Parameters
input_file: 20090724_LUd3_1_hg19_ensembl59_S_iCLIP_TIA1_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: 215076
[x-link sites] used in any map: 69164 (32.16%)
[single hits (=G+T), cDNA counts] total: 215076
[single hits (=G+T), cDNA counts] used in any map: 79071 (33.25%)

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	21461	9.98%	31.03%	22633	9.52%	28.62%
intron-exon	-300; 300	15527	7.22%	22.45%	16480	6.93%	20.84%
5-ncRNA	-1000; 300	3622	1.68%	5.24%	5582	2.35%	7.06%
ncRNA-3	-300; 1000	3669	1.71%	5.30%	5165	2.17%	6.53%
ORF-3UTR	-300; 300	10670	4.96%	15.43%	12854	5.41%	16.26%
5UTR-ORF	-300; 300	521	0.24%	0.75%	551	0.23%	0.70%
inter-5UTR	-1000; 300	1022	0.48%	1.48%	1319	0.55%	1.67%
3UTR-inter	-300; 1000	9931	4.62%	14.36%	11631	4.89%	14.71%
inter-5	-1000; 300	3406	1.58%	4.92%	4437	1.87%	5.61%
3-inter	-300; 1000	13152	6.12%	19.02%	16221	6.82%	20.51%
BP best in intron	-300; 100	8370	3.89%	12.10%	8668	3.65%	10.96%

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	20942	9.74%	30.28%	97.58%	15661	1.30806
anti	519	0.24%	0.75%	2.42%	376	0.0324172
both	21461	9.98%	31.03%	100.00%	16010	1.34047
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	21997	9.25%	27.82%	97.19%	15661	1.37395
anti	636	0.27%	0.80%	2.81%	376	0.0397252
both	22633	9.52%	28.62%	100.00%	16010	1.41368

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; 48	0; 141
chr7:128411528@+	-300; 107	CALU	33; 0	49; 0
chr3:41281934@+	-300; 300	CTNNB1	33; 0	52; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 31	0; 43
chr1:165624857@+	-127; 300	MGST3	28; 0	43; 0
chr12:50158717@+	-300; 300	TMBIM6	24; 0	42; 0
chr5:10401598@+	-300; 185	MARCH6	20; 0	28; 0
chr2:191800015@+	-300; 300	GLS	19; 0	21; 0
chr6:160527583@+	-300; 300	IGF2R	16; 0	21; 0
chr4:108534820@-	-291; 300	PAPSS1	16; 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)
chr1:45976739@+	-281; 300	MMACHC	0; 48	0; 141
chr7:139025365@+	-85; 256	C7orf55	9; 0	63; 0
chr3:41281934@+	-300; 300	CTNNB1	33; 0	52; 0
chr7:128411528@+	-300; 107	CALU	33; 0	49; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 31	0; 43
chr1:165624857@+	-127; 300	MGST3	28; 0	43; 0
chr12:50158717@+	-300; 300	TMBIM6	24; 0	42; 0
chr5:10401598@+	-300; 185	MARCH6	20; 0	28; 0
chr5:179048241@-	-78; 103	HNRNPH1	13; 0	25; 0
chr6:160527583@+	-300; 300	IGF2R	16; 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 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	15005	6.98%	21.69%	96.64%	11289	1.28412
anti	522	0.24%	0.75%	3.36%	427	0.0446727
both	15527	7.22%	22.45%	100.00%	11685	1.3288
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	15942	6.70%	20.16%	96.74%	11289	1.36431
anti	538	0.23%	0.68%	3.26%	427	0.0460419
both	16480	6.93%	20.84%	100.00%	11685	1.41036

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	49; 0	100; 0
chr9:131456919@+	-292; 300	SET	34; 0	98; 0
chr5:179041959@-	-293; 300	HNRNPH1	31; 0	48; 0
chr2:211542610@+	-300; 300	CPS1	26; 0	36; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	21; 0	30; 0
chr10:112657785@+	-300; 300	PDCD4	21; 0	28; 0
chr8:128753204@+	-241; 235	MYC	20; 0	32; 0
chr2:47387942@-	-300; 300	CALM2	20; 0	28; 0
chr17:57915655@+	-300; 51	TMEM49	19; 0	21; 0
chr1:26227577@-	-160; 260	STMN1	19; 0	33; 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	49; 0	100; 0
chr9:131456919@+	-292; 300	SET	34; 0	98; 0
chr5:179041959@-	-293; 300	HNRNPH1	31; 0	48; 0
chr2:211542610@+	-300; 300	CPS1	26; 0	36; 0
chr1:26227577@-	-160; 260	STMN1	19; 0	33; 0
chr8:128753204@+	-241; 235	MYC	20; 0	32; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	21; 0	30; 0
chr2:189876353@+	-300; 210	COL3A1	16; 0	29; 0
chr2:47387942@-	-300; 300	CALM2	20; 0	28; 0
chr12:54678332@+	-116; 300	HNRNPA1	10; 0	28; 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	1770	0.82%	2.56%	48.87%	827	1.00625
anti	1852	0.86%	2.68%	51.13%	961	1.05287
both	3622	1.68%	5.24%	100.00%	1759	2.05912
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	3468	1.46%	4.39%	62.13%	827	1.97157
anti	2114	0.89%	2.67%	37.87%	961	1.20182
both	5582	2.35%	7.06%	100.00%	1759	3.17339

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	244; 0	682; 0
chrUn_gl000220:109077@+	-758; 300	18S	68; 0	176; 0
chr8:128231332@-	-1000; 139	AC020688.1	61; 1	78; 1
chrUn_gl000220:113347@+	-585; 300	28S	41; 0	58; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 40	0; 46
chr1:205685227@+	-1000; 300	AC119673.2	0; 37	0; 42
chr3:49571651@-	-1000; 300	AC104452.1	0; 29	0; 37
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 28	0; 35
chr2:70315685@-	-1000; 62	AC136007.2	0; 26	0; 29
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 26	0; 38

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	244; 0	682; 0
chrUn_gl000220:109077@+	-758; 300	18S	68; 0	176; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	141; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	13; 0	140; 0
chr14:74055600@-	-1000; 36	AC005225.1	7; 0	137; 0
chr7:96770956@-	-1000; 35	AC073421.1	15; 0	111; 0
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	20; 0	111; 0
chr5:140105742@+	-1000; 44	Vault-ENSG00000202515	17; 0	89; 0
chr8:128231332@-	-1000; 139	AC020688.1	61; 1	78; 1
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	16; 0	79; 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	2148	1.00%	3.11%	58.54%	989	1.19799
anti	1521	0.71%	2.20%	41.46%	821	0.848299
both	3669	1.71%	5.30%	100.00%	1793	2.04629
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	3536	1.49%	4.47%	68.46%	989	1.97211
anti	1629	0.69%	2.06%	31.54%	821	0.908533
both	5165	2.17%	6.53%	100.00%	1793	2.88065

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	349; 0	821; 0
chrUn_gl000220:110946@+	-300; 539	18S	62; 0	133; 0
chrUn_gl000220:118417@+	-300; 1000	28S	42; 0	81; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 36	0; 46
chr11:62609089@-	-96; 978	U2-ENSG00000222328	35; 0	112; 0
chr2:191798136@-	-300; 1000	AC067945.1	0; 34	0; 42
chrY:21154137@-	-229; 1000	CD24L4, NCRNA00185	30; 0	30; 0
chr1:21070455@+	-63; 1000	RP5-930J4.4	0; 29	0; 29
chr10:112658486@-	-300; 1000	NCRNA00081	0; 28	0; 37
chr8:144939422@+	-300; 1000	AC105049.1	0; 25	0; 29

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	349; 0	821; 0
chrUn_gl000220:110946@+	-300; 539	18S	62; 0	133; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	35; 0	112; 0
chrUn_gl000220:118417@+	-300; 1000	28S	42; 0	81; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	18; 0	71; 0
chr14:74055527@-	-37; 1000	AC005225.1	2; 0	69; 0
chr1:17216097@+	-254; 1000	RP11-108M9.5	6; 0	66; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	13; 0	47; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 36	0; 46
chr2:191798136@-	-300; 1000	AC067945.1	0; 34	0; 42

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	10532	4.90%	15.23%	98.71%	3219	3.21
anti	138	0.06%	0.20%	1.29%	86	0.0420603
both	10670	4.96%	15.43%	100.00%	3281	3.25206
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	12695	5.34%	16.06%	98.76%	3219	3.86925
anti	159	0.07%	0.20%	1.24%	86	0.0484608
both	12854	5.41%	16.26%	100.00%	3281	3.91771

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	97; 0	205; 0
chr14:62213803@+	-76; 300	HIF1A	62; 0	99; 0
chr10:102120690@+	-100; 300	SCD	60; 0	103; 0
chr5:179156650@+	-145; 300	CANX	50; 0	97; 0
chr3:149087560@-	-53; 300	TM4SF1	45; 0	104; 0
chr1:35650053@-	-70; 300	SFPQ	43; 0	61; 0
chr1:156109094@+	-112; 233	LMNA	42; 0	65; 0
chr6:30692174@+	-300; 300	TUBB	39; 0	56; 0
chr21:27253823@-	-129; 300	APP	38; 0	56; 0
chr2:136872205@-	-300; 144	CXCR4	37; 0	45; 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)
chr19:13054727@+	-101; 288	CALR	97; 0	205; 0
chr17:4849191@-	-50; 123	PFN1	35; 0	192; 0
chr3:149087560@-	-53; 300	TM4SF1	45; 0	104; 0
chr10:102120690@+	-100; 300	SCD	60; 0	103; 0
chr14:62213803@+	-76; 300	HIF1A	62; 0	99; 0
chr5:179156650@+	-145; 300	CANX	50; 0	97; 0
chr1:156109094@+	-112; 233	LMNA	42; 0	65; 0
chr1:35650053@-	-70; 300	SFPQ	43; 0	61; 0
chr2:189876774@+	-211; 300	COL3A1	32; 0	60; 0
chr1:54497690@-	-144; 172	TMEM59	34; 0	60; 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	467	0.22%	0.68%	89.64%	321	1.33811
anti	54	0.03%	0.08%	10.36%	29	0.154728
both	521	0.24%	0.75%	100.00%	349	1.49284
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	493	0.21%	0.62%	89.47%	321	1.41261
anti	58	0.02%	0.07%	10.53%	29	0.166189
both	551	0.23%	0.70%	100.00%	349	1.5788

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	13; 0	16; 0
chr6:64286785@+	-92; 52	PTP4A1	11; 0	13; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 9	0; 10
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 8	0; 9
chr8:101733810@-	-252; 96	PABPC1	7; 0	8; 0
chr6:24718895@-	-300; 64	C6orf62	7; 0	7; 0
chr6:33168574@+	-177; 300	SLC39A7	7; 0	7; 0
chr5:180670946@-	-131; 134	GNB2L1	6; 0	7; 0
chr7:1608974@-	-300; 108	PSMG3	5; 0	5; 0
chr6:31508971@-	-66; 265	BAT1	5; 0	6; 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	13; 0	16; 0
chr6:64286785@+	-92; 52	PTP4A1	11; 0	13; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 9	0; 10
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 8	0; 9
chr8:101733810@-	-252; 96	PABPC1	7; 0	8; 0
chr6:24718895@-	-300; 64	C6orf62	7; 0	7; 0
chr6:33168574@+	-177; 300	SLC39A7	7; 0	7; 0
chr5:180670946@-	-131; 134	GNB2L1	6; 0	7; 0
chr2:211421442@+	-91; 70	CPS1	5; 0	7; 0
chr6:31508971@-	-66; 265	BAT1	5; 0	6; 0

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

RNAmap 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	340	0.16%	0.49%	33.27%	247	0.494186
anti	682	0.32%	0.99%	66.73%	454	0.991279
both	1022	0.48%	1.48%	100.00%	688	1.48547
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	379	0.16%	0.48%	28.73%	247	0.550872
anti	940	0.40%	1.19%	71.27%	454	1.36628
both	1319	0.55%	1.67%	100.00%	688	1.91715

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; 28	0; 45
chr8:101734314@-	-1000; 252	PABPC1	22; 0	45; 0
chr20:47894962@-	-1000; 248	ZNFX1	0; 12	0; 12
chr13:41635409@+	-1000; 200	WBP4	0; 12	0; 122
chr11:62623517@+	-1000; 112	SLC3A2	0; 12	0; 17
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 11	0; 11
chr5:32788944@+	-844; 281	C5orf23	10; 0	10; 0
chr8:33370702@-	-1000; 286	C8orf41	0; 9	0; 10
chr1:173837219@+	-1000; 87	ZBTB37	0; 9	0; 11
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 76

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; 12	0; 122
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 76
chr8:101734314@-	-1000; 252	PABPC1	22; 0	45; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 28	0; 45
chr11:62623517@+	-1000; 112	SLC3A2	0; 12	0; 17
chr15:89878025@-	-1000; 61	POLG	0; 4	0; 14
chr19:39903224@+	-1000; 300	PLEKHG2	0; 5	0; 13
chr20:47894962@-	-1000; 248	ZNFX1	0; 12	0; 12
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 11	0; 11
chr1:173837219@+	-1000; 87	ZBTB37	0; 9	0; 11

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	8434	3.92%	12.19%	84.93%	2994	2.4668
anti	1497	0.70%	2.16%	15.07%	571	0.437847
both	9931	4.62%	14.36%	100.00%	3419	2.90465
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	9691	4.08%	12.26%	83.32%	2994	2.83445
anti	1940	0.82%	2.45%	16.68%	571	0.567417
both	11631	4.89%	14.71%	100.00%	3419	3.40187

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; 73	0; 118
chr8:128753674@+	-235; 1000	MYC	52; 0	88; 0
chr15:45010359@+	-278; 1000	B2M	47; 0	79; 0
chr16:18802989@-	-300; 667	ARL6IP1	44; 0	64; 0
chr17:79476997@-	-300; 1000	ACTG1	38; 0	92; 0
chr21:44834393@-	-300; 1000	SIK1	37; 0	50; 0
chr14:62214976@+	-300; 1000	HIF1A	36; 0	54; 0
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 192
chr12:53874278@-	-300; 1000	MAP3K12	0; 33	0; 43
chr12:104744062@+	-300; 1000	TXNRD1	32; 0	50; 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; 35	0; 192
chr19:39220830@-	-300; 1000	CAPN12	0; 73	0; 118
chr17:79476997@-	-300; 1000	ACTG1	38; 0	92; 0
chr8:128753674@+	-235; 1000	MYC	52; 0	88; 0
chr15:45010359@+	-278; 1000	B2M	47; 0	79; 0
chr11:65622306@-	-249; 1000	CFL1	32; 0	66; 0
chr16:18802989@-	-300; 667	ARL6IP1	44; 0	64; 0
chr2:1635657@-	-300; 1000	PXDN	22; 0	63; 0
chr14:62214976@+	-300; 1000	HIF1A	36; 0	54; 0
chr21:44834393@-	-300; 1000	SIK1	37; 0	50; 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	1044	0.49%	1.51%	30.65%	604	0.568627
anti	2362	1.10%	3.42%	69.35%	1272	1.28649
both	3406	1.58%	4.92%	100.00%	1836	1.85512
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	1488	0.63%	1.88%	33.54%	604	0.810458
anti	2949	1.24%	3.73%	66.46%	1272	1.60621
both	4437	1.87%	5.61%	100.00%	1836	2.41667

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; 91	0; 172
chrUn_gl000220:109077@+	-758; 300	18S	68; 0	176; 0
chr8:128231332@-	-1000; 139	AC020688.1	61; 1	78; 1
chrUn_gl000220:113347@+	-585; 300	28S	41; 0	58; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 40	0; 46
chr1:205685227@+	-1000; 300	AC119673.2	0; 37	0; 42
chr3:49571651@-	-1000; 300	AC104452.1	0; 29	0; 37
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 28	0; 35
chr6:166401114@+	-1000; 249	AL132661.1	0; 27	0; 44
chr2:70315685@-	-1000; 62	AC136007.2	0; 26	0; 29

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_gl000220:109077@+	-758; 300	18S	68; 0	176; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 91	0; 172
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	17; 0	141; 0
chr13:41635409@+	-1000; 200	WBP4	0; 12	0; 122
chr8:128231332@-	-1000; 139	AC020688.1	61; 1	78; 1
chr11:66115160@-	-1000; 72	AP001107.2	0; 8	0; 76
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 6	0; 66
chrUn_gl000220:113347@+	-585; 300	28S	41; 0	58; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 40	0; 46
chr8:101734314@-	-1000; 252	PABPC1	22; 0	45; 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	10352	4.81%	14.97%	78.71%	3674	2.22719
anti	2800	1.30%	4.05%	21.29%	1147	0.60241
both	13152	6.12%	19.02%	100.00%	4648	2.8296
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	12805	5.39%	16.19%	78.94%	3674	2.75495
anti	3416	1.44%	4.32%	21.06%	1147	0.73494
both	16221	6.82%	20.51%	100.00%	4648	3.48989

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	349; 0	821; 0
chr1:169101767@-	-127; 1000	NME7	0; 84	0; 141
chr19:39220830@-	-300; 1000	CAPN12	0; 73	0; 118
chrUn_gl000220:110946@+	-300; 539	18S	62; 0	133; 0
chr8:128753674@+	-235; 1000	MYC	52; 0	88; 0
chr15:45010359@+	-278; 1000	B2M	47; 0	79; 0
chr7:5566780@-	-300; 1000	ACTB	44; 0	156; 0
chr16:18802989@-	-300; 667	ARL6IP1	44; 0	64; 0
chrUn_gl000220:118417@+	-300; 1000	28S	42; 0	81; 0
chr17:79476997@-	-300; 1000	ACTG1	38; 0	92; 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	349; 0	821; 0
chr17:4848518@+	-104; 1000	RNF167	0; 35	0; 192
chr7:5566780@-	-300; 1000	ACTB	44; 0	156; 0
chr1:169101767@-	-127; 1000	NME7	0; 84	0; 141
chrUn_gl000220:110946@+	-300; 539	18S	62; 0	133; 0
chr1:153516087@-	-156; 923	S100A4	24; 0	126; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 73	0; 118
chr17:79476997@-	-300; 1000	ACTG1	38; 0	92; 0
chr8:128753674@+	-235; 1000	MYC	52; 0	88; 0
chrUn_gl000220:118417@+	-300; 1000	28S	42; 0	81; 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	8050	3.74%	11.64%	96.18%	6719	1.15346
anti	320	0.15%	0.46%	3.82%	267	0.0458518
both	8370	3.89%	12.10%	100.00%	6979	1.19931
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	8334	3.50%	10.54%	96.15%	6719	1.19415
anti	334	0.14%	0.42%	3.85%	267	0.0478579
both	8668	3.65%	10.96%	100.00%	6979	1.24201

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)
chr5:179046653@-	-300; 100	HNRNPH1	17; 0	19; 0
chr1:1326494@-	-300; 100	CCNL2	17; 0	20; 0
chr5:10401919@+	-300; 100	MARCH6	14; 0	19; 0
chr1:70697488@+	-300; 100	SFRS11	10; 0	10; 0
chr1:28835317@+	-300; 22	SNHG3	10; 0	15; 0
chr15:66783435@-	-300; 100	SNAPC5	0; 9	0; 10
chr14:70237083@+	-300; 98	SFRS5	9; 0	9; 0
chr5:14290650@+	-300; 100	TRIO	8; 0	8; 0
chr3:186506588@+	-298; 100	EIF4A2	7; 1	7; 1
chr20:34326966@-	-300; 28	RBM39	8; 0	10; 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	7; 0	29; 0
chr1:1326494@-	-300; 100	CCNL2	17; 0	20; 0
chr5:179046653@-	-300; 100	HNRNPH1	17; 0	19; 0
chr5:10401919@+	-300; 100	MARCH6	14; 0	19; 0
chr1:28835317@+	-300; 22	SNHG3	10; 0	15; 0
chr20:34326966@-	-300; 28	RBM39	8; 0	10; 0
chr15:66783435@-	-300; 100	SNAPC5	0; 9	0; 10
chr1:70697488@+	-300; 100	SFRS11	10; 0	10; 0
chr7:26237431@-	-300; 80	HNRNPA2B1	6; 0	9; 0
chr14:70237083@+	-300; 98	SFRS5	9; 0	9; 0

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