Parameters
input_file: 20090715_LUh6_1_hg19_ensembl59_S_iCLIP_hnRNPC_HeLa_bedGraph-cDNA.bed.gz
input_res_type: single hits (=G+T), 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: 331908
[x-link sites] used in any map: 50432 (15.19%)
[single hits (=G+T), cDNA counts] total: 331908
[single hits (=G+T), cDNA counts] used in any map: 55036 (15.60%)

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 (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map
exon-intron	-300; 300	14195	4.28%	28.15%	14878	4.22%	27.03%
intron-exon	-300; 300	12958	3.90%	25.69%	13620	3.86%	24.75%
5-ncRNA	-1000; 300	4268	1.29%	8.46%	5347	1.52%	9.72%
ncRNA-3	-300; 1000	4608	1.39%	9.14%	5695	1.61%	10.35%
ORF-3UTR	-300; 300	2379	0.72%	4.72%	2580	0.73%	4.69%
5UTR-ORF	-300; 300	301	0.09%	0.60%	326	0.09%	0.59%
inter-5UTR	-1000; 300	1173	0.35%	2.33%	1291	0.37%	2.35%
3UTR-inter	-300; 1000	3452	1.04%	6.84%	3688	1.05%	6.70%
inter-5	-1000; 300	3725	1.12%	7.39%	4423	1.25%	8.04%
3-inter	-300; 1000	6047	1.82%	11.99%	6912	1.96%	12.56%
BP best in intron	-300; 100	13119	3.95%	26.01%	13767	3.90%	25.01%

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	13638	4.11%	27.04%	96.08%	10097	1.29184
anti	557	0.17%	1.10%	3.92%	486	0.0527612
both	14195	4.28%	28.15%	100.00%	10557	1.34461
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	14297	4.05%	25.98%	96.09%	10097	1.35427
anti	581	0.16%	1.06%	3.91%	486	0.0550346
both	14878	4.22%	27.03%	100.00%	10557	1.4093

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 (=G+T), 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 (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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	12239	3.69%	24.27%	94.45%	9320	1.23701
anti	719	0.22%	1.43%	5.55%	606	0.0726703
both	12958	3.90%	25.69%	100.00%	9894	1.30968
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	12875	3.65%	23.39%	94.53%	9320	1.30129
anti	745	0.21%	1.35%	5.47%	606	0.0752982
both	13620	3.86%	24.75%	100.00%	9894	1.37659

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 (=G+T), 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	14; 0	19; 0
chr22:38886440@-	-300; 39	DDX17	13; 0	18; 0
chr17:1248792@-	-300; 300	YWHAE	12; 0	15; 0
chr12:54678332@+	-116; 300	HNRNPA1	12; 0	21; 0
chr1:21101497@-	-222; 300	HP1BP3	12; 0	24; 0
chr16:29821927@-	-300; 92	AC009133.4	0; 11	0; 12
chr9:131456919@+	-292; 300	SET	10; 0	13; 0
chr5:145860712@+	-300; 300	TCERG1	10; 0	12; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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	21; 0
chr5:179041959@-	-293; 300	HNRNPH1	14; 0	19; 0
chr22:38886440@-	-300; 39	DDX17	13; 0	18; 0
chr1:43167651@+	-300; 184	YBX1	10; 0	18; 0
chr3:47702944@-	-300; 81	SMARCC1	10; 0	15; 0
chr17:1248792@-	-300; 300	YWHAE	12; 0	15; 0
chr2:122288320@-	-300; 249	CLASP1	0; 10	0; 14

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	2080	0.63%	4.12%	48.73%	963	0.936094
anti	2188	0.66%	4.34%	51.27%	1290	0.984698
both	4268	1.29%	8.46%	100.00%	2222	1.92079
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	3053	0.87%	5.55%	57.10%	963	1.37399
anti	2294	0.65%	4.17%	42.90%	1290	1.0324
both	5347	1.52%	9.72%	100.00%	2222	2.40639

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 (=G+T), 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
chrUn_gl000220:109077@+	-758; 300	18S	41; 0	54; 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
chrUn_gl000220:113347@+	-585; 300	28S	14; 0	17; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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
chrUn_gl000220:109077@+	-758; 300	18S	41; 0	54; 0
chr1:11969983@-	-628; 60	U5-ENSG00000201801	11; 0	51; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	9; 0	33; 0

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

RNAmap ncRNA-3

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

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	2284	0.69%	4.53%	49.57%	1040	0.965751
anti	2324	0.70%	4.61%	50.43%	1349	0.982664
both	4608	1.39%	9.14%	100.00%	2365	1.94841
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	3229	0.92%	5.87%	56.70%	1040	1.36533
anti	2466	0.70%	4.48%	43.30%	1349	1.04271
both	5695	1.61%	10.35%	100.00%	2365	2.40803

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 (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	233; 0	529; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 60	0; 91
chrUn_gl000220:118417@+	-300; 1000	28S	51; 0	72; 0
chrUn_gl000220:110946@+	-300; 539	18S	32; 0	55; 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

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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; 60	0; 91
chrUn_gl000220:118417@+	-300; 1000	28S	51; 0	72; 0
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	24; 0	56; 0
chrUn_gl000220:110946@+	-300; 539	18S	32; 0	55; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	31; 0	48; 0
chr11:10823012@-	-71; 189	EIF4G2, snoU97	16; 0	42; 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	2260	0.68%	4.48%	95.00%	1264	1.66544
anti	119	0.04%	0.24%	5.00%	103	0.0876934
both	2379	0.72%	4.72%	100.00%	1357	1.75313
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	2457	0.70%	4.46%	95.23%	1264	1.81061
anti	123	0.03%	0.22%	4.77%	103	0.0906411
both	2580	0.73%	4.69%	100.00%	1357	1.90125

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 (=G+T), 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 (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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	0.08%	0.55%	92.03%	174	1.45026
anti	24	0.01%	0.05%	7.97%	17	0.125654
both	301	0.09%	0.60%	100.00%	191	1.57592
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	302	0.09%	0.55%	92.64%	174	1.58115
anti	24	0.01%	0.04%	7.36%	17	0.125654
both	326	0.09%	0.59%	100.00%	191	1.70681

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 (=G+T), 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 (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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	322	0.10%	0.64%	27.45%	226	0.434548
anti	851	0.26%	1.69%	72.55%	536	1.14845
both	1173	0.35%	2.33%	100.00%	741	1.583
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	340	0.10%	0.62%	26.34%	226	0.458839
anti	951	0.27%	1.73%	73.66%	536	1.2834
both	1291	0.37%	2.35%	100.00%	741	1.74224

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 (=G+T), 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
chr7:66386211@+	-1000; 118	C7orf42	8; 0	9; 0
chr19:54960064@+	-920; 210	LENG8	0; 8	0; 9
chr16:88785022@+	-1000; 84	AC138028.2	0; 8	0; 9

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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
chr7:66386211@+	-1000; 118	C7orf42	8; 0	9; 0
chr19:54960064@+	-920; 210	LENG8	0; 8	0; 9
chr16:88785022@+	-1000; 84	AC138028.2	0; 8	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	2609	0.79%	5.17%	75.58%	1583	1.28081
anti	843	0.25%	1.67%	24.42%	515	0.413844
both	3452	1.04%	6.84%	100.00%	2037	1.69465
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	2788	0.79%	5.07%	75.60%	1583	1.36868
anti	900	0.26%	1.64%	24.40%	515	0.441826
both	3688	1.05%	6.70%	100.00%	2037	1.81051

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 (=G+T), 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
chr12:53874278@-	-300; 1000	MAP3K12	0; 14	0; 16
chr5:10435491@+	-300; 1000	MARCH6	13; 0	13; 0
chr12:10851674@-	-288; 1000	CSDA	12; 0	14; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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
chr12:53874278@-	-300; 1000	MAP3K12	0; 14	0; 16
chr11:47489944@-	-248; 1000	CELF1	15; 0	16; 0
chr12:10851674@-	-288; 1000	CSDA	12; 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 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	1017	0.31%	2.02%	27.30%	522	0.485442
anti	2708	0.82%	5.37%	72.70%	1616	1.2926
both	3725	1.12%	7.39%	100.00%	2095	1.77804
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	1367	0.39%	2.48%	30.91%	522	0.652506
anti	3056	0.87%	5.55%	69.09%	1616	1.45871
both	4423	1.25%	8.04%	100.00%	2095	2.11122

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 (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 90	0; 234
chr8:128231332@-	-1000; 139	AC020688.1	62; 1	126; 1
chrUn_gl000220:109077@+	-758; 300	18S	41; 0	54; 0
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
chrUn_gl000220:113347@+	-585; 300	28S	14; 0	17; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 90	0; 234
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
chrUn_gl000220:109077@+	-758; 300	18S	41; 0	54; 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

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	3605	1.09%	7.15%	59.62%	2006	1.09441
anti	2442	0.74%	4.84%	40.38%	1370	0.741348
both	6047	1.82%	11.99%	100.00%	3294	1.83576
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	4247	1.20%	7.72%	61.44%	2006	1.28931
anti	2665	0.76%	4.84%	38.56%	1370	0.809047
both	6912	1.96%	12.56%	100.00%	3294	2.09836

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 (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	233; 0	529; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 60	0; 91
chrUn_gl000220:118417@+	-300; 1000	28S	51; 0	72; 0
chr7:5566780@-	-300; 1000	ACTB	43; 0	106; 0
chr17:57917950@+	-300; 338	TMEM49	37; 0	63; 0
chr17:16344889@-	-300; 1000	C17orf76	0; 35	0; 88
chrUn_gl000220:110946@+	-300; 539	18S	32; 0	55; 0
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

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	233; 0	529; 0
chr7:5566780@-	-300; 1000	ACTB	43; 0	106; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 60	0; 91
chr17:16344889@-	-300; 1000	C17orf76	0; 35	0; 88
chrUn_gl000220:118417@+	-300; 1000	28S	51; 0	72; 0
chr17:57917950@+	-300; 338	TMEM49	37; 0	63; 0
chrUn_gl000220:110946@+	-300; 539	18S	32; 0	55; 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

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	12568	3.79%	24.92%	95.80%	9367	1.27854
anti	551	0.17%	1.09%	4.20%	479	0.0560529
both	13119	3.95%	26.01%	100.00%	9830	1.33459
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [BPs] in map	[single hits (=G+T), cDNA counts] per unique [BP]
same	13207	3.74%	24.00%	95.93%	9367	1.34354
anti	560	0.16%	1.02%	4.07%	479	0.0569685
both	13767	3.90%	25.01%	100.00%	9830	1.40051

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 (=G+T), 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	13; 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 (=G+T), cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), 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	13; 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.