Parameters
input_file: 20090724_LUd4_2_hg19_ensembl59_G_iCLIP_TIA1_HeLa_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: 142570
[x-link sites] used in any map: 47033 (32.99%)
[single hits in whole-genome, cDNA counts] total: 142570
[single hits in whole-genome, cDNA counts] used in any map: 52397 (33.85%)

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	13919	9.76%	29.59%	14584	9.42%	27.83%
intron-exon	-300; 300	10266	7.20%	21.83%	10872	7.02%	20.75%
5-ncRNA	-1000; 300	2223	1.56%	4.73%	3008	1.94%	5.74%
ncRNA-3	-300; 1000	2451	1.72%	5.21%	3204	2.07%	6.11%
ORF-3UTR	-300; 300	7944	5.57%	16.89%	9243	5.97%	17.64%
5UTR-ORF	-300; 300	246	0.17%	0.52%	263	0.17%	0.50%
inter-5UTR	-1000; 300	623	0.44%	1.32%	695	0.45%	1.33%
3UTR-inter	-300; 1000	7621	5.35%	16.20%	8637	5.58%	16.48%
inter-5	-1000; 300	2029	1.42%	4.31%	2492	1.61%	4.76%
3-inter	-300; 1000	9858	6.91%	20.96%	11630	7.51%	22.20%
BP best in intron	-300; 100	5550	3.89%	11.80%	5776	3.73%	11.02%

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	13615	9.55%	28.95%	97.82%	10664	1.25357
anti	304	0.21%	0.65%	2.18%	213	0.0279901
both	13919	9.76%	29.59%	100.00%	10861	1.28156
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	14218	9.18%	27.14%	97.49%	10664	1.30909
anti	366	0.24%	0.70%	2.51%	213	0.0336986
both	14584	9.42%	27.83%	100.00%	10861	1.34279

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)
chr1:45976739@+	-281; 300	MMACHC	0; 36	0; 88
chr3:41281934@+	-300; 300	CTNNB1	23; 0	30; 0
chr12:50158717@+	-300; 300	TMBIM6	22; 0	31; 0
chr7:128411528@+	-300; 107	CALU	21; 0	31; 0
chr5:177637967@-	-300; 300	AGXT2L2	1; 17	1; 19
chr5:10401598@+	-300; 185	MARCH6	16; 0	23; 0
chr12:98928321@+	-101; 300	TMPO	12; 0	13; 0
chr8:22280254@+	-300; 300	SLC39A14	11; 0	12; 0
chr2:191800015@+	-300; 300	GLS	11; 0	12; 0
chr1:165624857@+	-127; 300	MGST3	11; 0	17; 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)
chr1:45976739@+	-281; 300	MMACHC	0; 36	0; 88
chr7:139025365@+	-85; 256	C7orf55	4; 0	36; 0
chr7:128411528@+	-300; 107	CALU	21; 0	31; 0
chr12:50158717@+	-300; 300	TMBIM6	22; 0	31; 0
chr3:41281934@+	-300; 300	CTNNB1	23; 0	30; 0
chr5:10401598@+	-300; 185	MARCH6	16; 0	23; 0
chr5:177637967@-	-300; 300	AGXT2L2	1; 17	1; 19
chr1:165624857@+	-127; 300	MGST3	11; 0	17; 0
chr19:17513754@-	-189; 300	BST2	8; 0	14; 0
chr17:57915758@+	-52; 300	TMEM49	10; 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 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	9940	6.97%	21.13%	96.82%	7693	1.25063
anti	326	0.23%	0.69%	3.18%	277	0.0410166
both	10266	7.20%	21.83%	100.00%	7948	1.29165
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	10534	6.80%	20.10%	96.89%	7693	1.32536
anti	338	0.22%	0.65%	3.11%	277	0.0425264
both	10872	7.02%	20.75%	100.00%	7948	1.36789

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)
chr15:45009804@+	-300; 277	B2M	41; 0	65; 0
chr2:211542610@+	-300; 300	CPS1	23; 0	33; 0
chr9:131456919@+	-292; 300	SET	21; 1	38; 1
chr8:128753204@+	-241; 235	MYC	21; 0	31; 0
chr1:26227577@-	-160; 260	STMN1	20; 1	30; 1
chr10:112657785@+	-300; 300	PDCD4	20; 0	29; 0
chr17:57915655@+	-300; 51	TMEM49	19; 0	29; 0
chr2:189876353@+	-300; 210	COL3A1	17; 0	22; 0
chr4:24529663@-	-300; 283	DHX15	16; 0	24; 0
chr4:6643456@+	-236; 300	MRFAP1	16; 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)
chr15:45009804@+	-300; 277	B2M	41; 0	65; 0
chr9:131456919@+	-292; 300	SET	21; 1	38; 1
chr2:211542610@+	-300; 300	CPS1	23; 0	33; 0
chr8:128753204@+	-241; 235	MYC	21; 0	31; 0
chr1:26227577@-	-160; 260	STMN1	20; 1	30; 1
chr4:6643456@+	-236; 300	MRFAP1	16; 0	29; 0
chr17:57915655@+	-300; 51	TMEM49	19; 0	29; 0
chr10:112657785@+	-300; 300	PDCD4	20; 0	29; 0
chr4:24529663@-	-300; 283	DHX15	16; 0	24; 0
chr5:179041959@-	-293; 300	HNRNPH1	13; 0	22; 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	1004	0.70%	2.13%	45.16%	482	0.886143
anti	1219	0.86%	2.59%	54.84%	659	1.0759
both	2223	1.56%	4.73%	100.00%	1133	1.96205
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	1663	1.07%	3.17%	55.29%	482	1.46778
anti	1345	0.87%	2.57%	44.71%	659	1.18711
both	3008	1.94%	5.74%	100.00%	1133	2.6549

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	202; 0	374; 0
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	54; 1
chr2:70315685@-	-1000; 62	AC136007.2	0; 31	0; 39
chr1:205685227@+	-1000; 300	AC119673.2	0; 26	0; 29
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 23
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 20	0; 33
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 19	0; 22
chr17:57918626@+	-338; 36	hsa-mir-21	19; 0	28; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 17	0; 20
chr12:7052978@+	-748; 31	U7-ENSG00000238923	17; 0	96; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	202; 0	374; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	160; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	17; 0	96; 0
chr14:74055600@-	-1000; 36	AC005225.1	5; 0	62; 0
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	54; 1
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	14; 1	54; 1
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	13; 0	46; 0
chr2:70315685@-	-1000; 62	AC136007.2	0; 31	0; 39
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 20	0; 33
chrM:5890@-	-777; 32	J01415.32	4; 0	31; 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	1474	1.03%	3.13%	60.14%	708	1.18204
anti	977	0.69%	2.08%	39.86%	552	0.78348
both	2451	1.72%	5.21%	100.00%	1247	1.96552
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	2138	1.38%	4.08%	66.73%	708	1.71451
anti	1066	0.69%	2.03%	33.27%	552	0.854852
both	3204	2.07%	6.11%	100.00%	1247	2.56937

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	274; 0	567; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 26	0; 36
chrUn_gl000220:118417@+	-300; 1000	28S	24; 0	74; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 21	0; 27
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 20	0; 25
chr2:191798136@-	-300; 1000	AC067945.1	0; 18	0; 18
chr8:144939422@+	-300; 1000	AC105049.1	0; 16	0; 19
chr1:21070455@+	-63; 1000	RP5-930J4.4	0; 16	0; 17
chr1:17733878@+	-33; 1000	RP1-20B21.4	0; 16	0; 21
chr1:45187456@-	-59; 1000	U5-ENSG00000199377	14; 0	23; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	274; 0	567; 0
chrUn_gl000220:118417@+	-300; 1000	28S	24; 0	74; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	10; 0	52; 0
chr14:74055527@-	-37; 1000	AC005225.1	2; 0	42; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 26	0; 36
chr3:14530617@-	-300; 1000	GRIP2	0; 21	0; 27
chr1:94312467@+	-40; 1000	hsa-mir-760	7; 0	27; 0
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 20	0; 25
chr1:45187456@-	-59; 1000	U5-ENSG00000199377	14; 0	23; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	9; 0	21; 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	7821	5.49%	16.63%	98.45%	2607	2.92702
anti	123	0.09%	0.26%	1.55%	75	0.0460329
both	7944	5.57%	16.89%	100.00%	2672	2.97305
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	9111	5.89%	17.39%	98.57%	2607	3.40981
anti	132	0.09%	0.25%	1.43%	75	0.0494012
both	9243	5.97%	17.64%	100.00%	2672	3.45921

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)
chr19:13054727@+	-101; 288	CALR	69; 0	119; 0
chr1:35650053@-	-70; 300	SFPQ	53; 0	75; 0
chr3:149087560@-	-53; 300	TM4SF1	37; 0	55; 0
chr14:62213803@+	-76; 300	HIF1A	37; 0	55; 0
chr2:136872205@-	-300; 144	CXCR4	35; 0	43; 0
chrX:102931085@-	-300; 300	MORF4L2	34; 0	60; 0
chr1:54497690@-	-144; 172	TMEM59	31; 0	40; 0
chr11:64532857@-	-66; 300	SF1	30; 0	52; 0
chrX:114884310@+	-165; 300	PLS3	29; 0	41; 0
chr5:179156650@+	-145; 300	CANX	29; 0	42; 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)
chr19:13054727@+	-101; 288	CALR	69; 0	119; 0
chr17:4849191@-	-50; 123	PFN1	26; 0	81; 0
chr1:35650053@-	-70; 300	SFPQ	53; 0	75; 0
chrX:102931085@-	-300; 300	MORF4L2	34; 0	60; 0
chr3:149087560@-	-53; 300	TM4SF1	37; 0	55; 0
chr14:62213803@+	-76; 300	HIF1A	37; 0	55; 0
chr6:30692174@+	-300; 300	TUBB	27; 0	53; 0
chr11:64532857@-	-66; 300	SF1	30; 0	52; 0
chr1:207533847@+	-300; 231	CD55	25; 0	50; 0
chr2:189876774@+	-211; 300	COL3A1	29; 0	46; 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	207	0.15%	0.44%	84.15%	145	1.29375
anti	39	0.03%	0.08%	15.85%	16	0.24375
both	246	0.17%	0.52%	100.00%	160	1.5375
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	0.14%	0.42%	83.65%	145	1.375
anti	43	0.03%	0.08%	16.35%	16	0.26875
both	263	0.17%	0.50%	100.00%	160	1.64375

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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 16	0; 19
chr6:31508971@-	-66; 265	BAT1	11; 0	16; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 8	0; 8
chr6:24718895@-	-300; 64	C6orf62	7; 0	9; 0
chr6:64286785@+	-92; 52	PTP4A1	7; 0	7; 0
chr8:101733810@-	-252; 96	PABPC1	4; 0	4; 0
chr5:138643104@+	-89; 300	MATR3	4; 0	4; 0
chr8:126011645@+	-300; 145	SQLE	3; 0	3; 0
chr6:26271611@-	-216; 206	HIST1H3G	3; 0	4; 0
chr5:32789507@+	-282; 183	C5orf23	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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 16	0; 19
chr6:31508971@-	-66; 265	BAT1	11; 0	16; 0
chr6:24718895@-	-300; 64	C6orf62	7; 0	9; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 8	0; 8
chr6:64286785@+	-92; 52	PTP4A1	7; 0	7; 0
chr19:49468764@+	-100; 51	FTL	3; 0	5; 0
chr8:101733810@-	-252; 96	PABPC1	4; 0	4; 0
chr6:26271611@-	-216; 206	HIST1H3G	3; 0	4; 0
chr5:138643104@+	-89; 300	MATR3	4; 0	4; 0
chr8:126011645@+	-300; 145	SQLE	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 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	161	0.11%	0.34%	25.84%	129	0.378824
anti	462	0.32%	0.98%	74.16%	306	1.08706
both	623	0.44%	1.32%	100.00%	425	1.46588
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	166	0.11%	0.32%	23.88%	129	0.390588
anti	529	0.34%	1.01%	76.12%	306	1.24471
both	695	0.45%	1.33%	100.00%	425	1.63529

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)
chr11:62623517@+	-1000; 112	SLC3A2	0; 18	0; 19
chr6:166401114@+	-1000; 249	AL132661.1	0; 16	0; 23
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 13	0; 14
chr20:47894962@-	-1000; 248	ZNFX1	0; 10	0; 10
chr5:175815975@-	-1000; 188	NOP16	0; 9	0; 11
chr1:173837219@+	-1000; 87	ZBTB37	0; 9	0; 11
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 19
chr19:54960064@+	-920; 210	LENG8	0; 7	0; 7
chr15:89878025@-	-1000; 61	POLG	0; 7	0; 38
chr8:101734314@-	-1000; 252	PABPC1	6; 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)
chr15:89878025@-	-1000; 61	POLG	0; 7	0; 38
chr6:166401114@+	-1000; 249	AL132661.1	0; 16	0; 23
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 19
chr11:62623517@+	-1000; 112	SLC3A2	0; 18	0; 19
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 13	0; 14
chr5:175815975@-	-1000; 188	NOP16	0; 9	0; 11
chr1:173837219@+	-1000; 87	ZBTB37	0; 9	0; 11
chr20:47894962@-	-1000; 248	ZNFX1	0; 10	0; 10
chr8:101734314@-	-1000; 252	PABPC1	6; 0	7; 0
chr5:93954051@+	-1000; 151	ANKRD32	0; 5	0; 7

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	6529	4.58%	13.88%	85.67%	2527	2.26938
anti	1092	0.77%	2.32%	14.33%	423	0.379562
both	7621	5.35%	16.20%	100.00%	2877	2.64894
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	7354	4.75%	14.04%	85.15%	2527	2.55613
anti	1283	0.83%	2.45%	14.85%	423	0.445951
both	8637	5.58%	16.48%	100.00%	2877	3.00209

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)
chr19:39220830@-	-300; 1000	CAPN12	0; 49	0; 86
chr12:53874278@-	-300; 1000	MAP3K12	1; 38	1; 52
chr17:79476997@-	-300; 1000	ACTG1	35; 0	97; 0
chr16:18802989@-	-300; 667	ARL6IP1	34; 0	48; 0
chr17:4848518@+	-104; 1000	RNF167	0; 27	0; 82
chr8:128753674@+	-235; 1000	MYC	26; 0	32; 0
chr15:45010359@+	-278; 1000	B2M	26; 0	32; 0
chr12:104744062@+	-300; 1000	TXNRD1	26; 0	37; 0
chr6:31785723@+	-132; 1000	HSPA1A	24; 0	32; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 22	0; 24

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)
chr17:79476997@-	-300; 1000	ACTG1	35; 0	97; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 49	0; 86
chr17:4848518@+	-104; 1000	RNF167	0; 27	0; 82
chr12:53874278@-	-300; 1000	MAP3K12	1; 38	1; 52
chr16:18802989@-	-300; 667	ARL6IP1	34; 0	48; 0
chr2:1635657@-	-300; 1000	PXDN	19; 0	45; 0
chrX:70521018@+	-157; 282	NONO	14; 0	38; 0
chr12:104744062@+	-300; 1000	TXNRD1	26; 0	37; 0
chr17:79845715@-	-144; 1000	THOC4	19; 0	35; 0
chr8:128753674@+	-235; 1000	MYC	26; 0	32; 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	472	0.33%	1.00%	23.26%	312	0.408658
anti	1557	1.09%	3.31%	76.74%	860	1.34805
both	2029	1.42%	4.31%	100.00%	1155	1.75671
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	654	0.42%	1.25%	26.24%	312	0.566234
anti	1838	1.19%	3.51%	73.76%	860	1.59134
both	2492	1.61%	4.76%	100.00%	1155	2.15758

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)
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	54; 1
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 41	0; 113
chr2:70315685@-	-1000; 62	AC136007.2	0; 31	0; 39
chr1:205685227@+	-1000; 300	AC119673.2	0; 26	0; 29
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 23
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 20	0; 33
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 19	0; 22
chr11:62623517@+	-1000; 112	SLC3A2	0; 18	0; 19
chr3:49571651@-	-1000; 300	AC104452.1	0; 17	0; 20
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	160; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	160; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 41	0; 113
chr8:128231332@-	-1000; 139	AC020688.1	47; 1	54; 1
chr2:70315685@-	-1000; 62	AC136007.2	0; 31	0; 39
chr15:89878025@-	-1000; 61	POLG	0; 7	0; 38
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 20	0; 33
chrM:5903@+	-162; 300	J01415.8	0; 5	0; 32
chr1:205685227@+	-1000; 300	AC119673.2	0; 26	0; 29
chr6:166401114@+	-1000; 249	AL132661.1	0; 16	0; 23
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 23

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	7959	5.58%	16.92%	80.74%	3059	2.10779
anti	1899	1.33%	4.04%	19.26%	807	0.502913
both	9858	6.91%	20.96%	100.00%	3776	2.6107
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	9430	6.09%	18.00%	81.08%	3059	2.49735
anti	2200	1.42%	4.20%	18.92%	807	0.582627
both	11630	7.51%	22.20%	100.00%	3776	3.07998

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	274; 0	567; 0
chr1:169101767@-	-127; 1000	NME7	0; 64	0; 91
chr19:39220830@-	-300; 1000	CAPN12	0; 49	0; 86
chr12:53874278@-	-300; 1000	MAP3K12	1; 38	1; 52
chr17:79476997@-	-300; 1000	ACTG1	35; 0	97; 0
chr16:18802989@-	-300; 667	ARL6IP1	34; 0	48; 0
chr7:5566780@-	-300; 1000	ACTB	32; 0	75; 0
chr17:4848518@+	-104; 1000	RNF167	0; 27	0; 82
chr8:128753674@+	-235; 1000	MYC	26; 0	32; 0
chr15:45010359@+	-278; 1000	B2M	26; 0	32; 0

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

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	274; 0	567; 0
chr17:79476997@-	-300; 1000	ACTG1	35; 0	97; 0
chr1:169101767@-	-127; 1000	NME7	0; 64	0; 91
chr19:39220830@-	-300; 1000	CAPN12	0; 49	0; 86
chr6:26031876@-	-206; 1000	HIST1H3B	15; 0	85; 0
chr17:4848518@+	-104; 1000	RNF167	0; 27	0; 82
chr7:5566780@-	-300; 1000	ACTB	32; 0	75; 0
chrUn_gl000220:118417@+	-300; 1000	28S	24; 0	74; 0
chr1:153516087@-	-156; 923	S100A4	18; 0	68; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 38	1; 52

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	5357	3.76%	11.39%	96.52%	4570	1.13352
anti	193	0.14%	0.41%	3.48%	160	0.0408379
both	5550	3.89%	11.80%	100.00%	4726	1.17435
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	5577	3.60%	10.64%	96.55%	4570	1.18007
anti	199	0.13%	0.38%	3.45%	160	0.0421075
both	5776	3.73%	11.02%	100.00%	4726	1.22218

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)
chr9:86584384@-	-300; 90	HNRNPK	10; 0	24; 0
chr6:31508624@-	-300; 100	BAT1	10; 0	13; 0
chr5:10401919@+	-300; 100	MARCH6	10; 0	13; 0
chr20:34326966@-	-300; 28	RBM39	10; 0	10; 0
chr1:1326494@-	-300; 100	CCNL2	10; 0	10; 0
chr5:179048854@-	-300; 100	HNRNPH1	9; 0	9; 0
chr16:31199583@+	-300; 60	FUS	9; 0	10; 0
chr7:148514576@-	-149; 94	EZH2	7; 0	8; 0
chr6:144286222@-	-300; 100	PLAGL1	6; 0	7; 0
chr5:179045370@-	-300; 47	HNRNPH1	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)
chr9:86584384@-	-300; 90	HNRNPK	10; 0	24; 0
chr6:31508624@-	-300; 100	BAT1	10; 0	13; 0
chr5:10401919@+	-300; 100	MARCH6	10; 0	13; 0
chr5:179045370@-	-300; 47	HNRNPH1	6; 0	10; 0
chr20:34326966@-	-300; 28	RBM39	10; 0	10; 0
chr16:31199583@+	-300; 60	FUS	9; 0	10; 0
chr1:1326494@-	-300; 100	CCNL2	10; 0	10; 0
chr1:28835317@+	-300; 22	SNHG3	5; 0	10; 0
chr5:179048854@-	-300; 100	HNRNPH1	9; 0	9; 0
chr7:148514576@-	-149; 94	EZH2	7; 0	8; 0

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