Parameters
input_file: 20090724_LUd4_1_hg19_ensembl59_G_iCLIP_TIA1_HeLa_bedGraph-cDNA-hits-in-genome.bed.gz
input_res_type: single hits in whole-genome, cDNA counts
mapped_to: hg19
annot_ver: ensembl59
maxU_within: -300
maxD_within: 300
maxU_flanking: -1000
maxD_flanking: 1000
smoothing: 5

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 133321
[x-link sites] used in any map: 43089 (32.32%)
[single hits in whole-genome, cDNA counts] total: 133321
[single hits in whole-genome, cDNA counts] used in any map: 49250 (33.41%)

map	span (upstream; downstream)	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map
exon-intron	-300; 300	12571	9.43%	29.17%	13344	9.05%	27.09%
intron-exon	-300; 300	9490	7.12%	22.02%	10086	6.84%	20.48%
5-ncRNA	-1000; 300	2350	1.76%	5.45%	3776	2.56%	7.67%
ncRNA-3	-300; 1000	2553	1.91%	5.92%	3660	2.48%	7.43%
ORF-3UTR	-300; 300	7023	5.27%	16.30%	8115	5.50%	16.48%
5UTR-ORF	-300; 300	282	0.21%	0.65%	304	0.21%	0.62%
inter-5UTR	-1000; 300	597	0.45%	1.39%	805	0.55%	1.63%
3UTR-inter	-300; 1000	6599	4.95%	15.31%	7490	5.08%	15.21%
inter-5	-1000; 300	2108	1.58%	4.89%	2827	1.92%	5.74%
3-inter	-300; 1000	8748	6.56%	20.30%	10470	7.10%	21.26%
BP best in intron	-300; 100	5226	3.92%	12.13%	5462	3.70%	11.09%

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	12258	9.19%	28.45%	97.51%	9878	1.21643
anti	313	0.23%	0.73%	2.49%	225	0.0310608
both	12571	9.43%	29.17%	100.00%	10077	1.24749
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	12966	8.79%	26.33%	97.17%	9878	1.28669
anti	378	0.26%	0.77%	2.83%	225	0.0375112
both	13344	9.05%	27.09%	100.00%	10077	1.3242

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:45976739@+	-281; 300	MMACHC	0; 39	0; 90
chr7:128411528@+	-300; 107	CALU	26; 0	43; 0
chr3:41281934@+	-300; 300	CTNNB1	25; 0	42; 0
chr5:177637967@-	-300; 300	AGXT2L2	1; 23	1; 27
chr2:191800015@+	-300; 300	GLS	19; 0	19; 0
chr12:50158717@+	-300; 300	TMBIM6	18; 0	26; 0
chr4:108534820@-	-291; 300	PAPSS1	16; 0	19; 0
chr12:98928321@+	-101; 300	TMPO	13; 0	14; 0
chr1:71532457@-	-216; 300	ZRANB2	13; 0	13; 0
chr5:10401598@+	-300; 185	MARCH6	12; 0	16; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr1:45976739@+	-281; 300	MMACHC	0; 39	0; 90
chr7:139025365@+	-85; 256	C7orf55	7; 0	88; 0
chr7:128411528@+	-300; 107	CALU	26; 0	43; 0
chr3:41281934@+	-300; 300	CTNNB1	25; 0	42; 0
chr5:177637967@-	-300; 300	AGXT2L2	1; 23	1; 27
chr12:50158717@+	-300; 300	TMBIM6	18; 0	26; 0
chr4:108534820@-	-291; 300	PAPSS1	16; 0	19; 0
chr2:191800015@+	-300; 300	GLS	19; 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	9162	6.87%	21.26%	96.54%	7236	1.2229
anti	328	0.25%	0.76%	3.46%	267	0.04378
both	9490	7.12%	22.02%	100.00%	7492	1.26668
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	9750	6.61%	19.80%	96.67%	7236	1.30139
anti	336	0.23%	0.68%	3.33%	267	0.0448478
both	10086	6.84%	20.48%	100.00%	7492	1.34624

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr15:45009804@+	-300; 277	B2M	37; 0	53; 0
chr9:131456919@+	-292; 300	SET	26; 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
chr2:189876353@+	-300; 210	COL3A1	16; 0	19; 0
chr17:57915655@+	-300; 51	TMEM49	16; 0	22; 0
chr1:26227577@-	-160; 260	STMN1	15; 0	20; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr9:131456919@+	-292; 300	SET	26; 0	53; 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
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
chr1:26227577@-	-160; 260	STMN1	15; 0	20; 0
chr2:189876353@+	-300; 210	COL3A1	16; 0	19; 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	1162	0.87%	2.70%	49.45%	597	0.922222
anti	1188	0.89%	2.76%	50.55%	675	0.942857
both	2350	1.76%	5.45%	100.00%	1260	1.86508
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	2354	1.60%	4.78%	62.34%	597	1.86825
anti	1422	0.96%	2.89%	37.66%	675	1.12857
both	3776	2.56%	7.67%	100.00%	1260	2.99683

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	207; 0	500; 0
chr8:128231332@-	-1000; 139	AC020688.1	37; 0	43; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 30	0; 38
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 23
chr5:140090859@+	-1000; 49	Vault-ENSG00000199990	20; 0	139; 0
chr2:70315685@-	-1000; 62	AC136007.2	0; 20	0; 24
chr17:57918626@+	-338; 36	hsa-mir-21	20; 0	24; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 17	0; 20
chr12:7052978@+	-748; 31	U7-ENSG00000238923	17; 0	103; 0
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 17	0; 24

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	207; 0	500; 0
chr14:74055600@-	-1000; 36	AC005225.1	5; 0	161; 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	87; 0
chr1:17216143@-	-1000; 51	RP11-108M9.4	0; 10	0; 76
chr7:148638579@+	-1000; 39	Y_RNA-ENSG00000252310	15; 0	58; 0
chr5:140098509@+	-1000; 44	Vault-ENSG00000202111	13; 0	56; 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	1582	1.19%	3.67%	61.97%	744	1.18413
anti	971	0.73%	2.25%	38.03%	604	0.726796
both	2553	1.91%	5.92%	100.00%	1336	1.91093
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	2611	1.77%	5.30%	71.34%	744	1.95434
anti	1049	0.71%	2.13%	28.66%	604	0.78518
both	3660	2.48%	7.43%	100.00%	1336	2.73952

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	305; 0	641; 0
chrUn_gl000220:118417@+	-300; 1000	28S	34; 0	95; 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
chr1:230416056@-	-300; 1000	RP5-956O18.3	0; 15	0; 18

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	305; 0	641; 0
chrUn_gl000220:118417@+	-300; 1000	28S	34; 0	95; 0
chr1:17216097@+	-254; 1000	RP11-108M9.5	10; 0	76; 0
chr1:94312467@+	-40; 1000	hsa-mir-760	9; 0	72; 0
chr14:74055527@-	-37; 1000	AC005225.1	2; 0	65; 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
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	15; 0	46; 0
chr15:65597130@+	-58; 1000	U5-ENSG00000200156	15; 0	36; 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	6920	5.19%	16.06%	98.53%	2552	2.65236
anti	103	0.08%	0.24%	1.47%	69	0.0394787
both	7023	5.27%	16.30%	100.00%	2609	2.69184
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	8006	5.43%	16.26%	98.66%	2552	3.06861
anti	109	0.07%	0.22%	1.34%	69	0.0417785
both	8115	5.50%	16.48%	100.00%	2609	3.11039

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr19:13054727@+	-101; 288	CALR	69; 0	126; 0
chr1:35650053@-	-70; 300	SFPQ	41; 0	59; 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
chr3:49397638@-	-88; 300	RHOA	27; 0	36; 0
chr10:102120690@+	-100; 300	SCD	26; 0	41; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr19:13054727@+	-101; 288	CALR	69; 0	126; 0
chr17:4849191@-	-50; 123	PFN1	28; 0	121; 0
chr1:35650053@-	-70; 300	SFPQ	41; 0	59; 0
chr14:62213803@+	-76; 300	HIF1A	38; 0	53; 0
chr3:149087560@-	-53; 300	TM4SF1	33; 0	47; 0
chr1:245017433@-	-93; 300	HNRNPU	15; 0	43; 0
chr10:102120690@+	-100; 300	SCD	26; 0	41; 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	241	0.18%	0.56%	85.46%	181	1.205
anti	41	0.03%	0.10%	14.54%	21	0.205
both	282	0.21%	0.65%	100.00%	200	1.41
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	259	0.18%	0.53%	85.20%	181	1.295
anti	45	0.03%	0.09%	14.80%	21	0.225
both	304	0.21%	0.62%	100.00%	200	1.52

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
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 in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
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	196	0.15%	0.45%	32.83%	154	0.453704
anti	401	0.30%	0.93%	67.17%	289	0.928241
both	597	0.45%	1.39%	100.00%	432	1.38194
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	207	0.14%	0.42%	25.71%	154	0.479167
anti	598	0.41%	1.21%	74.29%	289	1.38426
both	805	0.55%	1.63%	100.00%	432	1.86343

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr6:166401114@+	-1000; 249	AL132661.1	0; 17	0; 20
chr5:32788944@+	-844; 281	C5orf23	10; 0	11; 0
chr15:89878025@-	-1000; 61	POLG	0; 10	0; 89
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
chr10:20105167@+	-1000; 300	PLXDC2	5; 0	6; 0
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 5	0; 5
chr8:33370702@-	-1000; 286	C8orf41	0; 4	0; 4
chr8:71485680@+	-1000; 300	AC120194.1	0; 4	0; 4

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr15:89878025@-	-1000; 61	POLG	0; 10	0; 89
chr11:66115160@-	-1000; 72	AP001107.2	0; 7	0; 71
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
chr17:4843462@-	-1000; 129	SLC25A11	0; 4	0; 6
chr12:63328929@-	-1000; 207	PPM1H	0; 2	0; 6

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	5627	4.22%	13.06%	85.27%	2419	2.05365
anti	972	0.73%	2.26%	14.73%	405	0.354745
both	6599	4.95%	15.31%	100.00%	2740	2.40839
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	6279	4.26%	12.75%	83.83%	2419	2.29161
anti	1211	0.82%	2.46%	16.17%	405	0.441971
both	7490	5.08%	15.21%	100.00%	2740	2.73358

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr19:39220830@-	-300; 1000	CAPN12	0; 51	0; 79
chr8:128753674@+	-235; 1000	MYC	34; 0	50; 0
chr14:62214976@+	-300; 1000	HIF1A	31; 0	45; 0
chr16:18802989@-	-300; 667	ARL6IP1	30; 0	44; 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
chr12:104744062@+	-300; 1000	TXNRD1	24; 0	36; 0
chr13:113978542@-	-129; 1000	GRTP1	1; 22	1; 27
chrX:24096088@+	-282; 1000	EIF2S3	22; 0	30; 0

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr17:4848518@+	-104; 1000	RNF167	1; 28	1; 121
chr19:39220830@-	-300; 1000	CAPN12	0; 51	0; 79
chr17:79476997@-	-300; 1000	ACTG1	28; 0	68; 0
chr2:1635657@-	-300; 1000	PXDN	20; 0	57; 0
chr8:128753674@+	-235; 1000	MYC	34; 0	50; 0
chr14:62214976@+	-300; 1000	HIF1A	31; 0	45; 0
chr16:18802989@-	-300; 667	ARL6IP1	30; 0	44; 0
chr17:8024297@-	-294; 1000	HES7	1; 8	8; 34
chr15:45010359@+	-278; 1000	B2M	27; 0	38; 0
chr11:65622306@-	-249; 1000	CFL1	21; 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 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	605	0.45%	1.40%	28.70%	416	0.477883
anti	1503	1.13%	3.49%	71.30%	870	1.1872
both	2108	1.58%	4.89%	100.00%	1266	1.66509
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	864	0.59%	1.75%	30.56%	416	0.682464
anti	1963	1.33%	3.99%	69.44%	870	1.55055
both	2827	1.92%	5.74%	100.00%	1266	2.23302

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 63	0; 158
chr8:128231332@-	-1000; 139	AC020688.1	37; 0	43; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 30	0; 38
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 22	0; 23
chr2:70315685@-	-1000; 62	AC136007.2	0; 20	0; 24
chr6:166401114@+	-1000; 249	AL132661.1	0; 17	0; 20
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 17	0; 20
chr1:230417638@-	-1000; 202	RP5-956O18.3	0; 17	0; 24
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 15	0; 17
chr19:54379302@-	-1000; 120	AC008440.5	0; 14	0; 15

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 63	0; 158
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
chr8:128231332@-	-1000; 139	AC020688.1	37; 0	43; 0
chr3:49571651@-	-1000; 300	AC104452.1	0; 30	0; 38
chrM:5903@+	-162; 300	J01415.8	0; 3	0; 31
chr2:70315685@-	-1000; 62	AC136007.2	0; 20	0; 24

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	6967	5.23%	16.17%	79.64%	2946	1.90355
anti	1781	1.34%	4.13%	20.36%	817	0.486612
both	8748	6.56%	20.30%	100.00%	3660	2.39016
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [junctions] in map	[single hits in whole-genome, cDNA counts] per unique [junction]
same	8363	5.67%	16.98%	79.88%	2946	2.28497
anti	2107	1.43%	4.28%	20.12%	817	0.575683
both	10470	7.10%	21.26%	100.00%	3660	2.86066

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	305; 0	641; 0
chr1:169101767@-	-127; 1000	NME7	0; 66	0; 81
chr19:39220830@-	-300; 1000	CAPN12	0; 51	0; 79
chrUn_gl000220:118417@+	-300; 1000	28S	34; 0	95; 0
chr8:128753674@+	-235; 1000	MYC	34; 0	50; 0
chr14:62214976@+	-300; 1000	HIF1A	31; 0	45; 0
chr7:5566780@-	-300; 1000	ACTB	30; 0	98; 0
chr16:18802989@-	-300; 667	ARL6IP1	30; 0	44; 0
chr17:4848518@+	-104; 1000	RNF167	1; 28	1; 121
chr4:57897324@+	-130; 1000	POLR2B	1; 27	1; 38

Top 10 junctions with largest [single hits in whole-genome, cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	305; 0	641; 0
chr17:4848518@+	-104; 1000	RNF167	1; 28	1; 121
chr7:5566780@-	-300; 1000	ACTB	30; 0	98; 0
chrUn_gl000220:118417@+	-300; 1000	28S	34; 0	95; 0
chr1:169101767@-	-127; 1000	NME7	0; 66	0; 81
chr19:39220830@-	-300; 1000	CAPN12	0; 51	0; 79
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
chr2:1635657@-	-300; 1000	PXDN	20; 0	57; 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	5014	3.76%	11.64%	95.94%	4381	1.10125
anti	212	0.16%	0.49%	4.06%	179	0.0465627
both	5226	3.92%	12.13%	100.00%	4553	1.14781
strand	[single hits in whole-genome, cDNA counts] used in map	[single hits in whole-genome, cDNA counts] % of total	[single hits in whole-genome, cDNA counts] % of used in any map	[single hits in whole-genome, cDNA counts] % of used in map	unique [BPs] in map	[single hits in whole-genome, cDNA counts] per unique [BP]
same	5240	3.55%	10.64%	95.94%	4381	1.15089
anti	222	0.15%	0.45%	4.06%	179	0.0487591
both	5462	3.70%	11.09%	100.00%	4553	1.19965

Top 10 BPs with largest x-link sites sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
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 in whole-genome, cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits in whole-genome, cDNA counts] (same; anti)
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.