Parameters
input_file: 20090724_LUe5_1_hg19_ensembl59_G_iCLIP_TDP-43_Brain-C25_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: 16780
[x-link sites] used in any map: 4347 (25.91%)
[single hits in whole-genome, cDNA counts] total: 16780
[single hits in whole-genome, cDNA counts] used in any map: 4934 (27.39%)

map	span (upstream; downstream)	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[single hits 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	895	5.33%	20.59%	934	5.18%	18.93%
intron-exon	-300; 300	1233	7.35%	28.36%	1295	7.19%	26.25%
5-ncRNA	-1000; 300	745	4.44%	17.14%	1060	5.88%	21.48%
ncRNA-3	-300; 1000	591	3.52%	13.60%	729	4.05%	14.78%
ORF-3UTR	-300; 300	270	1.61%	6.21%	284	1.58%	5.76%
5UTR-ORF	-300; 300	64	0.38%	1.47%	72	0.40%	1.46%
inter-5UTR	-1000; 300	87	0.52%	2.00%	92	0.51%	1.86%
3UTR-inter	-300; 1000	322	1.92%	7.41%	330	1.83%	6.69%
inter-5	-1000; 300	511	3.05%	11.76%	719	3.99%	14.57%
3-inter	-300; 1000	610	3.64%	14.03%	686	3.81%	13.90%
BP best in intron	-300; 100	489	2.91%	11.25%	520	2.89%	10.54%

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	866	5.16%	19.92%	96.76%	742	1.12468
anti	29	0.17%	0.67%	3.24%	28	0.0376623
both	895	5.33%	20.59%	100.00%	770	1.16234
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	904	5.02%	18.32%	96.79%	742	1.17403
anti	30	0.17%	0.61%	3.21%	28	0.038961
both	934	5.18%	18.93%	100.00%	770	1.21299

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)
chr17:72951885@-	-83; 300	C17orf28	7; 0	7; 0
chr3:116163722@-	-78; 300	LSAMP	6; 0	7; 0
chr22:38687371@-	-285; 177	CSNK1E	5; 0	5; 0
chr7:99951635@+	-160; 300	PILRB	4; 0	5; 0
chr6:17285396@+	-57; 300	RBM24	4; 0	4; 0
chr5:179048842@-	-53; 222	HNRNPH1	4; 0	4; 0
chr20:33969719@-	-54; 300	UQCC	4; 0	8; 0
chr1:9804451@-	-125; 194	CLSTN1	4; 0	4; 0
chr1:9795941@-	-79; 134	CLSTN1	4; 0	6; 0
chrX:28606164@+	-300; 300	IL1RAPL1	3; 0	3; 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)
chr20:33969719@-	-54; 300	UQCC	4; 0	8; 0
chr3:116163722@-	-78; 300	LSAMP	6; 0	7; 0
chr17:72951885@-	-83; 300	C17orf28	7; 0	7; 0
chr1:9795941@-	-79; 134	CLSTN1	4; 0	6; 0
chr7:99951635@+	-160; 300	PILRB	4; 0	5; 0
chr22:38687371@-	-285; 177	CSNK1E	5; 0	5; 0
chr6:17285396@+	-57; 300	RBM24	4; 0	4; 0
chr5:179048842@-	-53; 222	HNRNPH1	4; 0	4; 0
chr1:9804451@-	-125; 194	CLSTN1	4; 0	4; 0
chrX:48844531@-	-266; 120	GRIPAP1	1; 0	3; 0

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

RNAmap 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	1193	7.11%	27.44%	96.76%	1000	1.15154
anti	40	0.24%	0.92%	3.24%	36	0.03861
both	1233	7.35%	28.36%	100.00%	1036	1.19015
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	1255	6.97%	25.44%	96.91%	1000	1.21139
anti	40	0.22%	0.81%	3.09%	36	0.03861
both	1295	7.19%	26.25%	100.00%	1036	1.25

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)
chr9:97055255@+	-175; 300	ZNF169	7; 0	7; 0
chr5:94026899@+	-300; 231	ANKRD32	6; 0	6; 0
chr22:39715115@-	-130; 42	RPL3	6; 0	12; 0
chr1:84413308@-	-300; 251	TTLL7	5; 0	6; 0
chrX:47067960@+	-300; 300	UBA1	4; 0	4; 0
chr2:32822817@+	-300; 109	BIRC6	4; 0	4; 0
chr11:103104762@+	-300; 63	DYNC2H1	4; 0	4; 0
chr1:182353857@-	-300; 300	GLUL	4; 0	4; 0
chr9:80942966@+	-300; 69	PSAT1	3; 0	3; 0
chr8:27462851@-	-300; 206	CLU	3; 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)
chr22:39715115@-	-130; 42	RPL3	6; 0	12; 0
chr9:97055255@+	-175; 300	ZNF169	7; 0	7; 0
chr5:94026899@+	-300; 231	ANKRD32	6; 0	6; 0
chr1:84413308@-	-300; 251	TTLL7	5; 0	6; 0
chr11:18425240@+	-300; 59	LDHA	3; 0	5; 0
chrX:47067960@+	-300; 300	UBA1	4; 0	4; 0
chr8:27462851@-	-300; 206	CLU	3; 0	4; 0
chr5:136957814@-	-300; 300	KLHL3	3; 0	4; 0
chr3:110793741@+	-300; 174	PVRL3	3; 0	4; 0
chr2:32822817@+	-300; 109	BIRC6	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 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	639	3.81%	14.70%	85.77%	329	1.53237
anti	106	0.63%	2.44%	14.23%	88	0.254197
both	745	4.44%	17.14%	100.00%	417	1.78657
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	948	5.26%	19.21%	89.43%	329	2.27338
anti	112	0.62%	2.27%	10.57%	88	0.268585
both	1060	5.88%	21.48%	100.00%	417	2.54197

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	58; 0	146; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	13; 0	26; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	12; 0	42; 0
chr11:65269806@+	-1000; 29	MALAT1	11; 0	11; 0
chr7:80962916@+	-1000; 115	AC004866.1-ENSG00000239843	8; 0	11; 0
chr15:25346721@+	-990; 46	SNORD116-ENSG00000251896	8; 0	10; 0
chr15:25344645@+	-872; 48	SNORD116-ENSG00000251815	8; 0	9; 0
chr15:25342809@+	-1000; 46	SNORD116-ENSG00000252326	8; 0	11; 0
chr11:77597678@+	-1000; 37	AP002812.1	8; 0	9; 0
chr22:29729246@-	-503; 48	AP1B1, SNORD125	7; 0	15; 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	58; 0	146; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	12; 0	42; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	13; 0	26; 0
chr15:25336932@+	-886; 46	SNORD116-ENSG00000207375	5; 0	19; 0
chr1:8266656@-	-1000; 82	U1-ENSG00000200975	2; 0	16; 0
chr22:29729246@-	-503; 48	AP1B1, SNORD125	7; 0	15; 0
chr15:25332808@+	-522; 46	SNORD116-ENSG00000207259	5; 0	12; 0
chr7:80962916@+	-1000; 115	AC004866.1-ENSG00000239843	8; 0	11; 0
chr15:25342809@+	-1000; 46	SNORD116-ENSG00000252326	8; 0	11; 0
chr11:65269806@+	-1000; 29	MALAT1	11; 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 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	447	2.66%	10.28%	75.63%	243	1.34234
anti	144	0.86%	3.31%	24.37%	93	0.432432
both	591	3.52%	13.60%	100.00%	333	1.77477
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	566	3.14%	11.47%	77.64%	243	1.6997
anti	163	0.90%	3.30%	22.36%	93	0.489489
both	729	4.05%	14.78%	100.00%	333	2.18919

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)
chrUn_gl000220:118417@+	-300; 1000	28S	25; 0	54; 0
chr11:65271080@+	-300; 1000	MALAT1	21; 0	22; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	22; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	13; 0	17; 0
chr18:77773065@+	-110; 1000	AC090360.1	11; 0	17; 0
chrY:10036111@-	-300; 1000	RN18S1	0; 9	0; 10
chr3:160232693@-	-165; 362	KPNA4, snoU90	9; 0	12; 0
chr15:25344741@+	-48; 990	SNORD116-ENSG00000251815	7; 0	10; 0
chrX:108297359@-	-216; 1000	RN28S1	0; 6	0; 8
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	6; 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)
chrUn_gl000220:118417@+	-300; 1000	28S	25; 0	54; 0
chr11:65271080@+	-300; 1000	MALAT1	21; 0	22; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	22; 0
chr18:77773065@+	-110; 1000	AC090360.1	11; 0	17; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	13; 0	17; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	9; 0	12; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	6; 0	11; 0
chr4:144257786@-	-255; 1000	AC097658.1	0; 6	0; 11
chr10:68805209@-	-129; 1000	AL139240.1, CTNNA3	5; 0	11; 0
chrY:10036111@-	-300; 1000	RN18S1	0; 9	0; 10

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	259	1.54%	5.96%	95.93%	203	1.24519
anti	11	0.07%	0.25%	4.07%	5	0.0528846
both	270	1.61%	6.21%	100.00%	208	1.29808
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	272	1.51%	5.51%	95.77%	203	1.30769
anti	12	0.07%	0.24%	4.23%	5	0.0576923
both	284	1.58%	5.76%	100.00%	208	1.36538

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)
chr16:67472427@-	-82; 253	ATP6V0D1	13; 0	16; 0
chrX:139865739@-	-300; 158	CDR1	0; 7	0; 8
chr17:79477712@-	-73; 300	ACTG1	4; 0	4; 0
chr9:115232824@+	-57; 300	HSDL2	3; 0	3; 0
chr4:176554594@-	-300; 255	GPM6A	3; 0	3; 0
chr2:27599586@+	-57; 204	SNX17	3; 0	3; 0
chr18:9954208@+	-80; 300	VAPA	3; 0	3; 0
chr1:169100793@+	-132; 300	ATP1B1	3; 0	3; 0
chr1:78024416@+	-65; 300	AK5	3; 0	3; 0
chr8:143694438@-	-300; 297	ARC	2; 0	2; 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)
chr16:67472427@-	-82; 253	ATP6V0D1	13; 0	16; 0
chrX:139865739@-	-300; 158	CDR1	0; 7	0; 8
chr17:79477712@-	-73; 300	ACTG1	4; 0	4; 0
chr9:115232824@+	-57; 300	HSDL2	3; 0	3; 0
chr4:176554594@-	-300; 255	GPM6A	3; 0	3; 0
chr2:27599586@+	-57; 204	SNX17	3; 0	3; 0
chr18:9954208@+	-80; 300	VAPA	3; 0	3; 0
chr1:182352027@-	-300; 300	GLUL	2; 0	3; 0
chr1:169100793@+	-132; 300	ATP1B1	3; 0	3; 0
chr1:78024416@+	-65; 300	AK5	3; 0	3; 0

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

RNAmap 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	59	0.35%	1.36%	92.19%	45	1.25532
anti	5	0.03%	0.12%	7.81%	2	0.106383
both	64	0.38%	1.47%	100.00%	47	1.3617
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	67	0.37%	1.36%	93.06%	45	1.42553
anti	5	0.03%	0.10%	6.94%	2	0.106383
both	72	0.40%	1.46%	100.00%	47	1.53191

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)
chr4:71588290@+	-290; 89	RUFY3	6; 0	7; 0
chrX:139866530@-	-96; 300	CDR1	0; 4	0; 4
chr6:31508971@-	-66; 265	BAT1	3; 0	6; 0
chr12:121093613@+	-256; 231	CABP1	3; 0	3; 0
chrX:51149868@+	-51; 300	CXorf67	2; 0	3; 0
chr4:158141875@+	-70; 203	GRIA2	2; 0	2; 0
chr17:47755471@-	-62; 89	SPOP	2; 0	2; 0
chr15:91769493@+	-196; 225	SV2B	2; 0	2; 0
chr12:30906696@-	-300; 210	CAPRIN2	2; 0	2; 0
chrY:15591802@-	-300; 205	UTY	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)
chr4:71588290@+	-290; 89	RUFY3	6; 0	7; 0
chr6:31508971@-	-66; 265	BAT1	3; 0	6; 0
chrX:139866530@-	-96; 300	CDR1	0; 4	0; 4
chrX:51149868@+	-51; 300	CXorf67	2; 0	3; 0
chr14:86087858@+	-188; 300	FLRT2	1; 0	3; 0
chr12:121093613@+	-256; 231	CABP1	3; 0	3; 0
chr4:158141875@+	-70; 203	GRIA2	2; 0	2; 0
chr19:49926595@-	-51; 64	PTH2	1; 0	2; 0
chr17:47755471@-	-62; 89	SPOP	2; 0	2; 0
chr15:91769493@+	-196; 225	SV2B	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 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	48	0.29%	1.10%	55.17%	32	0.8
anti	39	0.23%	0.90%	44.83%	28	0.65
both	87	0.52%	2.00%	100.00%	60	1.45
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	53	0.29%	1.07%	57.61%	32	0.883333
anti	39	0.22%	0.79%	42.39%	28	0.65
both	92	0.51%	1.86%	100.00%	60	1.53333

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)
chr4:144257914@+	-1000; 213	GAB1	6; 0	11; 0
chrX:139866722@-	-1000; 96	CDR1	0; 5	0; 5
chr17:39623680@-	-1000; 52	KRT32	0; 3	0; 3
chr14:48143952@-	-1000; 80	MDGA2	3; 0	3; 0
chr12:14133052@-	-1000; 96	GRIN2B	3; 0	3; 0
chr11:62623517@+	-1000; 112	SLC3A2	0; 3	0; 3
chr5:24645086@-	-1000; 192	CDH10	2; 0	2; 0
chr19:55770362@-	-1000; 280	SAPS1	2; 0	2; 0
chr17:4843422@+	-1000; 116	RNF167	0; 2	0; 2
chr16:81040102@+	-1000; 300	CENPN	0; 2	0; 2

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)
chr4:144257914@+	-1000; 213	GAB1	6; 0	11; 0
chrX:139866722@-	-1000; 96	CDR1	0; 5	0; 5
chr17:39623680@-	-1000; 52	KRT32	0; 3	0; 3
chr14:48143952@-	-1000; 80	MDGA2	3; 0	3; 0
chr12:14133052@-	-1000; 96	GRIN2B	3; 0	3; 0
chr11:62623517@+	-1000; 112	SLC3A2	0; 3	0; 3
chr5:24645086@-	-1000; 192	CDH10	2; 0	2; 0
chr19:55770362@-	-1000; 280	SAPS1	2; 0	2; 0
chr17:4843422@+	-1000; 116	RNF167	0; 2	0; 2
chr16:81040102@+	-1000; 300	CENPN	0; 2	0; 2

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	252	1.50%	5.80%	78.26%	197	1.03279
anti	70	0.42%	1.61%	21.74%	47	0.286885
both	322	1.92%	7.41%	100.00%	244	1.31967
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	254	1.41%	5.15%	76.97%	197	1.04098
anti	76	0.42%	1.54%	23.03%	47	0.311475
both	330	1.83%	6.69%	100.00%	244	1.35246

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; 12	0; 14
chr22:39781593@+	-300; 1000	SYNGR1	5; 0	5; 0
chrX:139865423@-	-158; 1000	CDR1	0; 4	0; 4
chr22:39214455@-	-300; 1000	NPTXR	4; 0	4; 0
chr11:10818591@-	-300; 1000	EIF4G2	4; 0	4; 0
chr7:75956114@-	-300; 1000	YWHAG	3; 0	3; 0
chr7:73007522@-	-300; 1000	MLXIPL	3; 0	3; 0
chr5:32604185@+	-300; 1000	SUB1	3; 0	3; 0
chr2:27600096@-	-156; 1000	ZNF513	0; 3	0; 3
chr2:231743963@+	-300; 1000	ITM2C	3; 0	3; 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; 12	0; 14
chr22:39781593@+	-300; 1000	SYNGR1	5; 0	5; 0
chrX:139865423@-	-158; 1000	CDR1	0; 4	0; 4
chr22:39214455@-	-300; 1000	NPTXR	4; 0	4; 0
chr16:31000473@+	-300; 1000	HSD3B7	0; 2	0; 4
chr11:10818591@-	-300; 1000	EIF4G2	4; 0	4; 0
chr7:75956114@-	-300; 1000	YWHAG	3; 0	3; 0
chr7:73007522@-	-300; 1000	MLXIPL	3; 0	3; 0
chr5:32604185@+	-300; 1000	SUB1	3; 0	3; 0
chr2:27600096@-	-156; 1000	ZNF513	0; 3	0; 3

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	348	2.07%	8.01%	68.10%	196	1.2
anti	163	0.97%	3.75%	31.90%	94	0.562069
both	511	3.05%	11.76%	100.00%	290	1.76207
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	520	2.89%	10.54%	72.32%	196	1.7931
anti	199	1.10%	4.03%	27.68%	94	0.686207
both	719	3.99%	14.57%	100.00%	290	2.47931

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	58; 0	146; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 47	0; 78
chr7:80962916@+	-1000; 115	AC004866.1-ENSG00000239843	8; 0	11; 0
chr4:144257914@+	-1000; 213	GAB1	6; 0	11; 0
chr12:120729705@-	-597; 70	U4-ENSG00000202538	6; 0	8; 0
chrX:139866722@-	-1000; 96	CDR1	0; 5	0; 5
chr2:220455705@-	-1000; 149	7SK-ENSG00000222678	5; 0	6; 0
chr13:97601786@-	-1000; 142	7SK-ENSG00000222472	5; 0	6; 0
chrX:100889099@-	-1000; 53	U6-ENSG00000207291	4; 0	10; 0
chr5:6848574@-	-1000; 168	7SK-ENSG00000200243	4; 0	7; 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	58; 0	146; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 47	0; 78
chr1:8266656@-	-1000; 82	U1-ENSG00000200975	2; 0	16; 0
chr7:80962916@+	-1000; 115	AC004866.1-ENSG00000239843	8; 0	11; 0
chr4:144257914@+	-1000; 213	GAB1	6; 0	11; 0
chrX:100889099@-	-1000; 53	U6-ENSG00000207291	4; 0	10; 0
chr4:140606580@-	-1000; 150	7SK-ENSG00000201533	4; 0	8; 0
chr12:120729705@-	-597; 70	U4-ENSG00000202538	6; 0	8; 0
chr12:127805899@+	-1000; 87	U1-ENSG00000253089	1; 0	8; 0
chr5:6848574@-	-1000; 168	7SK-ENSG00000200243	4; 0	7; 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	447	2.66%	10.28%	73.28%	297	1.1175
anti	163	0.97%	3.75%	26.72%	104	0.4075
both	610	3.64%	14.03%	100.00%	400	1.525
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	504	2.80%	10.21%	73.47%	297	1.26
anti	182	1.01%	3.69%	26.53%	104	0.455
both	686	3.81%	13.90%	100.00%	400	1.715

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)
chrUn_gl000220:118417@+	-300; 1000	28S	25; 0	54; 0
chr11:65271080@+	-300; 1000	MALAT1	21; 0	22; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	22; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 12	0; 14
chr18:77773065@+	-110; 1000	AC090360.1	11; 0	17; 0
chrY:10036111@-	-300; 1000	RN18S1	0; 9	0; 10
chrX:108297359@-	-216; 1000	RN28S1	0; 6	0; 8
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	6; 0	11; 0
chr4:144257786@-	-255; 1000	AC097658.1	0; 6	0; 11
chr1:169101767@-	-127; 1000	NME7	0; 6	0; 6

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	25; 0	54; 0
chr11:65271080@+	-300; 1000	MALAT1	21; 0	22; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	22; 0
chr18:77773065@+	-110; 1000	AC090360.1	11; 0	17; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 12	0; 14
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	6; 0	11; 0
chr4:144257786@-	-255; 1000	AC097658.1	0; 6	0; 11
chrY:10036111@-	-300; 1000	RN18S1	0; 9	0; 10
chrX:108297359@-	-216; 1000	RN28S1	0; 6	0; 8
chr1:169101767@-	-127; 1000	NME7	0; 6	0; 6

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	456	2.72%	10.49%	93.25%	342	1.22911
anti	33	0.20%	0.76%	6.75%	29	0.0889488
both	489	2.91%	11.25%	100.00%	371	1.31806
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	485	2.69%	9.83%	93.27%	342	1.30728
anti	35	0.19%	0.71%	6.73%	29	0.0943396
both	520	2.89%	10.54%	100.00%	371	1.40162

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	10; 0	10; 0
chr9:97055216@+	-216; 37	ZNF169	7; 0	7; 0
chr5:94026903@+	-300; 100	ANKRD32	6; 0	6; 0
chr20:2634908@+	-300; 100	SNORD110	6; 0	9; 0
chr11:85418922@-	-300; 100	SYTL2	6; 0	6; 0
chr19:613070@+	-300; 100	HCN2	5; 0	5; 0
chr5:179048854@-	-300; 100	HNRNPH1	4; 0	4; 0
chr3:52725453@+	-133; 100	SNORD19-ENSG00000222345	4; 0	4; 0
chr2:175216709@-	-300; 100	CIR1	4; 0	4; 0
chr19:12953892@+	-300; 100	MAST1	4; 0	4; 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	10; 0	10; 0
chr20:2634908@+	-300; 100	SNORD110	6; 0	9; 0
chr9:97055216@+	-216; 37	ZNF169	7; 0	7; 0
chr1:235622562@-	-300; 100	B3GALNT2	4; 0	7; 0
chr9:140676322@+	-300; 100	EHMT1	2; 0	6; 0
chr5:94026903@+	-300; 100	ANKRD32	6; 0	6; 0
chr11:85418922@-	-300; 100	SYTL2	6; 0	6; 0
chr19:613070@+	-300; 100	HCN2	5; 0	5; 0
chr5:179048854@-	-300; 100	HNRNPH1	4; 0	4; 0
chr3:52725453@+	-133; 100	SNORD19-ENSG00000222345	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.