1108	1.26%	6.35%	65.91%	483	1.39021
anti	573	0.65%	3.29%	34.09%	319	0.718946
both	1681	1.91%	9.64%	100.00%	797	2.10916
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	1825	1.84%	8.58%	69.15%	483	2.28984
anti	814	0.82%	3.83%	30.85%	319	1.02133
both	2639	2.67%	12.40%	100.00%	797	3.31117

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	107; 0	145; 0
chrUn_gl000220:118417@+	-300; 1000	28S	69; 0	250; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	36; 0	49; 0
chr14:101323580@-	-300; 1000	AL117190.1-ENSG00000214512	0; 35	0; 49
chrM:15953@+	-33; 309	J01415.6	8; 20	41; 126
chr14:101318824@+	-49; 1000	MEG3, hsa-mir-770	24; 0	26; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	23; 0	36; 0
chr1:109643234@+	-210; 1000	snoU2-25	22; 0	43; 0
chrM:15954@-	-34; 606	J01415.14	12; 9	57; 67
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	19; 0	31; 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)
chrUn_gl000220:118417@+	-300; 1000	28S	69; 0	250; 0
chrM:15953@+	-33; 309	J01415.6	8; 20	41; 126
chr11:65271080@+	-300; 1000	MALAT1	107; 0	145; 0
chrM:15954@-	-34; 606	J01415.14	12; 9	57; 67
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	14; 0	95; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	10; 0	70; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	36; 0	49; 0
chr14:101323580@-	-300; 1000	AL117190.1-ENSG00000214512	0; 35	0; 49
chr1:109643234@+	-210; 1000	snoU2-25	22; 0	43; 0
chrM:4327@-	-36; 1000	J01415.13	0; 17	0; 41

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	1300	1.48%	7.45%	97.31%	839	1.4977
anti	36	0.04%	0.21%	2.69%	30	0.0414747
both	1336	1.52%	7.66%	100.00%	868	1.53917
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	1466	1.48%	6.89%	97.28%	839	1.68894
anti	41	0.04%	0.19%	2.72%	30	0.047235
both	1507	1.52%	7.08%	100.00%	868	1.73618

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr10:73822514@-	-74; 300	SPOCK2	44; 0	87; 0
chr16:67472427@-	-82; 253	ATP6V0D1	22; 0	39; 0
chr10:22825820@-	-195; 300	PIP5K2A	21; 0	27; 0
chr5:73925375@-	-221; 300	ENC1	19; 0	23; 0
chr11:35275966@-	-194; 300	SLC1A2	14; 0	15; 0
chr1:41092185@-	-108; 300	RIMS3	12; 0	14; 0
chr1:20809678@-	-267; 300	CAMK2N1	10; 0	11; 0
chr2:55199719@-	-300; 198	RTN4	9; 0	10; 0
chr16:23478907@-	-57; 300	GGA2	9; 0	15; 0
chr5:58147354@+	-182; 300	RAB3C	8; 0	11; 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)
chr10:73822514@-	-74; 300	SPOCK2	44; 0	87; 0
chr16:67472427@-	-82; 253	ATP6V0D1	22; 0	39; 0
chr10:22825820@-	-195; 300	PIP5K2A	21; 0	27; 0
chr5:73925375@-	-221; 300	ENC1	19; 0	23; 0
chr16:23478907@-	-57; 300	GGA2	9; 0	15; 0
chr11:35275966@-	-194; 300	SLC1A2	14; 0	15; 0
chr1:41092185@-	-108; 300	RIMS3	12; 0	14; 0
chr3:5025377@+	-300; 300	BHLHE40	7; 0	13; 0
chr5:58147354@+	-182; 300	RAB3C	8; 0	11; 0
chr1:20809678@-	-267; 300	CAMK2N1	10; 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 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	324	0.37%	1.86%	93.64%	216	1.38462
anti	22	0.03%	0.13%	6.36%	20	0.0940171
both	346	0.39%	1.98%	100.00%	234	1.47863
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	380	0.38%	1.79%	94.53%	216	1.62393
anti	22	0.02%	0.10%	5.47%	20	0.0940171
both	402	0.41%	1.89%	100.00%	234	1.71795

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)
chr4:158141875@+	-70; 203	GRIA2	23; 0	30; 0
chr4:71588290@+	-290; 89	RUFY3	15; 0	24; 0
chr2:61764828@-	-277; 66	XPO1	15; 0	23; 0
chr12:121093613@+	-256; 231	CABP1	9; 0	16; 0
chr6:31508971@-	-66; 265	BAT1	8; 0	15; 0
chr18:35145603@-	-198; 143	CELF4	5; 0	5; 0
chr5:86564268@+	-282; 269	RASA1	4; 0	4; 0
chr17:47755471@-	-62; 89	SPOP	4; 0	5; 0
chr11:66115015@-	-73; 300	AP001107.2	4; 0	5; 0
chrX:139866530@-	-96; 300	CDR1	0; 3	0; 3

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)
chr4:158141875@+	-70; 203	GRIA2	23; 0	30; 0
chr4:71588290@+	-290; 89	RUFY3	15; 0	24; 0
chr2:61764828@-	-277; 66	XPO1	15; 0	23; 0
chr12:121093613@+	-256; 231	CABP1	9; 0	16; 0
chr6:31508971@-	-66; 265	BAT1	8; 0	15; 0
chr7:91763677@-	-83; 96	CYP51A1	3; 0	5; 0
chr18:35145603@-	-198; 143	CELF4	5; 0	5; 0
chr17:47755471@-	-62; 89	SPOP	4; 0	5; 0
chr11:66115015@-	-73; 300	AP001107.2	4; 0	5; 0
chr5:86564268@+	-282; 269	RASA1	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 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	412	0.47%	2.36%	60.23%	213	1.09867
anti	272	0.31%	1.56%	39.77%	162	0.725333
both	684	0.78%	3.92%	100.00%	375	1.824
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	519	0.52%	2.44%	55.21%	213	1.384
anti	421	0.43%	1.98%	44.79%	162	1.12267
both	940	0.95%	4.42%	100.00%	375	2.50667

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)
chr6:40555203@-	-1000; 262	LRFN2	27; 0	34; 0
chr15:80737492@-	-1000; 74	AC016705.1	0; 26	0; 33
chr14:65569226@-	-1000; 85	MAX	26; 0	41; 0
chr13:26828275@+	-1000; 251	CDK8	25; 0	66; 0
chr14:48143952@-	-1000; 80	MDGA2	22; 0	30; 0
chr12:122459860@+	-1000; 68	BCL7A	19; 0	29; 0
chr4:144257914@+	-1000; 213	GAB1	13; 0	14; 0
chr21:38445469@-	-1000; 90	PIGP	0; 9	0; 9
chr19:36705503@+	-1000; 297	ZNF146	0; 9	0; 11
chr15:89878025@-	-1000; 61	POLG	0; 9	0; 71

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr15:89878025@-	-1000; 61	POLG	0; 9	0; 71
chr13:26828275@+	-1000; 251	CDK8	25; 0	66; 0
chr14:65569226@-	-1000; 85	MAX	26; 0	41; 0
chr11:66115160@-	-1000; 72	AP001107.2	0; 7	0; 39
chr6:40555203@-	-1000; 262	LRFN2	27; 0	34; 0
chr15:80737492@-	-1000; 74	AC016705.1	0; 26	0; 33
chr14:48143952@-	-1000; 80	MDGA2	22; 0	30; 0
chr12:122459860@+	-1000; 68	BCL7A	19; 0	29; 0
chr17:37026255@+	-1000; 93	LASP1	0; 3	0; 22
chr4:144257914@+	-1000; 213	GAB1	13; 0	14; 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	1076	1.22%	6.17%	83.15%	749	1.19158
anti	218	0.25%	1.25%	16.85%	163	0.241417
both	1294	1.47%	7.42%	100.00%	903	1.433
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	1183	1.19%	5.56%	82.73%	749	1.31008
anti	247	0.25%	1.16%	17.27%	163	0.273533
both	1430	1.44%	6.72%	100.00%	903	1.58361

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)
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 38
chr3:9543479@-	-206; 1000	LHFPL4	20; 0	23; 0
chr22:39781593@+	-300; 1000	SYNGR1	15; 0	23; 0
chr22:39214455@-	-300; 1000	NPTXR	13; 0	16; 0
chr11:35272751@-	-300; 1000	SLC1A2	13; 0	13; 0
chr12:7311526@+	-300; 1000	CLSTN3	12; 0	15; 0
chr7:30199534@+	-192; 1000	C7orf41	9; 0	13; 0
chr6:43149243@+	-300; 334	SRF	7; 0	7; 0
chr2:69686412@-	-300; 1000	AC114772.2	7; 0	9; 0
chr18:72102961@-	-300; 1000	FAM69C	7; 0	11; 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)
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 38
chr3:9543479@-	-206; 1000	LHFPL4	20; 0	23; 0
chr22:39781593@+	-300; 1000	SYNGR1	15; 0	23; 0
chr22:39214455@-	-300; 1000	NPTXR	13; 0	16; 0
chr12:7311526@+	-300; 1000	CLSTN3	12; 0	15; 0
chr7:30199534@+	-192; 1000	C7orf41	9; 0	13; 0
chr11:35272751@-	-300; 1000	SLC1A2	13; 0	13; 0
chr18:72102961@-	-300; 1000	FAM69C	7; 0	11; 0
chr5:73923232@-	-300; 1000	ENC1	5; 0	9; 0
chr2:69686412@-	-300; 1000	AC114772.2	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 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	914	1.04%	5.24%	49.03%	459	0.931702
anti	950	1.08%	5.45%	50.97%	527	0.9684
both	1864	2.12%	10.69%	100.00%	981	1.9001
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	1976	2.00%	9.29%	57.93%	459	2.01427
anti	1435	1.45%	6.74%	42.07%	527	1.46279
both	3411	3.45%	16.03%	100.00%	981	3.47706

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	124; 0	879; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 116	0; 345
chr9:138900081@+	-1000; 300	AL355574.1	0; 53	0; 89
chr6:40555203@-	-1000; 262	LRFN2	27; 0	34; 0
chr15:80737492@-	-1000; 74	AC016705.1	0; 26	0; 33
chr14:65569226@-	-1000; 85	MAX	26; 0	41; 0
chr13:26828275@+	-1000; 251	CDK8	25; 0	66; 0
chr14:48143952@-	-1000; 80	MDGA2	22; 0	30; 0
chr1:159172176@-	-1000; 69	CTA-134P22.2	0; 20	0; 24
chr12:122459860@+	-1000; 68	BCL7A	19; 0	29; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	879; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 116	0; 345
chr9:138900081@+	-1000; 300	AL355574.1	0; 53	0; 89
chr15:89878025@-	-1000; 61	POLG	0; 9	0; 71
chr13:26828275@+	-1000; 251	CDK8	25; 0	66; 0
chrM:5903@+	-162; 300	J01415.8	5; 7	5; 47
chr14:65569226@-	-1000; 85	MAX	26; 0	41; 0
chr11:66115160@-	-1000; 72	AP001107.2	0; 7	0; 39
chr6:36607448@-	-1000; 64	U1-ENSG00000238554	9; 0	36; 0
chr6:40555203@-	-1000; 262	LRFN2	27; 0	34; 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	1545	1.76%	8.86%	71.00%	940	1.16078
anti	631	0.72%	3.62%	29.00%	405	0.47408
both	2176	2.47%	12.48%	100.00%	1331	1.63486
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	1946	1.97%	9.15%	73.46%	940	1.46206
anti	703	0.71%	3.30%	26.54%	405	0.528174
both	2649	2.68%	12.45%	100.00%	1331	1.99023

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	107; 0	145; 0
chrUn_gl000220:118417@+	-300; 1000	28S	69; 0	250; 0
chr14:101323580@-	-300; 1000	AL117190.1-ENSG00000214512	0; 35	0; 49
chr1:109643234@+	-210; 1000	snoU2-25	22; 0	43; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 38
chr3:9543479@-	-206; 1000	LHFPL4	20; 0	23; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	19; 0	31; 0
chr22:39781593@+	-300; 1000	SYNGR1	15; 0	23; 0
chr10:133994727@-	-160; 1000	RP11-140A10.3	0; 15	0; 16
chr4:144257786@-	-255; 1000	AC097658.1	0; 13	0; 14

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)
chrUn_gl000220:118417@+	-300; 1000	28S	69; 0	250; 0
chr11:65271080@+	-300; 1000	MALAT1	107; 0	145; 0
chr14:101323580@-	-300; 1000	AL117190.1-ENSG00000214512	0; 35	0; 49
chr1:109643234@+	-210; 1000	snoU2-25	22; 0	43; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 38
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	19; 0	31; 0
chr3:9543479@-	-206; 1000	LHFPL4	20; 0	23; 0
chr22:39781593@+	-300; 1000	SYNGR1	15; 0	23; 0
chr22:39214455@-	-300; 1000	NPTXR	13; 0	16; 0
chr10:133994727@-	-160; 1000	RP11-140A10.3	0; 15	0; 16

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	2002	2.28%	11.48%	94.21%	1493	1.2458
anti	123	0.14%	0.71%	5.79%	114	0.0765401
both	2125	2.42%	12.18%	100.00%	1607	1.32234
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	2189	2.21%	10.29%	94.23%	1493	1.36217
anti	134	0.14%	0.63%	5.77%	114	0.0833852
both	2323	2.35%	10.92%	100.00%	1607	1.44555

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	21; 0	48; 0
chr2:127811623@-	-300; 36	BIN1	20; 0	26; 0
chr19:2337060@+	-300; 100	AC004410.1	16; 0	17; 0
chr7:31117581@+	-300; 22	ADCYAP1R1	14; 0	14; 0
chr12:113566108@-	-300; 100	RASAL1	13; 0	15; 0
chr19:11467032@+	-172; 100	AC024575.1	11; 0	12; 0
chr17:7107644@-	-300; 74	DLG4	11; 0	15; 0
chr12:52446230@+	-300; 47	NR4A1	11; 0	11; 0
chr6:161574570@-	-285; 40	AGPAT4	10; 0	11; 0
chr17:78867401@+	-300; 100	RPTOR	10; 0	10; 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	21; 0	48; 0
chr2:127811623@-	-300; 36	BIN1	20; 0	26; 0
chr19:2337060@+	-300; 100	AC004410.1	16; 0	17; 0
chr12:121093851@+	-300; 42	CABP1	10; 0	17; 0
chr17:7107644@-	-300; 74	DLG4	11; 0	15; 0
chr12:113566108@-	-300; 100	RASAL1	13; 0	15; 0
chr7:31117581@+	-300; 22	ADCYAP1R1	14; 0	14; 0
chr19:11467032@+	-172; 100	AC024575.1	11; 0	12; 0
chr10:88649475@+	-300; 100	U1-ENSG00000200176	2; 0	12; 0
chr6:161574570@-	-285; 40	AGPAT4	10; 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.