Parameters
input_file: 20090724_LUd3_3_hg19_ensembl59_S_iCLIP_TIAL1_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: 444451
[x-link sites] used in any map: 139440 (31.37%)
[single hits (=G+T), cDNA counts] total: 444451
[single hits (=G+T), cDNA counts] used in any map: 159738 (32.53%)

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	49576	11.15%	35.55%	53041	10.80%	33.20%
intron-exon	-300; 300	32814	7.38%	23.53%	35156	7.16%	22.01%
5-ncRNA	-1000; 300	6692	1.51%	4.80%	10082	2.05%	6.31%
ncRNA-3	-300; 1000	6948	1.56%	4.98%	10252	2.09%	6.42%
ORF-3UTR	-300; 300	17557	3.95%	12.59%	21397	4.36%	13.40%
5UTR-ORF	-300; 300	988	0.22%	0.71%	1051	0.21%	0.66%
inter-5UTR	-1000; 300	1888	0.42%	1.35%	2338	0.48%	1.46%
3UTR-inter	-300; 1000	16778	3.77%	12.03%	19960	4.06%	12.50%
inter-5	-1000; 300	6104	1.37%	4.38%	7773	1.58%	4.87%
3-inter	-300; 1000	22552	5.07%	16.17%	28805	5.87%	18.03%
BP best in intron	-300; 100	18328	4.12%	13.14%	19103	3.89%	11.96%

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	48584	10.93%	34.84%	98.00%	28798	1.65252
anti	992	0.22%	0.71%	2.00%	718	0.0337415
both	49576	11.15%	35.55%	100.00%	29400	1.68626
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	51786	10.54%	32.42%	97.63%	28798	1.76143
anti	1255	0.26%	0.79%	2.37%	718	0.0426871
both	53041	10.80%	33.20%	100.00%	29400	1.80412

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)
chr1:45976739@+	-281; 300	MMACHC	0; 75	0; 279
chr3:41281934@+	-300; 300	CTNNB1	50; 0	87; 0
chr7:128411528@+	-300; 107	CALU	48; 0	116; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 40	0; 60
chr2:191800015@+	-300; 300	GLS	36; 0	46; 0
chr5:10401598@+	-300; 185	MARCH6	35; 0	61; 0
chr3:186506209@+	-300; 300	EIF4A2	31; 0	33; 0
chr12:50158717@+	-300; 300	TMBIM6	31; 0	70; 0
chr6:18225699@-	-124; 192	DEK	29; 0	35; 0
chr5:179047674@-	-181; 300	HNRNPH1	23; 0	27; 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)
chr1:45976739@+	-281; 300	MMACHC	0; 75	0; 279
chr7:128411528@+	-300; 107	CALU	48; 0	116; 0
chr7:139025365@+	-85; 256	C7orf55	10; 0	106; 0
chr3:41281934@+	-300; 300	CTNNB1	50; 0	87; 0
chr12:50158717@+	-300; 300	TMBIM6	31; 0	70; 0
chr5:10401598@+	-300; 185	MARCH6	35; 0	61; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 40	0; 60
chr2:191800015@+	-300; 300	GLS	36; 0	46; 0
chr17:57915758@+	-52; 300	TMEM49	23; 0	40; 0
chr1:165624857@+	-127; 300	MGST3	22; 0	38; 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	31761	7.15%	22.78%	96.79%	20667	1.48631
anti	1053	0.24%	0.76%	3.21%	796	0.049277
both	32814	7.38%	23.53%	100.00%	21369	1.53559
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	34048	6.93%	21.31%	96.85%	20667	1.59334
anti	1108	0.23%	0.69%	3.15%	796	0.0518508
both	35156	7.16%	22.01%	100.00%	21369	1.64519

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)
chr15:45009804@+	-300; 277	B2M	82; 0	202; 0
chr9:131456919@+	-292; 300	SET	52; 0	160; 0
chr5:179041959@-	-293; 300	HNRNPH1	43; 0	105; 0
chr8:128753204@+	-241; 235	MYC	41; 0	63; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	38; 0	81; 0
chr2:211542610@+	-300; 300	CPS1	34; 0	48; 0
chr7:5568349@-	-150; 219	ACTB	33; 0	38; 0
chr17:57915655@+	-300; 51	TMEM49	29; 0	45; 0
chr1:165697357@-	-300; 292	TMCO1	29; 0	37; 0
chr1:26227577@-	-160; 260	STMN1	28; 0	60; 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)
chr15:45009804@+	-300; 277	B2M	82; 0	202; 0
chr9:131456919@+	-292; 300	SET	52; 0	160; 0
chr5:179041959@-	-293; 300	HNRNPH1	43; 0	105; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	38; 0	81; 0
chr11:64540976@-	-300; 241	SF1	17; 0	68; 0
chr8:128753204@+	-241; 235	MYC	41; 0	63; 0
chr17:57917128@+	-300; 72	TMEM49	27; 0	63; 0
chr1:26227577@-	-160; 260	STMN1	28; 0	60; 0
chr7:6502805@-	-300; 300	KDELR2	27; 0	56; 0
chr10:112657785@+	-300; 300	PDCD4	25; 0	53; 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	3142	0.71%	2.25%	46.95%	1292	1.09975
anti	3550	0.80%	2.55%	53.05%	1623	1.24256
both	6692	1.51%	4.80%	100.00%	2857	2.34232
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	6063	1.23%	3.80%	60.14%	1292	2.12216
anti	4019	0.82%	2.52%	39.86%	1623	1.40672
both	10082	2.05%	6.31%	100.00%	2857	3.52888

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	479; 0	1596; 0
chr8:128231332@-	-1000; 139	AC020688.1	150; 1	206; 1
chrUn_gl000220:109077@+	-758; 300	18S	73; 0	157; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 53	0; 67
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 52	0; 60
chr17:57918626@+	-338; 36	hsa-mir-21	49; 0	103; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 43	0; 51
chr1:205685227@+	-1000; 300	AC119673.2	0; 38	0; 48
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 36	0; 41
chr2:70315685@-	-1000; 62	AC136007.2	0; 33	0; 39

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	479; 0	1596; 0
chr8:128231332@-	-1000; 139	AC020688.1	150; 1	206; 1
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	20; 0	182; 0
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	21; 0	163; 0
chrUn_gl000220:109077@+	-758; 300	18S	73; 0	157; 0
chr14:74055600@-	-1000; 36	AC005225.1	7; 0	148; 0
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 10	0; 148
chr5:135416285@-	-1000; 50	Vault-ENSG00000202030	11; 0	124; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	15; 0	122; 0
chr7:96770956@-	-1000; 35	AC073421.1	12; 1	111; 1

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	3860	0.87%	2.77%	55.56%	1569	1.31203
anti	3088	0.69%	2.21%	44.44%	1420	1.04963
both	6948	1.56%	4.98%	100.00%	2942	2.36166
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	6869	1.40%	4.30%	67.00%	1569	2.33481
anti	3383	0.69%	2.12%	33.00%	1420	1.1499
both	10252	2.09%	6.42%	100.00%	2942	3.4847

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	628; 0	1996; 0
chrUn_gl000220:110946@+	-300; 539	18S	75; 0	175; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 55	0; 72
chr11:62609089@-	-96; 978	U2-ENSG00000222328	51; 0	264; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 47	0; 69
chr3:14530617@-	-300; 1000	GRIP2	0; 45	0; 60
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 41	0; 54
chrY:21154137@-	-229; 1000	CD24L4, NCRNA00185	40; 0	58; 0
chrUn_gl000220:118417@+	-300; 1000	28S	40; 0	92; 0
chr8:144939422@+	-300; 1000	AC105049.1	0; 36	0; 44

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	628; 0	1996; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	51; 0	264; 0
chrUn_gl000220:110946@+	-300; 539	18S	75; 0	175; 0
chr1:17216097@+	-254; 1000	RP11-108M9.5	10; 0	148; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	26; 0	133; 0
chrUn_gl000220:118417@+	-300; 1000	28S	40; 0	92; 0
chr10:103124600@-	-96; 1000	U2-ENSG00000222414	16; 0	84; 0
chr5:135416184@-	-51; 1000	Vault-ENSG00000202030	14; 0	79; 0
chr14:74055527@-	-37; 1000	AC005225.1	4; 0	74; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 55	0; 72

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	17254	3.88%	12.37%	98.27%	4148	4.02943
anti	303	0.07%	0.22%	1.73%	198	0.0707613
both	17557	3.95%	12.59%	100.00%	4282	4.10019
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	21075	4.29%	13.19%	98.50%	4148	4.92177
anti	322	0.07%	0.20%	1.50%	198	0.0751985
both	21397	4.36%	13.40%	100.00%	4282	4.99696

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)
chr19:13054727@+	-101; 288	CALR	104; 0	211; 0
chr10:102120690@+	-100; 300	SCD	71; 0	133; 0
chr14:62213803@+	-76; 300	HIF1A	70; 0	165; 0
chr5:179156650@+	-145; 300	CANX	68; 0	142; 0
chr21:27253823@-	-129; 300	APP	67; 0	97; 0
chr3:149087560@-	-53; 300	TM4SF1	63; 0	162; 0
chr1:35650053@-	-70; 300	SFPQ	55; 0	91; 0
chr1:156109094@+	-112; 233	LMNA	50; 0	98; 0
chr7:148700882@-	-209; 300	PDIA4	48; 0	63; 0
chr17:4849191@-	-50; 123	PFN1	47; 0	244; 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)
chr17:4849191@-	-50; 123	PFN1	47; 0	244; 0
chr19:13054727@+	-101; 288	CALR	104; 0	211; 0
chr14:62213803@+	-76; 300	HIF1A	70; 0	165; 0
chr3:149087560@-	-53; 300	TM4SF1	63; 0	162; 0
chr5:179156650@+	-145; 300	CANX	68; 0	142; 0
chr10:102120690@+	-100; 300	SCD	71; 0	133; 0
chr1:156109094@+	-112; 233	LMNA	50; 0	98; 0
chr21:27253823@-	-129; 300	APP	67; 0	97; 0
chr1:35650053@-	-70; 300	SFPQ	55; 0	91; 0
chr1:245017433@-	-93; 300	HNRNPU	40; 0	89; 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	888	0.20%	0.64%	89.88%	551	1.50254
anti	100	0.02%	0.07%	10.12%	44	0.169205
both	988	0.22%	0.71%	100.00%	591	1.67174
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	941	0.19%	0.59%	89.53%	551	1.59222
anti	110	0.02%	0.07%	10.47%	44	0.186125
both	1051	0.21%	0.66%	100.00%	591	1.77834

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)
chr17:4851688@-	-300; 66	PFN1	33; 0	43; 0
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 22	0; 25
chr8:101733810@-	-252; 96	PABPC1	14; 0	15; 0
chr6:64286785@+	-92; 52	PTP4A1	13; 0	15; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 10	0; 12
chr6:24718895@-	-300; 64	C6orf62	10; 0	11; 0
chr11:3012265@+	-300; 90	AC131971.1	0; 10	0; 12
chr6:166401613@+	-250; 300	AL132661.1	0; 9	0; 11
chr2:211421442@+	-91; 70	CPS1	8; 0	13; 0
chr1:12677352@-	-192; 97	DHRS3	8; 0	9; 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)
chr17:4851688@-	-300; 66	PFN1	33; 0	43; 0
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 22	0; 25
chr8:101733810@-	-252; 96	PABPC1	14; 0	15; 0
chr6:64286785@+	-92; 52	PTP4A1	13; 0	15; 0
chr2:211421442@+	-91; 70	CPS1	8; 0	13; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 10	0; 12
chr11:3012265@+	-300; 90	AC131971.1	0; 10	0; 12
chr6:24718895@-	-300; 64	C6orf62	10; 0	11; 0
chr6:166401613@+	-250; 300	AL132661.1	0; 9	0; 11
chr6:33168574@+	-177; 300	SLC39A7	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 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	665	0.15%	0.48%	35.22%	471	0.607306
anti	1223	0.28%	0.88%	64.78%	682	1.11689
both	1888	0.42%	1.35%	100.00%	1095	1.7242
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	718	0.15%	0.45%	30.71%	471	0.655708
anti	1620	0.33%	1.01%	69.29%	682	1.47945
both	2338	0.48%	1.46%	100.00%	1095	2.13516

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; 58	0; 110
chr8:101734314@-	-1000; 252	PABPC1	30; 0	70; 0
chr5:32788944@+	-844; 281	C5orf23	23; 0	26; 0
chr11:62623517@+	-1000; 112	SLC3A2	0; 21	0; 28
chr8:71485680@+	-1000; 300	AC120194.1	0; 19	0; 21
chr20:47894962@-	-1000; 248	ZNFX1	0; 15	0; 23
chr17:7387865@+	-741; 109	POLR2A	13; 1	13; 1
chr13:41635409@+	-1000; 200	WBP4	0; 14	0; 147
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 14	0; 16
chr8:33370702@-	-1000; 286	C8orf41	0; 12	0; 21

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)
chr13:41635409@+	-1000; 200	WBP4	0; 14	0; 147
chr6:166401114@+	-1000; 249	AL132661.1	0; 58	0; 110
chr11:66115160@-	-1000; 72	AP001107.2	0; 12	0; 90
chr8:101734314@-	-1000; 252	PABPC1	30; 0	70; 0
chr19:39903224@+	-1000; 300	PLEKHG2	0; 6	0; 39
chr11:62623517@+	-1000; 112	SLC3A2	0; 21	0; 28
chr5:32788944@+	-844; 281	C5orf23	23; 0	26; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 15	0; 23
chr8:33370702@-	-1000; 286	C8orf41	0; 12	0; 21
chr8:71485680@+	-1000; 300	AC120194.1	0; 19	0; 21

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	13994	3.15%	10.04%	83.41%	3951	3.09602
anti	2784	0.63%	2.00%	16.59%	864	0.615929
both	16778	3.77%	12.03%	100.00%	4520	3.71195
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	16504	3.36%	10.33%	82.69%	3951	3.65133
anti	3456	0.70%	2.16%	17.31%	864	0.764602
both	19960	4.06%	12.50%	100.00%	4520	4.41593

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)
chr19:39220830@-	-300; 1000	CAPN12	0; 93	0; 160
chr8:128753674@+	-235; 1000	MYC	68; 0	151; 0
chr15:45010359@+	-278; 1000	B2M	65; 0	151; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 56	1; 99
chr16:18802989@-	-300; 667	ARL6IP1	53; 0	76; 0
chr22:38879452@+	-263; 1000	KDELR3	0; 52	0; 60
chr17:4848518@+	-104; 1000	RNF167	0; 47	0; 244
chr16:87863620@-	-300; 1000	SLC7A5	43; 0	96; 0
chr12:104744062@+	-300; 1000	TXNRD1	43; 0	70; 0
chr21:44834393@-	-300; 1000	SIK1	41; 0	66; 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)
chr17:4848518@+	-104; 1000	RNF167	0; 47	0; 244
chr19:39220830@-	-300; 1000	CAPN12	0; 93	0; 160
chr8:128753674@+	-235; 1000	MYC	68; 0	151; 0
chr15:45010359@+	-278; 1000	B2M	65; 0	151; 0
chr17:79476997@-	-300; 1000	ACTG1	38; 0	108; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 56	1; 99
chr16:87863620@-	-300; 1000	SLC7A5	43; 0	96; 0
chr17:38613983@+	-300; 1000	IGFBP4	26; 0	92; 0
chr2:1635657@-	-300; 1000	PXDN	28; 0	87; 0
chr16:18802989@-	-300; 667	ARL6IP1	53; 0	76; 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	1818	0.41%	1.30%	29.78%	1019	0.610682
anti	4286	0.96%	3.07%	70.22%	2068	1.4397
both	6104	1.37%	4.38%	100.00%	2977	2.05039
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	2589	0.53%	1.62%	33.31%	1019	0.869667
anti	5184	1.06%	3.25%	66.69%	2068	1.74135
both	7773	1.58%	4.87%	100.00%	2977	2.61102

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)
chr8:128231332@-	-1000; 139	AC020688.1	150; 1	206; 1
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 76	0; 158
chrUn_gl000220:109077@+	-758; 300	18S	73; 0	157; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 57	0; 109
chr3:49571651@-	-1000; 300	AC104452.1	0; 53	0; 67
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 52	0; 60
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 43	0; 51
chr1:205685227@+	-1000; 300	AC119673.2	0; 38	0; 48
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 36	0; 41
chr2:70315685@-	-1000; 62	AC136007.2	0; 33	0; 39

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)
chr8:128231332@-	-1000; 139	AC020688.1	150; 1	206; 1
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	20; 0	182; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 76	0; 158
chrUn_gl000220:109077@+	-758; 300	18S	73; 0	157; 0
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 10	0; 148
chr13:41635409@+	-1000; 200	WBP4	0; 14	0; 147
chr5:135416285@-	-1000; 50	Vault-ENSG00000202030	11; 0	124; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 57	0; 109
chr11:66115160@-	-1000; 72	AP001107.2	0; 12	0; 90
chr6:89773408@-	-1000; 95	U2-ENSG00000223001	4; 0	75; 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	17150	3.86%	12.30%	76.05%	4896	2.68556
anti	5402	1.22%	3.87%	23.95%	1849	0.845913
both	22552	5.07%	16.17%	100.00%	6386	3.53148
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	22349	4.55%	13.99%	77.59%	4896	3.49969
anti	6456	1.31%	4.04%	22.41%	1849	1.01096
both	28805	5.87%	18.03%	100.00%	6386	4.51065

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	628; 0	1996; 0
chr1:169101767@-	-127; 1000	NME7	0; 131	0; 202
chr19:39220830@-	-300; 1000	CAPN12	0; 93	0; 160
chrUn_gl000220:110946@+	-300; 539	18S	75; 0	175; 0
chr8:128753674@+	-235; 1000	MYC	68; 0	151; 0
chr15:45010359@+	-278; 1000	B2M	65; 0	151; 0
chr7:5566780@-	-300; 1000	ACTB	60; 0	220; 0
chr12:53874278@-	-300; 1000	MAP3K12	1; 56	1; 99
chr2:191798136@-	-300; 1000	AC067945.1	0; 55	0; 72
chr16:18802989@-	-300; 667	ARL6IP1	53; 0	76; 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	628; 0	1996; 0
chr17:4848518@+	-104; 1000	RNF167	0; 47	0; 244
chr7:5566780@-	-300; 1000	ACTB	60; 0	220; 0
chr1:169101767@-	-127; 1000	NME7	0; 131	0; 202
chrUn_gl000220:110946@+	-300; 539	18S	75; 0	175; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 93	0; 160
chr8:128753674@+	-235; 1000	MYC	68; 0	151; 0
chr15:45010359@+	-278; 1000	B2M	65; 0	151; 0
chr1:17216097@+	-254; 1000	RP11-108M9.5	10; 0	148; 0
chr1:153516087@-	-156; 923	S100A4	26; 0	141; 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	17684	3.98%	12.68%	96.49%	13050	1.30664
anti	644	0.14%	0.46%	3.51%	521	0.0475839
both	18328	4.12%	13.14%	100.00%	13534	1.35422
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	18413	3.75%	11.53%	96.39%	13050	1.3605
anti	690	0.14%	0.43%	3.61%	521	0.0509827
both	19103	3.89%	11.96%	100.00%	13534	1.41148

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)
chr3:186506588@+	-298; 100	EIF4A2	26; 0	28; 0
chr5:179046653@-	-300; 100	HNRNPH1	22; 0	27; 0
chr5:179048854@-	-300; 100	HNRNPH1	21; 0	23; 0
chr1:1326494@-	-300; 100	CCNL2	21; 0	31; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	20; 0	20; 0
chr5:10401919@+	-300; 100	MARCH6	20; 0	34; 0
chr2:61413393@+	-229; 100	AHSA2	18; 0	27; 0
chr14:70237083@+	-300; 98	SFRS5	18; 0	20; 0
chr20:34326966@-	-300; 28	RBM39	17; 0	20; 0
chr1:70697488@+	-300; 100	SFRS11	17; 0	22; 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)
chr9:86584384@-	-300; 90	HNRNPK	14; 0	86; 0
chr5:10401919@+	-300; 100	MARCH6	20; 0	34; 0
chr1:1326494@-	-300; 100	CCNL2	21; 0	31; 0
chr3:186506588@+	-298; 100	EIF4A2	26; 0	28; 0
chr5:179046653@-	-300; 100	HNRNPH1	22; 0	27; 0
chr2:61413393@+	-229; 100	AHSA2	18; 0	27; 0
chr1:28835317@+	-300; 22	SNHG3	14; 0	27; 0
chr5:179048854@-	-300; 100	HNRNPH1	21; 0	23; 0
chr1:70697488@+	-300; 100	SFRS11	17; 0	22; 0
chr7:26237690@-	-300; 100	HNRNPA2B1	20; 0	20; 0

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