Parameters
input_file: 20090724_LUd4_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: 138090
[x-link sites] used in any map: 44436 (32.18%)
[single hits (=G+T), cDNA counts] total: 138090
[single hits (=G+T), cDNA counts] used in any map: 51822 (33.35%)

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	12699	9.20%	28.58%	13598	8.75%	26.24%
intron-exon	-300; 300	9650	6.99%	21.72%	10294	6.62%	19.86%
5-ncRNA	-1000; 300	2597	1.88%	5.84%	4655	3.00%	8.98%
ncRNA-3	-300; 1000	2714	1.97%	6.11%	4012	2.58%	7.74%
ORF-3UTR	-300; 300	7310	5.29%	16.45%	8452	5.44%	16.31%
5UTR-ORF	-300; 300	286	0.21%	0.64%	308	0.20%	0.59%
inter-5UTR	-1000; 300	625	0.45%	1.41%	967	0.62%	1.87%
3UTR-inter	-300; 1000	6883	4.98%	15.49%	7862	5.06%	15.17%
inter-5	-1000; 300	2301	1.67%	5.18%	3291	2.12%	6.35%
3-inter	-300; 1000	9170	6.64%	20.64%	11088	7.14%	21.40%
BP best in intron	-300; 100	5293	3.83%	11.91%	5532	3.56%	10.68%

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	12370	8.96%	27.84%	97.41%	9946	1.21824
anti	329	0.24%	0.74%	2.59%	235	0.032401
both	12699	9.20%	28.58%	100.00%	10154	1.25064
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	13204	8.50%	25.48%	97.10%	9946	1.30037
anti	394	0.25%	0.76%	2.90%	235	0.0388024
both	13598	8.75%	26.24%	100.00%	10154	1.33918

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; 41	0; 92
chr7:128411528@+	-300; 107	CALU	26; 0	43; 0
chr5:177637967@-	-300; 300	AGXT2L2	1; 24	1; 28
chr3:41281934@+	-300; 300	CTNNB1	25; 0	42; 0
chr2:191800015@+	-300; 300	GLS	19; 1	19; 1
chr12:50158717@+	-300; 300	TMBIM6	18; 0	26; 0
chr4:108534820@-	-291; 300	PAPSS1	16; 0	19; 0
chr7:139025365@+	-85; 256	C7orf55	13; 0	215; 0
chr12:98928321@+	-101; 300	TMPO	13; 0	14; 0
chr1:71532457@-	-216; 300	ZRANB2	13; 0	13; 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)
chr7:139025365@+	-85; 256	C7orf55	13; 0	215; 0
chr1:45976739@+	-281; 300	MMACHC	0; 41	0; 92
chr7:128411528@+	-300; 107	CALU	26; 0	43; 0
chr3:41281934@+	-300; 300	CTNNB1	25; 0	42; 0
chr5:177637967@-	-300; 300	AGXT2L2	1; 24	1; 28
chr12:50158717@+	-300; 300	TMBIM6	18; 0	26; 0
chr2:191800015@+	-300; 300	GLS	19; 1	19; 1
chr4:108534820@-	-291; 300	PAPSS1	16; 0	19; 0
chr5:10401598@+	-300; 185	MARCH6	12; 0	16; 0
chr1:165624857@+	-127; 300	MGST3	11; 0	16; 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	9306	6.74%	20.94%	96.44%	7299	1.22965
anti	344	0.25%	0.77%	3.56%	282	0.0454545
both	9650	6.99%	21.72%	100.00%	7568	1.27511
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	9942	6.40%	19.18%	96.58%	7299	1.31369
anti	352	0.23%	0.68%	3.42%	282	0.0465116
both	10294	6.62%	19.86%	100.00%	7568	1.3602

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)
chr9:131456919@+	-292; 300	SET	38; 0	70; 0
chr15:45009804@+	-300; 277	B2M	37; 0	53; 0
chr2:211542610@+	-300; 300	CPS1	21; 0	24; 0
chr5:179041959@-	-293; 300	HNRNPH1	19; 0	28; 0
chr8:128753204@+	-241; 235	MYC	18; 0	25; 0
chr10:112657785@+	-300; 300	PDCD4	18; 0	21; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	17; 0	21; 0
chr2:47387942@-	-300; 300	CALM2	16; 0	20; 0
chr2:189876353@+	-300; 210	COL3A1	16; 0	19; 0
chr17:1248792@-	-300; 300	YWHAE	16; 0	19; 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)
chr9:131456919@+	-292; 300	SET	38; 0	70; 0
chr15:45009804@+	-300; 277	B2M	37; 0	53; 0
chr5:179041959@-	-293; 300	HNRNPH1	19; 0	28; 0
chr8:128753204@+	-241; 235	MYC	18; 0	25; 0
chr2:211542610@+	-300; 300	CPS1	21; 0	24; 0
chr12:54678332@+	-116; 300	HNRNPA1	10; 0	23; 0
chr2:27274290@+	-196; 66	AGBL5	3; 0	22; 0
chr17:57915655@+	-300; 51	TMEM49	16; 0	22; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	17; 0	21; 0
chr10:112657785@+	-300; 300	PDCD4	18; 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 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	1355	0.98%	3.05%	52.18%	636	1.02964
anti	1242	0.90%	2.80%	47.82%	693	0.943769
both	2597	1.88%	5.84%	100.00%	1316	1.9734
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	3128	2.01%	6.04%	67.20%	636	2.3769
anti	1527	0.98%	2.95%	32.80%	693	1.16033
both	4655	3.00%	8.98%	100.00%	1316	3.53723

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	207; 0	500; 0
chrUn_gl000220:109077@+	-758; 300	18S	76; 0	180; 0
chr8:128231332@-	-1000; 139	AC020688.1	37; 0	43; 0
chrUn_gl000220:113347@+	-585; 300	28S	35; 0	56; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 30	0; 38
chr2:70315685@-	-1000; 62	AC136007.2	0; 23	0; 28
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 23
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	20; 0	139; 0
chr17:57918626@+	-338; 36	hsa-mir-21	20; 0	24; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 17	0; 20

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	207; 0	500; 0
chr7:96770956@-	-1000; 35	AC073421.1	11; 0	218; 0
chr14:74055600@-	-1000; 36	AC005225.1	6; 0	215; 0
chrUn_gl000220:109077@+	-758; 300	18S	76; 0	180; 0
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	20; 0	139; 0
chr5:135416285@-	-1000; 50	Vault-ENSG00000202030	12; 0	105; 0
chr12:7052978@+	-748; 31	U7-ENSG00000238923	17; 0	103; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	13; 0	103; 0
chr19:58024440@-	-1000; 33	hsa-mir-1274b	4; 0	93; 0
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 10	0; 76

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	1724	1.25%	3.88%	63.52%	785	1.24207
anti	990	0.72%	2.23%	36.48%	615	0.713256
both	2714	1.97%	6.11%	100.00%	1388	1.95533
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	2944	1.89%	5.68%	73.38%	785	2.12104
anti	1068	0.69%	2.06%	26.62%	615	0.769452
both	4012	2.58%	7.74%	100.00%	1388	2.89049

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	305; 0	641; 0
chrUn_gl000220:110946@+	-300; 539	18S	47; 0	94; 0
chrUn_gl000220:118417@+	-300; 1000	28S	35; 0	96; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 23	0; 27
chr11:62609089@-	-96; 978	U2-ENSG00000222328	21; 0	51; 0
chr5:135416184@-	-51; 1000	Vault-ENSG00000202030	16; 0	60; 0
chr1:28835512@-	-182; 1000	AL513497.3	0; 16	0; 19
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	15; 0	60; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	15; 0	46; 0
chr15:65597130@+	-58; 1000	U5-ENSG00000200156	15; 0	36; 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	305; 0	641; 0
chrUn_gl000220:118417@+	-300; 1000	28S	35; 0	96; 0
chrUn_gl000220:110946@+	-300; 539	18S	47; 0	94; 0
chr14:74055527@-	-37; 1000	AC005225.1	4; 0	93; 0
chr1:17216097@+	-254; 1000	RP11-108M9.5	10; 0	76; 0
chr1:94312467@+	-40; 1000	hsa-mir-760	9; 0	72; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	15; 0	60; 0
chr5:135416184@-	-51; 1000	Vault-ENSG00000202030	16; 0	60; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	21; 0	51; 0
chr17:38273551@-	-37; 1000	AC068669.1	3; 0	49; 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	7204	5.22%	16.21%	98.55%	2596	2.71439
anti	106	0.08%	0.24%	1.45%	71	0.0399397
both	7310	5.29%	16.45%	100.00%	2654	2.75433
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	8339	5.37%	16.09%	98.66%	2596	3.14205
anti	113	0.07%	0.22%	1.34%	71	0.0425772
both	8452	5.44%	16.31%	100.00%	2654	3.18463

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	70; 0	130; 0
chr10:102120690@+	-100; 300	SCD	47; 0	81; 0
chr1:35650053@-	-70; 300	SFPQ	42; 0	60; 0
chr14:62213803@+	-76; 300	HIF1A	38; 0	53; 0
chr3:149087560@-	-53; 300	TM4SF1	33; 0	47; 0
chr5:179156650@+	-145; 300	CANX	31; 0	40; 0
chr7:148700882@-	-209; 300	PDIA4	29; 0	38; 0
chr21:27253823@-	-129; 300	APP	29; 0	39; 0
chr17:4849191@-	-50; 123	PFN1	28; 0	121; 0
chr6:30692174@+	-300; 300	TUBB	27; 0	36; 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	70; 0	130; 0
chr17:4849191@-	-50; 123	PFN1	28; 0	121; 0
chr10:102120690@+	-100; 300	SCD	47; 0	81; 0
chr1:35650053@-	-70; 300	SFPQ	42; 0	60; 0
chr14:62213803@+	-76; 300	HIF1A	38; 0	53; 0
chr1:245017433@-	-93; 300	HNRNPU	23; 0	53; 0
chr3:149087560@-	-53; 300	TM4SF1	33; 0	47; 0
chr5:179156650@+	-145; 300	CANX	31; 0	40; 0
chr21:27253823@-	-129; 300	APP	29; 0	39; 0
chr7:148700882@-	-209; 300	PDIA4	29; 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 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	245	0.18%	0.55%	85.66%	184	1.2069
anti	41	0.03%	0.09%	14.34%	21	0.20197
both	286	0.21%	0.64%	100.00%	203	1.40887
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	263	0.17%	0.51%	85.39%	184	1.29557
anti	45	0.03%	0.09%	14.61%	21	0.221675
both	308	0.20%	0.59%	100.00%	203	1.51724

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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 11	0; 11
chr7:135612307@+	-300; 127	AC015987.2	0; 6	0; 8
chr8:101733810@-	-252; 96	PABPC1	4; 0	6; 0
chr8:126011645@+	-300; 145	SQLE	4; 0	4; 0
chr6:64286785@+	-92; 52	PTP4A1	4; 0	6; 0
chr4:83350842@-	-226; 221	HNRPDL	4; 0	4; 0
chr2:211421442@+	-91; 70	CPS1	4; 0	6; 0
chr16:24551947@+	-300; 83	RBBP6	4; 0	4; 0
chr9:21974825@-	-136; 176	CDKN2A	3; 0	3; 0
chr6:24718895@-	-300; 64	C6orf62	3; 0	3; 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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 11	0; 11
chr7:135612307@+	-300; 127	AC015987.2	0; 6	0; 8
chr8:101733810@-	-252; 96	PABPC1	4; 0	6; 0
chr6:64286785@+	-92; 52	PTP4A1	4; 0	6; 0
chr2:211421442@+	-91; 70	CPS1	4; 0	6; 0
chr8:126011645@+	-300; 145	SQLE	4; 0	4; 0
chr4:83350842@-	-226; 221	HNRPDL	4; 0	4; 0
chr16:24551947@+	-300; 83	RBBP6	4; 0	4; 0
chr11:61734896@-	-103; 57	FTH1	3; 0	4; 0
chr9:21974825@-	-136; 176	CDKN2A	3; 0	3; 0

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

RNAmap inter-5UTR

junction is at position zero.
upstream is regions of type: inter, telo
downstream is regions of type: 5UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	212	0.15%	0.48%	33.92%	156	0.486239
anti	413	0.30%	0.93%	66.08%	291	0.947248
both	625	0.45%	1.41%	100.00%	436	1.43349
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	233	0.15%	0.45%	24.10%	156	0.534404
anti	734	0.47%	1.42%	75.90%	291	1.68349
both	967	0.62%	1.87%	100.00%	436	2.21789

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)
chr8:101734314@-	-1000; 252	PABPC1	17; 0	28; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 17	0; 20
chr5:32788944@+	-844; 281	C5orf23	10; 0	11; 0
chr15:89878025@-	-1000; 61	POLG	0; 10	0; 89
chr13:41635409@+	-1000; 200	WBP4	0; 10	0; 134
chr11:62623517@+	-1000; 112	SLC3A2	0; 9	0; 9
chr5:147647742@+	-1000; 164	SPINK5L3	7; 0	7; 0
chr11:66115160@-	-1000; 72	AP001107.2	0; 7	0; 71
chr20:47894962@-	-1000; 248	ZNFX1	0; 5	0; 6
chr10:20105167@+	-1000; 300	PLXDC2	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)
chr13:41635409@+	-1000; 200	WBP4	0; 10	0; 134
chr15:89878025@-	-1000; 61	POLG	0; 10	0; 89
chr11:66115160@-	-1000; 72	AP001107.2	0; 7	0; 71
chr8:101734314@-	-1000; 252	PABPC1	17; 0	28; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 17	0; 20
chr19:39903224@+	-1000; 300	PLEKHG2	0; 3	0; 19
chr17:37026255@+	-1000; 93	LASP1	0; 1	0; 14
chr5:32788944@+	-844; 281	C5orf23	10; 0	11; 0
chr11:62623517@+	-1000; 112	SLC3A2	0; 9	0; 9
chr5:147647742@+	-1000; 164	SPINK5L3	7; 0	7; 0

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	5867	4.25%	13.20%	85.24%	2457	2.10891
anti	1016	0.74%	2.29%	14.76%	411	0.365205
both	6883	4.98%	15.49%	100.00%	2782	2.47412
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	6561	4.22%	12.66%	83.45%	2457	2.35838
anti	1301	0.84%	2.51%	16.55%	411	0.467649
both	7862	5.06%	15.17%	100.00%	2782	2.82602

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; 54	0; 83
chr8:128753674@+	-235; 1000	MYC	34; 0	50; 0
chr16:18802989@-	-300; 667	ARL6IP1	32; 0	49; 0
chr14:62214976@+	-300; 1000	HIF1A	31; 0	45; 0
chr17:4848518@+	-104; 1000	RNF167	1; 28	1; 121
chr17:79476997@-	-300; 1000	ACTG1	28; 0	68; 0
chr15:45010359@+	-278; 1000	B2M	27; 0	38; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 26	0; 39
chrX:24096088@+	-282; 1000	EIF2S3	24; 0	32; 0
chr12:104744062@+	-300; 1000	TXNRD1	24; 0	36; 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	1; 28	1; 121
chr19:39220830@-	-300; 1000	CAPN12	0; 54	0; 83
chr17:79476997@-	-300; 1000	ACTG1	28; 0	68; 0
chr17:8024297@-	-294; 1000	HES7	1; 9	8; 56
chr2:1635657@-	-300; 1000	PXDN	20; 0	57; 0
chr8:128753674@+	-235; 1000	MYC	34; 0	50; 0
chr16:18802989@-	-300; 667	ARL6IP1	32; 0	49; 0
chr14:62214976@+	-300; 1000	HIF1A	31; 0	45; 0
chr12:53874278@-	-300; 1000	MAP3K12	0; 26	0; 39
chr11:65622306@-	-249; 1000	CFL1	22; 0	39; 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	744	0.54%	1.67%	32.33%	429	0.575851
anti	1557	1.13%	3.50%	67.67%	884	1.20511
both	2301	1.67%	5.18%	100.00%	1292	1.78096
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	1141	0.73%	2.20%	34.67%	429	0.883127
anti	2150	1.38%	4.15%	65.33%	884	1.66409
both	3291	2.12%	6.35%	100.00%	1292	2.54721

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_gl000220:109077@+	-758; 300	18S	76; 0	180; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 67	0; 166
chr8:128231332@-	-1000; 139	AC020688.1	37; 0	43; 0
chrUn_gl000220:113347@+	-585; 300	28S	35; 0	56; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 30	0; 38
chr2:70315685@-	-1000; 62	AC136007.2	0; 23	0; 28
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 23
chr8:101734314@-	-1000; 252	PABPC1	17; 0	28; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 17	0; 20
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 17	0; 20

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	76; 0	180; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 67	0; 166
chr13:41635409@+	-1000; 200	WBP4	0; 10	0; 134
chr5:135416285@-	-1000; 50	Vault-ENSG00000202030	12; 0	105; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	13; 0	103; 0
chr15:89878025@-	-1000; 61	POLG	0; 10	0; 89
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 10	0; 76
chr11:66115160@-	-1000; 72	AP001107.2	0; 7	0; 71
chrUn_gl000220:113347@+	-585; 300	28S	35; 0	56; 0
chr8:128231332@-	-1000; 139	AC020688.1	37; 0	43; 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	7319	5.30%	16.47%	79.81%	3008	1.96062
anti	1851	1.34%	4.17%	20.19%	831	0.495848
both	9170	6.64%	20.64%	100.00%	3733	2.45647
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	8853	5.70%	17.08%	79.84%	3008	2.37155
anti	2235	1.44%	4.31%	20.16%	831	0.598714
both	11088	7.14%	21.40%	100.00%	3733	2.97027

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	305; 0	641; 0
chr1:169101767@-	-127; 1000	NME7	1; 66	1; 81
chr19:39220830@-	-300; 1000	CAPN12	0; 54	0; 83
chrUn_gl000220:110946@+	-300; 539	18S	47; 0	94; 0
chr7:5566780@-	-300; 1000	ACTB	43; 0	138; 0
chrUn_gl000220:118417@+	-300; 1000	28S	35; 0	96; 0
chr8:128753674@+	-235; 1000	MYC	34; 0	50; 0
chr16:18802989@-	-300; 667	ARL6IP1	32; 0	49; 0
chr14:62214976@+	-300; 1000	HIF1A	31; 0	45; 0
chr17:4848518@+	-104; 1000	RNF167	1; 28	1; 121

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	305; 0	641; 0
chr7:5566780@-	-300; 1000	ACTB	43; 0	138; 0
chr17:4848518@+	-104; 1000	RNF167	1; 28	1; 121
chrUn_gl000220:118417@+	-300; 1000	28S	35; 0	96; 0
chrUn_gl000220:110946@+	-300; 539	18S	47; 0	94; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 54	0; 83
chr1:169101767@-	-127; 1000	NME7	1; 66	1; 81
chr1:17216097@+	-254; 1000	RP11-108M9.5	10; 0	76; 0
chr17:79476997@-	-300; 1000	ACTG1	28; 0	68; 0
chr1:153516087@-	-156; 923	S100A4	19; 0	67; 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	5063	3.67%	11.39%	95.65%	4425	1.09707
anti	230	0.17%	0.52%	4.35%	197	0.0498375
both	5293	3.83%	11.91%	100.00%	4615	1.14691
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	5290	3.40%	10.21%	95.63%	4425	1.14626
anti	242	0.16%	0.47%	4.37%	197	0.0524377
both	5532	3.56%	10.68%	100.00%	4615	1.1987

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)
chr1:1326494@-	-300; 100	CCNL2	11; 0	12; 0
chr5:179046653@-	-300; 100	HNRNPH1	10; 0	10; 0
chr5:10401919@+	-300; 100	MARCH6	9; 0	12; 0
chr15:66783435@-	-300; 100	SNAPC5	0; 9	0; 9
chr1:21100194@-	-300; 92	HP1BP3	9; 0	10; 0
chr1:28835317@+	-300; 22	SNHG3	8; 0	9; 0
chr20:34326966@-	-300; 28	RBM39	7; 0	7; 0
chr17:79478678@-	-111; 27	ACTG1	7; 0	7; 0
chr9:86584384@-	-300; 90	HNRNPK	6; 0	11; 0
chr2:110301957@-	-300; 57	SEPT10	6; 0	7; 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)
chr5:10401919@+	-300; 100	MARCH6	9; 0	12; 0
chr1:1326494@-	-300; 100	CCNL2	11; 0	12; 0
chr9:86584384@-	-300; 90	HNRNPK	6; 0	11; 0
chr5:179046653@-	-300; 100	HNRNPH1	10; 0	10; 0
chr1:21100194@-	-300; 92	HP1BP3	9; 0	10; 0
chr15:66783435@-	-300; 100	SNAPC5	0; 9	0; 9
chr1:28835317@+	-300; 22	SNHG3	8; 0	9; 0
chr1:70697488@+	-300; 100	SFRS11	6; 0	8; 0
chr20:34326966@-	-300; 28	RBM39	7; 0	7; 0
chr2:110301957@-	-300; 57	SEPT10	6; 0	7; 0

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