Parameters
input_file: 20090715_LUh6_1_hg19_ensembl59_G_iCLIP_hnRNPC_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: 321762
[x-link sites] used in any map: 49299 (15.32%)
[single hits in whole-genome, cDNA counts] total: 321762
[single hits in whole-genome, cDNA counts] used in any map: 53780 (15.74%)

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	13923	4.33%	28.24%	14591	4.27%	27.13%
intron-exon	-300; 300	12749	3.96%	25.86%	13392	3.92%	24.90%
5-ncRNA	-1000; 300	4123	1.28%	8.36%	5184	1.52%	9.64%
ncRNA-3	-300; 1000	4451	1.38%	9.03%	5506	1.61%	10.24%
ORF-3UTR	-300; 300	2326	0.72%	4.72%	2522	0.74%	4.69%
5UTR-ORF	-300; 300	298	0.09%	0.60%	323	0.09%	0.60%
inter-5UTR	-1000; 300	1159	0.36%	2.35%	1274	0.37%	2.37%
3UTR-inter	-300; 1000	3394	1.05%	6.88%	3625	1.06%	6.74%
inter-5	-1000; 300	3598	1.12%	7.30%	4276	1.25%	7.95%
3-inter	-300; 1000	5892	1.83%	11.95%	6715	1.97%	12.49%
BP best in intron	-300; 100	12817	3.98%	26.00%	13446	3.93%	25.00%

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	13408	4.17%	27.20%	96.30%	9936	1.29408
anti	515	0.16%	1.04%	3.70%	449	0.0497056
both	13923	4.33%	28.24%	100.00%	10361	1.34379
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	14053	4.11%	26.13%	96.31%	9936	1.35634
anti	538	0.16%	1.00%	3.69%	449	0.0519255
both	14591	4.27%	27.13%	100.00%	10361	1.40826

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)
chr5:179049848@-	-158; 300	HNRNPH1	32; 0	57; 0
chr2:66663000@+	-300; 300	MEIS1	16; 0	18; 0
chr10:96322633@+	-33; 300	HELLS	13; 0	18; 0
chr5:78909906@+	-75; 300	PAPD4	12; 0	18; 0
chr19:17450408@+	-83; 300	GTPBP3	12; 0	12; 0
chrX:24168936@+	-157; 300	ZFX	10; 0	11; 0
chr6:13925597@+	-87; 300	RNF182	10; 0	14; 0
chr1:21101941@-	-278; 222	HP1BP3	10; 0	11; 0
chr7:138710450@-	-300; 300	ZC3HAV1L	9; 0	10; 0
chr7:95045186@-	-211; 300	PON2	9; 0	10; 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)
chr5:179049848@-	-158; 300	HNRNPH1	32; 0	57; 0
chr5:78909906@+	-75; 300	PAPD4	12; 0	18; 0
chr2:66663000@+	-300; 300	MEIS1	16; 0	18; 0
chr10:96322633@+	-33; 300	HELLS	13; 0	18; 0
chr6:13925597@+	-87; 300	RNF182	10; 0	14; 0
chr19:17450408@+	-83; 300	GTPBP3	12; 0	12; 0
chr17:79652719@+	-43; 300	HGS	7; 0	12; 0
chrX:24168936@+	-157; 300	ZFX	10; 0	11; 0
chr2:198354919@-	-188; 300	HSPD1	7; 0	11; 0
chr17:62498126@-	-30; 300	DDX5	7; 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 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	12103	3.76%	24.55%	94.93%	9237	1.24146
anti	646	0.20%	1.31%	5.07%	541	0.0662632
both	12749	3.96%	25.86%	100.00%	9749	1.30772
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	12720	3.72%	23.65%	94.98%	9237	1.30475
anti	672	0.20%	1.25%	5.02%	541	0.0689301
both	13392	3.92%	24.90%	100.00%	9749	1.37368

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)
chr17:57915655@+	-300; 51	TMEM49	27; 0	41; 0
chr1:1413405@+	-300; 300	ATAD3B	23; 0	37; 0
chr5:179041959@-	-293; 300	HNRNPH1	13; 0	18; 0
chr22:38886440@-	-300; 39	DDX17	13; 0	18; 0
chr12:54678332@+	-116; 300	HNRNPA1	12; 0	19; 0
chr1:21101497@-	-222; 300	HP1BP3	12; 0	24; 0
chr16:29821927@-	-300; 92	AC009133.4	0; 11	0; 12
chr5:145860712@+	-300; 300	TCERG1	10; 0	12; 0
chr3:47702944@-	-300; 81	SMARCC1	10; 0	15; 0
chr2:122288320@-	-300; 249	CLASP1	0; 10	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)
chr17:57915655@+	-300; 51	TMEM49	27; 0	41; 0
chr1:1413405@+	-300; 300	ATAD3B	23; 0	37; 0
chr1:21101497@-	-222; 300	HP1BP3	12; 0	24; 0
chr12:54678332@+	-116; 300	HNRNPA1	12; 0	19; 0
chr5:179041959@-	-293; 300	HNRNPH1	13; 0	18; 0
chr22:38886440@-	-300; 39	DDX17	13; 0	18; 0
chr3:47702944@-	-300; 81	SMARCC1	10; 0	15; 0
chr2:122288320@-	-300; 249	CLASP1	0; 10	0; 14
chr9:131456919@+	-292; 300	SET	9; 0	12; 0
chr5:145860712@+	-300; 300	TCERG1	10; 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 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	1989	0.62%	4.03%	48.24%	934	0.918707
anti	2134	0.66%	4.33%	51.76%	1260	0.985681
both	4123	1.28%	8.36%	100.00%	2165	1.90439
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	2944	0.86%	5.47%	56.79%	934	1.35982
anti	2240	0.66%	4.17%	43.21%	1260	1.03464
both	5184	1.52%	9.64%	100.00%	2165	2.39446

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	156; 0	403; 0
chr8:128231332@-	-1000; 139	AC020688.1	62; 1	126; 1
chr17:57918626@+	-338; 36	hsa-mir-21	57; 0	213; 0
chr17:41445449@-	-1000; 87	AC087650.5	35; 0	89; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	24; 0	55; 0
chr20:47896855@+	-555; 45	C20orf199, SNORD12-ENSG00000222365	20; 0	73; 0
chr1:45187573@-	-1000; 58	U5-ENSG00000199377	16; 0	30; 0
chr7:1609708@+	-1000; 230	AC093734.11	0; 15	0; 18
chr5:87514707@+	-1000; 34	AC010243.1	0; 13	0; 13
chrM:576@+	-288; 35	J01415.1	2; 10	2; 12

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	156; 0	403; 0
chr17:57918626@+	-338; 36	hsa-mir-21	57; 0	213; 0
chr8:128231332@-	-1000; 139	AC020688.1	62; 1	126; 1
chr17:41445449@-	-1000; 87	AC087650.5	35; 0	89; 0
chr20:47896855@+	-555; 45	C20orf199, SNORD12-ENSG00000222365	20; 0	73; 0
chr20:47895476@+	-101; 44	C20orf199, SNORD12-ENSG00000209042	12; 0	60; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	24; 0	55; 0
chr1:11969983@-	-628; 60	U5-ENSG00000201801	11; 0	51; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	9; 0	33; 0
chr1:45187573@-	-1000; 58	U5-ENSG00000199377	16; 0	30; 0

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

RNAmap 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	2191	0.68%	4.44%	49.22%	1004	0.952195
anti	2260	0.70%	4.58%	50.78%	1315	0.982182
both	4451	1.38%	9.03%	100.00%	2301	1.93438
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	3109	0.91%	5.78%	56.47%	1004	1.35115
anti	2397	0.70%	4.46%	43.53%	1315	1.04172
both	5506	1.61%	10.24%	100.00%	2301	2.39287

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	233; 0	529; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 59	0; 90
chrUn_gl000220:118417@+	-300; 1000	28S	51; 0	72; 0
chr1:11969863@-	-60; 1000	U5-ENSG00000201801	32; 0	145; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	31; 0	48; 0
chr1:11968328@+	-60; 1000	U5-ENSG00000199347	26; 0	37; 0
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	24; 0	56; 0
chr12:120729564@-	-71; 1000	U4-ENSG00000202538	22; 0	37; 0
chr15:65588504@+	-58; 1000	U5-ENSG00000199568	20; 0	21; 0
chr1:45187456@-	-59; 1000	U5-ENSG00000199377	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)
chr11:65271080@+	-300; 1000	MALAT1	233; 0	529; 0
chr1:11969863@-	-60; 1000	U5-ENSG00000201801	32; 0	145; 0
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	11; 1	112; 1
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	12; 0	102; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 59	0; 90
chrUn_gl000220:118417@+	-300; 1000	28S	51; 0	72; 0
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	24; 0	56; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	31; 0	48; 0
chr11:10823012@-	-71; 189	EIF4G2, snoU97	16; 0	42; 0
chr12:120729564@-	-71; 1000	U4-ENSG00000202538	22; 0	37; 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	2214	0.69%	4.49%	95.18%	1244	1.66092
anti	112	0.03%	0.23%	4.82%	97	0.084021
both	2326	0.72%	4.72%	100.00%	1333	1.74494
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	2407	0.70%	4.48%	95.44%	1244	1.8057
anti	115	0.03%	0.21%	4.56%	97	0.0862716
both	2522	0.74%	4.69%	100.00%	1333	1.89197

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)
chr17:57917272@+	-72; 300	TMEM49	29; 0	50; 0
chr1:35650053@-	-70; 300	SFPQ	19; 0	21; 0
chr19:19105798@-	-145; 252	SFRS14	18; 0	19; 0
chr12:46754890@-	-51; 300	SLC38A2	18; 0	23; 0
chr22:38881684@-	-300; 300	DDX17	13; 0	17; 0
chr17:4849191@-	-50; 123	PFN1	13; 0	32; 0
chrX:77381764@+	-239; 300	PGK1	10; 0	11; 0
chr2:172180296@-	-288; 268	METTL8	10; 0	10; 0
chr2:189876774@+	-211; 300	COL3A1	10; 0	15; 0
chr10:120069924@-	-248; 300	C10orf84	10; 0	12; 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)
chr17:57917272@+	-72; 300	TMEM49	29; 0	50; 0
chr17:4849191@-	-50; 123	PFN1	13; 0	32; 0
chr12:46754890@-	-51; 300	SLC38A2	18; 0	23; 0
chr1:35650053@-	-70; 300	SFPQ	19; 0	21; 0
chr19:19105798@-	-145; 252	SFRS14	18; 0	19; 0
chr22:38881684@-	-300; 300	DDX17	13; 0	17; 0
chr2:189876774@+	-211; 300	COL3A1	10; 0	15; 0
chr10:120069924@-	-248; 300	C10orf84	10; 0	12; 0
chrX:77381764@+	-239; 300	PGK1	10; 0	11; 0
chr18:9954208@+	-80; 300	VAPA	9; 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	277	0.09%	0.56%	92.95%	174	1.45789
anti	21	0.01%	0.04%	7.05%	16	0.110526
both	298	0.09%	0.60%	100.00%	190	1.56842
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	302	0.09%	0.56%	93.50%	174	1.58947
anti	21	0.01%	0.04%	6.50%	16	0.110526
both	323	0.09%	0.60%	100.00%	190	1.7

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)
chr7:1608974@-	-300; 108	PSMG3	11; 0	13; 0
chr11:70268614@+	-197; 61	CTTN	10; 0	15; 0
chr17:43226557@+	-300; 300	HEXIM1	9; 0	10; 0
chr7:23509978@-	-54; 212	IGF2BP3	8; 0	9; 0
chr5:138643104@+	-89; 300	MATR3	8; 0	10; 0
chr6:31508971@-	-66; 265	BAT1	7; 0	10; 0
chr5:179050164@-	-215; 158	HNRNPH1	5; 0	5; 0
chr1:46597623@-	-300; 53	PIK3R3	5; 0	5; 0
chr2:61764828@-	-277; 66	XPO1	4; 0	4; 0
chr13:31037816@-	-300; 237	HMGB1	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)
chr11:70268614@+	-197; 61	CTTN	10; 0	15; 0
chr7:1608974@-	-300; 108	PSMG3	11; 0	13; 0
chr6:31508971@-	-66; 265	BAT1	7; 0	10; 0
chr5:138643104@+	-89; 300	MATR3	8; 0	10; 0
chr17:43226557@+	-300; 300	HEXIM1	9; 0	10; 0
chr7:23509978@-	-54; 212	IGF2BP3	8; 0	9; 0
chr5:179050164@-	-215; 158	HNRNPH1	5; 0	5; 0
chr1:46597623@-	-300; 53	PIK3R3	5; 0	5; 0
chr6:31725905@+	-300; 82	MSH5	2; 0	4; 0
chr21:35467497@+	-168; 300	SLC5A3	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-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	313	0.10%	0.63%	27.01%	221	0.427012
anti	846	0.26%	1.72%	72.99%	533	1.15416
both	1159	0.36%	2.35%	100.00%	733	1.58117
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	330	0.10%	0.61%	25.90%	221	0.450205
anti	944	0.28%	1.76%	74.10%	533	1.28786
both	1274	0.37%	2.37%	100.00%	733	1.73806

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)
chr6:166401114@+	-1000; 249	AL132661.1	0; 32	0; 46
chr20:47894962@-	-1000; 248	ZNFX1	0; 18	0; 67
chr11:62623517@+	-1000; 112	SLC3A2	0; 14	0; 15
chr1:173837219@+	-1000; 87	ZBTB37	0; 14	0; 19
chr8:33370702@-	-1000; 286	C8orf41	0; 12	0; 13
chr5:147647742@+	-1000; 164	SPINK5L3	11; 0	13; 0
chr1:156307104@+	-1000; 118	C1orf182	0; 10	0; 11
chr19:54960064@+	-920; 210	LENG8	0; 8	0; 9
chr16:88785022@+	-1000; 84	AC138028.2	0; 8	0; 9
chr1:17380664@-	-1000; 69	SDHB	0; 8	0; 8

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)
chr20:47894962@-	-1000; 248	ZNFX1	0; 18	0; 67
chr6:166401114@+	-1000; 249	AL132661.1	0; 32	0; 46
chr1:173837219@+	-1000; 87	ZBTB37	0; 14	0; 19
chr11:62623517@+	-1000; 112	SLC3A2	0; 14	0; 15
chr8:33370702@-	-1000; 286	C8orf41	0; 12	0; 13
chr5:147647742@+	-1000; 164	SPINK5L3	11; 0	13; 0
chr1:156307104@+	-1000; 118	C1orf182	0; 10	0; 11
chr19:54960064@+	-920; 210	LENG8	0; 8	0; 9
chr16:88785022@+	-1000; 84	AC138028.2	0; 8	0; 9
chr11:118889240@+	-1000; 132	TRAPPC4	0; 5	0; 9

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	2567	0.80%	5.21%	75.63%	1560	1.27775
anti	827	0.26%	1.68%	24.37%	507	0.411648
both	3394	1.05%	6.88%	100.00%	2009	1.6894
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	2741	0.80%	5.10%	75.61%	1560	1.36436
anti	884	0.26%	1.64%	24.39%	507	0.44002
both	3625	1.06%	6.74%	100.00%	2009	1.80438

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)
chr17:57917950@+	-300; 338	TMEM49	37; 0	63; 0
chr17:79476997@-	-300; 1000	ACTG1	20; 0	35; 0
chr21:44834393@-	-300; 1000	SIK1	18; 0	20; 0
chr19:54972979@-	-144; 1000	LENG9	0; 17	0; 20
chr22:38879452@+	-263; 1000	KDELR3	0; 16	0; 18
chr11:47489944@-	-248; 1000	CELF1	15; 0	16; 0
chr17:4848518@+	-104; 1000	RNF167	0; 14	0; 33
chr5:10435491@+	-300; 1000	MARCH6	13; 0	13; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 13	0; 15
chr2:210886300@+	-300; 1000	RPE	10; 1	10; 1

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)
chr17:57917950@+	-300; 338	TMEM49	37; 0	63; 0
chr17:79476997@-	-300; 1000	ACTG1	20; 0	35; 0
chr17:4848518@+	-104; 1000	RNF167	0; 14	0; 33
chr21:44834393@-	-300; 1000	SIK1	18; 0	20; 0
chr19:54972979@-	-144; 1000	LENG9	0; 17	0; 20
chr22:38879452@+	-263; 1000	KDELR3	0; 16	0; 18
chr19:39220830@-	-300; 1000	CAPN12	0; 10	0; 16
chr11:47489944@-	-248; 1000	CELF1	15; 0	16; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 13	0; 15
chrX:24096088@+	-282; 1000	EIF2S3	9; 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 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	933	0.29%	1.89%	25.93%	498	0.454678
anti	2665	0.83%	5.41%	74.07%	1596	1.29873
both	3598	1.12%	7.30%	100.00%	2052	1.75341
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	1266	0.37%	2.35%	29.61%	498	0.616959
anti	3010	0.88%	5.60%	70.39%	1596	1.46686
both	4276	1.25%	7.95%	100.00%	2052	2.08382

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; 87	0; 230
chr8:128231332@-	-1000; 139	AC020688.1	62; 1	126; 1
chr17:41445449@-	-1000; 87	AC087650.5	35; 0	89; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 31	0; 45
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	24; 0	55; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 18	0; 67
chr1:45187573@-	-1000; 58	U5-ENSG00000199377	16; 0	30; 0
chr7:1609708@+	-1000; 230	AC093734.11	0; 15	0; 18
chr11:62623517@+	-1000; 112	SLC3A2	0; 14	0; 15
chr1:173837219@+	-1000; 87	ZBTB37	0; 14	0; 19

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; 87	0; 230
chr8:128231332@-	-1000; 139	AC020688.1	62; 1	126; 1
chr17:41445449@-	-1000; 87	AC087650.5	35; 0	89; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 18	0; 67
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	24; 0	55; 0
chr1:11969983@-	-628; 60	U5-ENSG00000201801	11; 0	51; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 31	0; 45
chr1:45187573@-	-1000; 58	U5-ENSG00000199377	16; 0	30; 0
chr1:11968208@+	-1000; 60	U5-ENSG00000199347	11; 0	30; 0
chr12:120729705@-	-597; 70	U4-ENSG00000202538	8; 0	25; 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	3503	1.09%	7.11%	59.45%	1967	1.08284
anti	2389	0.74%	4.85%	40.55%	1345	0.738485
both	5892	1.83%	11.95%	100.00%	3235	1.82133
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	4108	1.20%	7.64%	61.18%	1967	1.26986
anti	2607	0.76%	4.85%	38.82%	1345	0.805873
both	6715	1.97%	12.49%	100.00%	3235	2.07573

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	233; 0	529; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 59	0; 90
chrUn_gl000220:118417@+	-300; 1000	28S	51; 0	72; 0
chr17:57917950@+	-300; 338	TMEM49	37; 0	63; 0
chr7:5566780@-	-300; 1000	ACTB	35; 0	89; 0
chr17:16344889@-	-300; 1000	C17orf76	0; 35	0; 87
chr17:79476997@-	-300; 1000	ACTG1	20; 0	35; 0
chr1:169101767@-	-127; 1000	NME7	0; 19	0; 22
chr21:44834393@-	-300; 1000	SIK1	18; 0	20; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 17	0; 19

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	233; 0	529; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 59	0; 90
chr7:5566780@-	-300; 1000	ACTB	35; 0	89; 0
chr17:16344889@-	-300; 1000	C17orf76	0; 35	0; 87
chrUn_gl000220:118417@+	-300; 1000	28S	51; 0	72; 0
chr17:57917950@+	-300; 338	TMEM49	37; 0	63; 0
chr17:79476997@-	-300; 1000	ACTG1	20; 0	35; 0
chr17:4848518@+	-104; 1000	RNF167	0; 14	0; 33
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	13; 0	24; 0
chr1:169101767@-	-127; 1000	NME7	0; 19	0; 22

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	12339	3.83%	25.03%	96.27%	9212	1.28411
anti	478	0.15%	0.97%	3.73%	413	0.049745
both	12817	3.98%	26.00%	100.00%	9609	1.33385
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	12960	3.79%	24.10%	96.39%	9212	1.34874
anti	486	0.14%	0.90%	3.61%	413	0.0505776
both	13446	3.93%	25.00%	100.00%	9609	1.39931

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)
chr17:57915352@+	-300; 100	TMEM49	17; 0	42; 0
chr21:44842114@-	-300; 100	SIK1	13; 0	13; 0
chr8:128752542@+	-300; 97	MYC	11; 0	14; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	11; 0	11; 0
chr17:62496969@-	-300; 79	DDX5	11; 0	12; 0
chr5:170817954@+	-235; 100	NPM1	10; 0	13; 0
chr20:34320265@-	-300; 100	RBM39	10; 0	10; 0
chr11:70268819@+	-300; 100	CTTN	10; 0	15; 0
chr11:47259214@+	-300; 100	DDB2	10; 0	10; 0
chr1:1413786@+	-300; 100	ATAD3B	10; 0	19; 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)
chr17:57915352@+	-300; 100	TMEM49	17; 0	42; 0
chr16:70571951@+	-300; 100	SNORD111-ENSG00000221066	5; 0	19; 0
chr1:1413786@+	-300; 100	ATAD3B	10; 0	19; 0
chr11:70268819@+	-300; 100	CTTN	10; 0	15; 0
chr8:128752542@+	-300; 97	MYC	11; 0	14; 0
chr5:170817954@+	-235; 100	NPM1	10; 0	13; 0
chr21:44842114@-	-300; 100	SIK1	13; 0	13; 0
chr17:62496969@-	-300; 79	DDX5	11; 0	12; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	11; 0	11; 0
chr5:179045370@-	-300; 47	HNRNPH1	9; 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.