Parameters
input_file: 20090724_LUjt2_1_hg19_ensembl59_G_iCLIP_TDP-43_Brain-F24_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: 5

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 82773
[x-link sites] used in any map: 15600 (18.85%)
[single hits in whole-genome, cDNA counts] total: 82773
[single hits in whole-genome, cDNA counts] used in any map: 19135 (21.22%)

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	3838	4.64%	24.60%	4022	4.46%	21.02%
intron-exon	-300; 300	4249	5.13%	27.24%	4385	4.86%	22.92%
5-ncRNA	-1000; 300	2091	2.53%	13.40%	3658	4.06%	19.12%
ncRNA-3	-300; 1000	1740	2.10%	11.15%	2957	3.28%	15.45%
ORF-3UTR	-300; 300	968	1.17%	6.21%	997	1.11%	5.21%
5UTR-ORF	-300; 300	229	0.28%	1.47%	243	0.27%	1.27%
inter-5UTR	-1000; 300	375	0.45%	2.40%	585	0.65%	3.06%
3UTR-inter	-300; 1000	1088	1.31%	6.97%	1120	1.24%	5.85%
inter-5	-1000; 300	1671	2.02%	10.71%	3458	3.83%	18.07%
3-inter	-300; 1000	2123	2.56%	13.61%	2804	3.11%	14.65%
BP best in intron	-300; 100	2168	2.62%	13.90%	2277	2.52%	11.90%

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	3620	4.37%	23.21%	94.32%	3348	1.01828
anti	218	0.26%	1.40%	5.68%	209	0.0613221
both	3838	4.64%	24.60%	100.00%	3555	1.07961
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	3798	4.21%	19.85%	94.43%	3348	1.06835
anti	224	0.25%	1.17%	5.57%	209	0.0630098
both	4022	4.46%	21.02%	100.00%	3555	1.13136

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr7:139025365@+	-85; 256	C7orf55	14; 0	74; 0
chr19:17740047@-	-42; 300	UNC13A	9; 0	9; 0
chr5:883069@-	-226; 300	BRD9	7; 0	7; 0
chr22:38687371@-	-285; 177	CSNK1E	7; 0	7; 0
chr19:46815910@+	-247; 300	HIF3A	7; 0	8; 0
chr16:57662765@+	-174; 300	GPR56	7; 0	8; 0
chr10:103590823@-	-50; 300	KCNIP2	7; 0	7; 0
chr7:1479559@-	-300; 300	MICALL2	5; 0	5; 0
chr3:116163722@-	-78; 300	LSAMP	5; 0	5; 0
chr3:65595417@-	-112; 300	MAGI1	5; 0	5; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr7:139025365@+	-85; 256	C7orf55	14; 0	74; 0
chr19:17740047@-	-42; 300	UNC13A	9; 0	9; 0
chr19:46815910@+	-247; 300	HIF3A	7; 0	8; 0
chr16:57662765@+	-174; 300	GPR56	7; 0	8; 0
chr5:883069@-	-226; 300	BRD9	7; 0	7; 0
chr22:38687371@-	-285; 177	CSNK1E	7; 0	7; 0
chr10:103590823@-	-50; 300	KCNIP2	7; 0	7; 0
chr2:127827569@-	-48; 300	BIN1	4; 0	6; 0
chr11:497969@-	-86; 300	RNH1	5; 0	6; 0
chr1:1158622@-	-57; 300	SDF4	4; 0	6; 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	4038	4.88%	25.88%	95.03%	3763	1.02073
anti	211	0.25%	1.35%	4.97%	199	0.0533367
both	4249	5.13%	27.24%	100.00%	3956	1.07406
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	4154	4.61%	21.71%	94.73%	3763	1.05005
anti	231	0.26%	1.21%	5.27%	199	0.0583923
both	4385	4.86%	22.92%	100.00%	3956	1.10844

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr22:39715115@-	-130; 42	RPL3	9; 0	16; 0
chr12:113565982@-	-300; 57	RASAL1	9; 0	9; 0
chr20:10286776@+	-300; 300	SNAP25	8; 0	8; 0
chr2:127811587@-	-300; 54	BIN1	6; 0	6; 0
chr4:863744@-	-300; 300	GAK	5; 0	5; 0
chr2:175665014@-	-300; 300	CHN1	5; 0	5; 0
chr2:47387942@-	-300; 300	CALM2	5; 0	6; 0
chr19:46834412@+	-300; 93	HIF3A	5; 0	8; 0
chr4:158284586@+	-135; 300	GRIA2	4; 0	4; 0
chr19:2337038@-	-300; 78	AC004490.1	0; 4	0; 4

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	9; 0	16; 0
chr8:26221236@+	-300; 85	PPP2R2A	1; 1	10; 5
chr1:182356426@-	-300; 259	GLUL	1; 1	1; 11
chr12:113565982@-	-300; 57	RASAL1	9; 0	9; 0
chr20:10286776@+	-300; 300	SNAP25	8; 0	8; 0
chr19:46834412@+	-300; 93	HIF3A	5; 0	8; 0
chr2:127811587@-	-300; 54	BIN1	6; 0	6; 0
chr2:47387942@-	-300; 300	CALM2	5; 0	6; 0
chr4:863744@-	-300; 300	GAK	5; 0	5; 0
chr2:175665014@-	-300; 300	CHN1	5; 0	5; 0

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

RNAmap 5-ncRNA

junction is at position zero.
upstream is regions of type: intron, inter, telo
downstream is regions of type: ncRNA

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	1513	1.83%	9.70%	72.36%	601	1.42333
anti	578	0.70%	3.71%	27.64%	472	0.543744
both	2091	2.53%	13.40%	100.00%	1063	1.96707
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	3028	3.36%	15.82%	82.78%	601	2.84854
anti	630	0.70%	3.29%	17.22%	472	0.592662
both	3658	4.06%	19.12%	100.00%	1063	3.4412

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	142; 0	196; 0
chr1:109642814@+	-1000; 210	snoU2-25	108; 0	461; 0
chrM:16022@-	-274; 34	J01415.14	25; 2	168; 2
chr14:20811565@-	-1000; 166	RNaseP_nuc-ENSG00000252678	23; 0	38; 0
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	21; 0	74; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	20; 0	24; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	18; 0	25; 0
chr2:230045665@-	-1000; 89	AC006368.1, PID1	18; 0	48; 0
chr1:235291251@-	-329; 67	SNORA14-ENSG00000207181, TOMM20	18; 0	54; 0
chr6:36607448@-	-1000; 64	U1-ENSG00000238554	17; 0	73; 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	108; 0	461; 0
chr11:65269806@+	-1000; 29	MALAT1	142; 0	196; 0
chrM:16022@-	-274; 34	J01415.14	25; 2	168; 2
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	21; 0	74; 0
chr6:36607448@-	-1000; 64	U1-ENSG00000238554	17; 0	73; 0
chr1:8266656@-	-1000; 82	U1-ENSG00000200975	9; 0	68; 0
chr1:148241464@+	-1000; 82	U1-ENSG00000207501	13; 0	68; 0
chr20:62540307@+	-1000; 82	DNAJC5, U1-ENSG00000199805	13; 0	66; 0
chr12:63244680@-	-1000; 82	PPM1H, U1-ENSG00000200296	8; 0	61; 0
chr1:235291251@-	-329; 67	SNORA14-ENSG00000207181, TOMM20	18; 0	54; 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	1192	1.44%	7.64%	68.51%	485	1.37963
anti	548	0.66%	3.51%	31.49%	384	0.634259
both	1740	2.10%	11.15%	100.00%	864	2.01389
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	2167	2.40%	11.32%	73.28%	485	2.5081
anti	790	0.88%	4.13%	26.72%	384	0.914352
both	2957	3.28%	15.45%	100.00%	864	3.42245

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	199; 0	287; 0
chrUn_gl000220:118417@+	-300; 1000	28S	110; 0	479; 0
chr1:109643234@+	-210; 1000	snoU2-25	33; 0	42; 0
chr14:20811232@-	-167; 1000	RNaseP_nuc-ENSG00000252678	32; 0	49; 0
chrM:15953@+	-33; 309	J01415.6	6; 25	49; 160
chr11:62609089@-	-96; 978	U2-ENSG00000222328	30; 0	61; 0
chrM:4327@-	-36; 1000	J01415.13	0; 23	0; 57
chrM:15954@-	-34; 606	J01415.14	6; 15	25; 66
chr12:127650451@-	-268; 1000	AC079949.1	18; 0	59; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	15; 0	49; 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	110; 0	479; 0
chr11:65271080@+	-300; 1000	MALAT1	199; 0	287; 0
chrM:15953@+	-33; 309	J01415.6	6; 25	49; 160
chrM:15954@-	-34; 606	J01415.14	6; 15	25; 66
chr11:62609089@-	-96; 978	U2-ENSG00000222328	30; 0	61; 0
chr12:127650451@-	-268; 1000	AC079949.1	18; 0	59; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	11; 0	58; 0
chrM:4327@-	-36; 1000	J01415.13	0; 23	0; 57
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	15; 0	49; 0
chr14:20811232@-	-167; 1000	RNaseP_nuc-ENSG00000252678	32; 0	49; 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	914	1.10%	5.86%	94.42%	742	1.17029
anti	54	0.07%	0.35%	5.58%	42	0.0691421
both	968	1.17%	6.21%	100.00%	781	1.23944
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	943	1.05%	4.93%	94.58%	742	1.20743
anti	54	0.06%	0.28%	5.42%	42	0.0691421
both	997	1.11%	5.21%	100.00%	781	1.27657

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)
chr10:22825820@-	-195; 300	PIP5K2A	15; 0	18; 0
chrX:139865739@-	-300; 158	CDR1	0; 11	0; 11
chr10:73822514@-	-74; 300	SPOCK2	10; 0	11; 0
chrX:103045717@+	-132; 300	PLP1	6; 0	6; 0
chr2:55199719@-	-300; 198	RTN4	5; 0	5; 0
chr17:8063722@-	-233; 300	VAMP2	5; 0	5; 0
chr16:67472427@-	-82; 253	ATP6V0D1	5; 0	8; 0
chr16:89981552@+	-300; 300	AC092143.1	5; 0	5; 0
chrX:148564273@-	-173; 300	IDS	4; 0	4; 0
chr9:124094881@+	-85; 120	GSN	4; 0	4; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr10:22825820@-	-195; 300	PIP5K2A	15; 0	18; 0
chrX:139865739@-	-300; 158	CDR1	0; 11	0; 11
chr10:73822514@-	-74; 300	SPOCK2	10; 0	11; 0
chr16:67472427@-	-82; 253	ATP6V0D1	5; 0	8; 0
chrX:103045717@+	-132; 300	PLP1	6; 0	6; 0
chr2:55199719@-	-300; 198	RTN4	5; 0	5; 0
chr17:8063722@-	-233; 300	VAMP2	5; 0	5; 0
chr16:89981552@+	-300; 300	AC092143.1	5; 0	5; 0
chrX:148564273@-	-173; 300	IDS	4; 0	4; 0
chrX:119572929@-	-109; 300	LAMP2	3; 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 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	208	0.25%	1.33%	90.83%	168	1.13661
anti	21	0.03%	0.13%	9.17%	15	0.114754
both	229	0.28%	1.47%	100.00%	183	1.25137
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	220	0.24%	1.15%	90.53%	168	1.20219
anti	23	0.03%	0.12%	9.47%	15	0.125683
both	243	0.27%	1.27%	100.00%	183	1.32787

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)
chr6:31508971@-	-66; 265	BAT1	11; 0	17; 0
chr2:61764828@-	-277; 66	XPO1	8; 0	8; 0
chrX:139866530@-	-96; 300	CDR1	0; 7	0; 7
chr4:71588290@+	-290; 89	RUFY3	5; 0	6; 0
chr16:89980628@+	-52; 300	AC092143.1	4; 0	4; 0
chr16:1756340@+	-74; 159	MAPK8IP3	3; 0	3; 0
chr13:45010763@-	-109; 62	TSC22D1	3; 0	3; 0
chrX:148586666@-	-105; 51	IDS	2; 0	2; 0
chr4:158141875@+	-70; 203	GRIA2	2; 0	2; 0
chr3:192445111@-	-80; 221	FGF12	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)
chr6:31508971@-	-66; 265	BAT1	11; 0	17; 0
chr2:61764828@-	-277; 66	XPO1	8; 0	8; 0
chrX:139866530@-	-96; 300	CDR1	0; 7	0; 7
chr4:71588290@+	-290; 89	RUFY3	5; 0	6; 0
chr16:89980628@+	-52; 300	AC092143.1	4; 0	4; 0
chr16:1756340@+	-74; 159	MAPK8IP3	3; 0	3; 0
chr15:31196866@+	-76; 300	MTMR15	2; 0	3; 0
chr13:45010763@-	-109; 62	TSC22D1	3; 0	3; 0
chrX:148586666@-	-105; 51	IDS	2; 0	2; 0
chr9:35748969@-	-128; 300	GBA2	1; 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	165	0.20%	1.06%	44.00%	148	0.559322
anti	210	0.25%	1.35%	56.00%	151	0.711864
both	375	0.45%	2.40%	100.00%	295	1.27119
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	172	0.19%	0.90%	29.40%	148	0.583051
anti	413	0.46%	2.16%	70.60%	151	1.4
both	585	0.65%	3.06%	100.00%	295	1.98305

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)
chr15:89878025@-	-1000; 61	POLG	0; 15	0; 150
chr11:66115160@-	-1000; 72	AP001107.2	0; 10	0; 51
chr15:80737492@-	-1000; 74	AC016705.1	0; 7	0; 8
chr11:62623517@+	-1000; 112	SLC3A2	0; 7	0; 8
chrX:139866722@-	-1000; 96	CDR1	0; 6	0; 7
chr20:47894962@-	-1000; 248	ZNFX1	0; 6	0; 6
chr8:33370702@-	-1000; 286	C8orf41	0; 5	0; 5
chr1:151030233@+	-1000; 300	MLLT11	1; 4	1; 4
chr18:47340272@-	-1000; 209	ACAA2	0; 4	0; 4
chr16:89980524@+	-1000; 52	AC092143.1	4; 0	4; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr15:89878025@-	-1000; 61	POLG	0; 15	0; 150
chr11:66115160@-	-1000; 72	AP001107.2	0; 10	0; 51
chr17:37026255@+	-1000; 93	LASP1	0; 2	0; 18
chr15:80737492@-	-1000; 74	AC016705.1	0; 7	0; 8
chr11:62623517@+	-1000; 112	SLC3A2	0; 7	0; 8
chrX:139866722@-	-1000; 96	CDR1	0; 6	0; 7
chr20:47894962@-	-1000; 248	ZNFX1	0; 6	0; 6
chr8:33370702@-	-1000; 286	C8orf41	0; 5	0; 5
chr1:151030233@+	-1000; 300	MLLT11	1; 4	1; 4
chr18:47340272@-	-1000; 209	ACAA2	0; 4	0; 4

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	891	1.08%	5.71%	81.89%	749	0.992205
anti	197	0.24%	1.26%	18.11%	156	0.219376
both	1088	1.31%	6.97%	100.00%	898	1.21158
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	913	1.01%	4.77%	81.52%	749	1.0167
anti	207	0.23%	1.08%	18.48%	156	0.230512
both	1120	1.24%	5.85%	100.00%	898	1.24722

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)
chrX:139865423@-	-158; 1000	CDR1	0; 8	0; 9
chr17:8024297@-	-294; 1000	HES7	6; 0	10; 0
chr5:71502853@+	-300; 1000	MAP1B	5; 0	5; 0
chr3:115528639@-	-241; 1000	LSAMP	5; 0	5; 0
chr18:72102961@-	-300; 1000	FAM69C	5; 0	6; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 5	0; 8
chr9:111899165@-	-283; 1000	C9orf4	4; 0	4; 0
chr5:139496321@+	-300; 1000	PURA	4; 0	4; 0
chr3:9543479@-	-206; 1000	LHFPL4	4; 0	4; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 4	0; 4

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)
chr17:8024297@-	-294; 1000	HES7	6; 0	10; 0
chrX:139865423@-	-158; 1000	CDR1	0; 8	0; 9
chr16:67471456@+	-275; 1000	HSD11B2	0; 5	0; 8
chr18:72102961@-	-300; 1000	FAM69C	5; 0	6; 0
chr5:71502853@+	-300; 1000	MAP1B	5; 0	5; 0
chr3:115528639@-	-241; 1000	LSAMP	5; 0	5; 0
chr9:111899165@-	-283; 1000	C9orf4	4; 0	4; 0
chr9:77302117@+	-300; 1000	RORB	3; 0	4; 0
chr7:75956114@-	-300; 1000	YWHAG	3; 0	4; 0
chr6:76427997@+	-300; 1000	SENP6	3; 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-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	781	0.94%	5.01%	46.74%	413	0.829087
anti	890	1.08%	5.71%	53.26%	538	0.944798
both	1671	2.02%	10.71%	100.00%	942	1.77389
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	1637	1.82%	8.56%	47.34%	413	1.73779
anti	1821	2.02%	9.52%	52.66%	538	1.93312
both	3458	3.83%	18.07%	100.00%	942	3.67091

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_gl000220:117814@-	-1000; 67	AL592188.5	0; 213	0; 899
chr1:109642814@+	-1000; 210	snoU2-25	108; 0	461; 0
chr14:20811565@-	-1000; 166	RNaseP_nuc-ENSG00000252678	23; 0	38; 0
chr6:36607448@-	-1000; 64	U1-ENSG00000238554	17; 0	73; 0
chr9:79186648@+	-1000; 151	AL161626.1	16; 0	44; 0
chr15:89878025@-	-1000; 61	POLG	0; 15	0; 150
chr22:43011249@+	-1000; 75	U12-ENSG00000199382	14; 0	31; 0
chr9:35658013@-	-429; 132	RNase_MRP-ENSG00000199916	13; 0	19; 0
chr8:23934670@-	-1000; 81	U1-ENSG00000207201	13; 0	43; 0
chr1:148241464@+	-1000; 82	U1-ENSG00000207501	13; 0	68; 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_gl000220:117814@-	-1000; 67	AL592188.5	0; 213	0; 899
chr1:109642814@+	-1000; 210	snoU2-25	108; 0	461; 0
chr15:89878025@-	-1000; 61	POLG	0; 15	0; 150
chr6:36607448@-	-1000; 64	U1-ENSG00000238554	17; 0	73; 0
chr1:8266656@-	-1000; 82	U1-ENSG00000200975	9; 0	68; 0
chr1:148241464@+	-1000; 82	U1-ENSG00000207501	13; 0	68; 0
chr11:66115160@-	-1000; 72	AP001107.2	0; 10	0; 51
chr8:136754737@-	-1000; 76	U1-ENSG00000199652	3; 0	47; 0
chr9:79186648@+	-1000; 151	AL161626.1	16; 0	44; 0
chr8:23934670@-	-1000; 81	U1-ENSG00000207201	13; 0	43; 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	1554	1.88%	9.96%	73.20%	954	1.13846
anti	569	0.69%	3.65%	26.80%	419	0.41685
both	2123	2.56%	13.61%	100.00%	1365	1.55531
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	2201	2.44%	11.50%	78.50%	954	1.61245
anti	603	0.67%	3.15%	21.50%	419	0.441758
both	2804	3.11%	14.65%	100.00%	1365	2.05421

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	199; 0	287; 0
chrUn_gl000220:118417@+	-300; 1000	28S	110; 0	479; 0
chr1:109643234@+	-210; 1000	snoU2-25	33; 0	42; 0
chr14:20811232@-	-167; 1000	RNaseP_nuc-ENSG00000252678	32; 0	49; 0
chr12:127650451@-	-268; 1000	AC079949.1	18; 0	59; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	15; 0	49; 0
chrX:108297359@-	-216; 1000	RN28S1	0; 11	0; 15
chr10:133994727@-	-160; 1000	RP11-140A10.3	0; 11	0; 11
chrY:10036111@-	-300; 1000	RN18S1	0; 8	0; 11
chrX:139865423@-	-158; 1000	CDR1	0; 8	0; 9

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	110; 0	479; 0
chr11:65271080@+	-300; 1000	MALAT1	199; 0	287; 0
chr12:127650451@-	-268; 1000	AC079949.1	18; 0	59; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	15; 0	49; 0
chr14:20811232@-	-167; 1000	RNaseP_nuc-ENSG00000252678	32; 0	49; 0
chr1:109643234@+	-210; 1000	snoU2-25	33; 0	42; 0
chr9:79186950@+	-151; 1000	AL161626.1	6; 0	35; 0
chr6:26574925@+	-300; 1000	AL121936.1	3; 0	16; 0
chrX:108297359@-	-216; 1000	RN28S1	0; 11	0; 15
chr9:35657749@-	-132; 1000	RNase_MRP-ENSG00000199916	8; 0	12; 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	2013	2.43%	12.90%	92.85%	1748	1.06003
anti	155	0.19%	0.99%	7.15%	151	0.0816219
both	2168	2.62%	13.90%	100.00%	1899	1.14165
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	2119	2.35%	11.07%	93.06%	1748	1.11585
anti	158	0.18%	0.83%	6.94%	151	0.0832017
both	2277	2.52%	11.90%	100.00%	1899	1.19905

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	18; 0	22; 0
chr13:27829210@+	-300; 100	SNORD102	11; 0	19; 0
chr12:113566108@-	-300; 100	RASAL1	10; 0	10; 0
chr5:138614713@+	-297; 24	MATR3	9; 0	9; 0
chr20:2634908@+	-300; 100	SNORD110	9; 0	10; 0
chr19:2337060@+	-300; 100	AC004410.1	9; 0	9; 0
chr12:6619768@+	-224; 24	NCAPD2	8; 0	9; 0
chr9:130210892@-	-238; 100	SNORA65	7; 0	11; 0
chr11:8707006@+	-177; 100	SNORA3-ENSG00000212607	7; 0	7; 0
chr9:125642528@-	-109; 100	SNORD90	6; 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)
chr10:88649475@+	-300; 100	U1-ENSG00000200176	5; 0	33; 0
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	18; 0	22; 0
chr13:27829210@+	-300; 100	SNORD102	11; 0	19; 0
chr9:130210892@-	-238; 100	SNORA65	7; 0	11; 0
chr9:125642528@-	-109; 100	SNORD90	6; 0	10; 0
chr20:2634908@+	-300; 100	SNORD110	9; 0	10; 0
chr12:113566108@-	-300; 100	RASAL1	10; 0	10; 0
chr5:138614713@+	-297; 24	MATR3	9; 0	9; 0
chr19:2337060@+	-300; 100	AC004410.1	9; 0	9; 0
chr12:6619768@+	-224; 24	NCAPD2	8; 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.