miR-Intess: classification

other hairpins

novel_multiarm_loopOverlap_mirtron (2 loci)

sblock6196 [novel_multiarm_loopOverlap_mirtron]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.095	no	no	0.52/0.62	21/23/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	41 11	-9 17	5arm_loop_3arm 3arm	1 1	38 0	0.48 0.29	9 3	2	2	na	na

		reads	miRBase family seed
seed	------------------------------------------CAUGGCG----------------------------------------------------------------	1	novel
seed	----------------------------------------------------------------------------------ACAUAUG------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	-----------------------------------------TCATGGCGGGTGTTGGTATAGAG-------------------------------------------------	23	1	-
	---------------------------------------------------------------------------------CACATATGCCCTGCCCTCCAG-----------	21	-	1
rat	gcaggtggctgggcacagggcgggtgttggtatagagagcaTCATGGCGGGTGTTGGTATAGAGagcatcatggcggaactCACATATGCCCTGCCCTCCAGctcaggcctgc
	*****************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>	ENSRNOT00000027263 ENSRNOG00000020058 Celsr2
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>	ENSRNOT00000055873 ENSRNOG00000020058 Celsr2
rat	((((((..((((((..(((((((.....((((((..(((..((.((.((((((((.........)))))).)).)))).)))...)))))))))))))...))))))))))))	0.510 -45.10

rat

chromosome:2:203963346:203963458:-1

Same_strand|Intronic_coding|ENSRNOT00000055873|ENSRNOG00000020058 ## ENSRNOG00000020058|protein_coding|Celsr2|Cadherin EGF LAG seven-pass G-type receptor 2 (Multiple epidermal growth factor-like domains 3) (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:Q9QYP2] ## {Repeats: trf 14 37 0 class=trf}

novel_rep_cloningOK (2 loci)

block2435039 [novel_rep_cloningOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.041	no	LINE/L1	0.79/0.80	19/20/0.71	0.0	0.2	11	0	4	0	16	7	3arm	2	nd	0.21	2	14	4	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GGGGUGG----------------------------	14	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S2
	------------------------------------------------------------------------TGGGGTGGGGGGTGGGACCC----------------	20	6	1	3	-
	------------------------------------------------------------------------TGGGGTGGGGGGTGGGACC-----------------	19	2	-	1	1
rat	CTGGCTCACGAAGTGTTAATGAAGTCCAAGCCTCTCACCTGACCAG------TAGGG----TGGAATTGGGATGGGGTGGGGGGTGGGACCCTGAGCTTGAGAGAAAG
mouse	---------GAAGCA----------CCTAACCCCTCAAGAGACTGGAGGCCTCAGGGAGTTTAGAGGTCAGGTGGGGTGGGGGGTGGGAGCATC--------------
	** * * * **** * ** * * ***************** * *
rat	((..(((.((.(((.........((((..(((((((((((..(((( (.... ....)))))....))))))))))).)))).....))))).)))..))	0.420 -33.34
mouse	...((. (((.((((((((....(((...((((((..........)))))).)))....))))))))))).))...	1.000 -31.50

rat	chromosome:8:92027668:92027765:1	intergenic
mouse	chromosome:12:10727086:10727223:-1	intergenic ## {Repeats: Lx3_Mus 1 class=LINE/L1}

block234814 [novel_rep_cloningOK]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.314	no	SINE/B2	0.48/0.55	20/25/0.93	0.0	0.0	15	0	4	0	23	8	5arm	1	nd	0.20	2	27	4	na	na

		reads	miRBase family seed
seed	------------------------GUCUCUG-------------------------------------------------------------------------------------------	19	novel
seed	--------------AGCCUCU-----------------------------------------------------------------------------------------------------	4	novel
seed	----------------------UUGUCUC---------------------------------------------------------------------------------------------	3	novel
seed	---------------------CUUGUCU----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T5S1	T5S2
	-----------------------TGTCTCTGCATCACAGTGTG-------------------------------------------------------------------------------	20	1	1	15	2
	---------------------CTTGTCTCTGCATCACAGTGTG-------------------------------------------------------------------------------	22	-	2	1	-
	-------------CAGCCTCTCTTGTCTCTGCATCACA------------------------------------------------------------------------------------	25	-	1	1	-
	--------------------TCTTGTCTCTGCATCACAGTGTG-------------------------------------------------------------------------------	23	-	-	1	-
	-------------CAGCCTCTCTTGTCTCTGCATC---------------------------------------------------------------------------------------	22	-	-	1	-
	-------------CAGCCTCTCTTGTCTCTGCA-----------------------------------------------------------------------------------------	20	-	-	1	-
rat	CGTGAGGTAGGGTCAGCCTCTCTTGTCTCTGCATCACAGTGTGCTCCAGTCTCAGCCGGCTGGACAGCGGATTC--TGTGGATGCTGGGTCTCATCAGGAAGACTGCTGTTCCTCTGAGTGG
mouse	-----------------------TGTCTCTGCATCACATGTGGGGCTGGTACC------CTGGTGATGAGCTTCCATGTGGGTGCCGGGAAT------------------------------
	*************** * * ** * **** * * * * * *** *
rat	(((..((.(((..((((.(((((((.(((.(((((((((..((((((((((......)))))))..)))....) )))).)))).)))......))))).))..))))..)))))..))).	0.950 -41.80
mouse	..((((.((((((((((.((((((.((((. ...)).)).))))))))))))).))).))))..	1.000 -28.20

rat	chromosome:12:44302568:44302687:1	intergenic
mouse	chromosome:17:28681722:28681881:-1	intergenic ## {Repeats: dust 0 class=dust,trf 0 class=trf,(CAAAA)n -1 class=Simple_repeat,B3 -1 class=SINE/B2}

novel_shortStem_5varHIGH_loopOverlap_bulgeHIGH (2 loci)

block2089138 [novel_shortStem_5varHIGH_loopOverlap_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.027	no	no	0.45/0.54	20/26/0.75	4.8	4.2	4	0	2	0	2	-8	5arm_loop	3	nd	0.29	4	4	2	na	na

		reads	miRBase family seed
seed	---GAACAAU--------------------------------------------------------------	2	novel
seed	----------GCGGUGC-------------------------------------------------------	1	novel
seed	---------------GCUCACU--------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	--TGAACAATGCGGTGCTCACTCCCA----------------------------------------------	24	-	2
	---------TGCGGTGCTCACTCCCATACTTTCTT-------------------------------------	26	1	-
	--------------TGCTCACTCCCATACTTTCT--------------------------------------	20	-	1
rat	tgTGAACAATGCGGTGCTCACTCCCATACTTTCTTacccattcatggggttctgtatcctgcctctttcaca
	************************************************************************
rat	.(((((....(((((((..((.(((((................)))))))...))).)).))....))))).	0.990 -15.99

rat

chromosome:7:17360524:17360595:-1

intergenic

block2090786 [novel_shortStem_5varHIGH_loopOverlap_bulgeHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.027	no	no	0.45/0.54	20/26/0.75	4.8	4.2	4	0	2	0	2	-8	5arm_loop	3	nd	0.29	4	4	2	na	na

		reads	miRBase family seed
seed	---GAACAAU--------------------------------------------------------------	2	novel
seed	----------GCGGUGC-------------------------------------------------------	1	novel
seed	---------------GCUCACU--------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	--TGAACAATGCGGTGCTCACTCCCA----------------------------------------------	24	-	2
	---------TGCGGTGCTCACTCCCATACTTTCTT-------------------------------------	26	1	-
	--------------TGCTCACTCCCATACTTTCT--------------------------------------	20	-	1
rat	tgTGAACAATGCGGTGCTCACTCCCATACTTTCTTacccattcatggggttctgtatcctgcctctttcaca
	************************************************************************
rat	.(((((....(((((((..((.(((((................)))))))...))).)).))....))))).	0.990 -15.99

rat

chromosome:7:18800651:18800722:-1

intergenic

novel_shortStem_5varHIGH_loopOverlap_nonpairedHIGH (2 loci)

block594382 [novel_shortStem_5varHIGH_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.594	no	no	0.50/0.50	20/24/1.00	2.5	0.5	2	0	2	0	3	-2	5arm_loop	2	nd	0.40	3	2	2	na	na

		reads	miRBase family seed
seed	---------GCUCCAA--------------------------------------------	1	novel
seed	----CUCAAGC-------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S2
	--------AGCTCCAAAGCACAGGAAGA--------------------------------	20	1	-
	---ACTCAAGCTCCAAAGCACAGGAAG---------------------------------	24	-	1
rat	ggtACTCAAGCTCCAAAGCACAGGAAGAtcattccagaaggctgtgtagttcttgtcatc
	************************************************************
rat	(((((...((((.((.(((...((((.....)))).....))).)).))))...)).)))	0.830 -10.50

rat

chromosome:17:4458269:4458328:-1

intergenic

block1640202 [novel_shortStem_5varHIGH_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.239	no	no	0.57/0.62	21/21/1.00	1.5	1.5	2	0	2	0	1	-20	3arm_loop	1	nd	0.33	3	2	2	na	na

		reads	miRBase family seed
seed	-------------------AGCUUCC-----------------	1	novel
seed	----------------------UUCCACG--------------	1	novel
		len	cloning frequencies
			T3S2	T5S2
	---------------------CTTCCACGTTGCGACTCAGCC-	21	-	1
	------------------GAGCTTCCACGTTGCGACTCA----	21	1	-
rat	cggagcggtgcctgcgtgGAGCTTCCACGTTGCGACTCAGCCg
	*******************************************
rat	(((...(((((..((((((.....)))))).)).)))...)))	1.000 -17.00

rat

chromosome:4:56144540:56144582:1

intergenic

novel_shortStem_5varHIGH_mirtron (2 loci)

block893921 [novel_shortStem_5varHIGH_mirtron]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.025	no	no	0.45/0.57	20/24/1.00	2.0	2.7	3	0	1	0	4	29	5arm	4	1	0.29	3	3	1	na	na

		reads	miRBase family seed
seed	-----GGCAGGU------------------------------------------------------------------------------------------------------------	2	novel
seed	-----------UUGGUAU------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----GGGCAGGTTGGTATCCAGGTT-----------------------------------------------------------------------------------------------	21	1
	----------GTTGGTATCCAGGTTACAAG------------------------------------------------------------------------------------------	20	1
	----GGGCAGGTTGGTATCCAGGTTACA--------------------------------------------------------------------------------------------	24	1
rat	ccctGGGCAGGTTGGTATCCAGGTTACAAGgcaagtagaagtttggtgcttggagacagaggtctgctttccagcaggtactaacttttattgtatcctggctatgtttccctttgtagg
	************************************************************************************************************************
	>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>	ENSRNOT00000044783 ENSRNOG00000033465 Hbb
rat	.((((...(((..((((((((((.((((......(((((((.(((((((((((((((((....))).))))))...))))))))))))))))))).)))))..)))))..)))...))))	0.960 -39.10

rat

chromosome:1:161619945:161620064:-1

block974813 [novel_shortStem_5varHIGH_mirtron]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.031	no	no	0.53/0.59	19/23/0.71	1.4	3.0	7	0	4	0	0	3	3arm	1	0	0.26	2	7	4	na	na

		reads	miRBase family seed
seed	----------------------------------------UGGCUCA-----------------	4	novel
seed	---------------------------------------AUGGCUC------------------	2	novel
seed	---------------------------------------------CACCAUC------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T5S2
	--------------------------------------------TCACCATCTCTGTGCCACAG	20	-	1	-	-
	---------------------------------------ATGGCTCACCATCTCTGTG------	19	-	-	-	1
	--------------------------------------CATGGCTCACCATCTCTGT-------	19	-	-	1	-
	---------------------------------------ATGGCTCACCATCTCTGTGCC----	21	1	-	-	-
	---------------------------------------ATGGCTCACCATCTCTGTGC-----	20	-	-	1	-
	--------------------------------------CATGGCTCACCATCTCTGTGCC----	22	-	1	-	-
	---------------------------------------ATGGCTCACCATCTCTGTGCCAC--	23	-	-	-	1
rat	actggggccagagtgggttccaggacggagcagcgtgtCATGGCTCACCATCTCTGTGCCACAG
	****************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>	ENSRNOT00000002044 ENSRNOG00000001494 Napa
rat	.(((.(((((((((((...(((.((((........)))).)))....))).))))).))).)))	0.650 -26.40

rat

chromosome:1:76456489:76456552:1

novel_shortStem_loopOverlap_mirtron (2 loci)

block74302 [novel_shortStem_loopOverlap_mirtron]

Hairpin parameters
miRNA	randfold	RNA	rep	GC min/max	len min/max/mir_range	5'var	3'var	reads	reads edited	libs	libs edited	base distance	loop distance	position	locations	exon distance	unpaired	max bulge	total reads	total libs	dicer	drosha
no	0.031	no	no	0.58/0.58	24/24/1.00	0.0	0.0	1	0	1	0	4	-3	3arm_loop	1	0	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------AAGCCUU--------------------	1	novel
		len	cloning frequencies
			T3S1
	-------------------------------CAAGCCTTGTGGTCTCCCTTGCAG----	24	1
rat	aggtctaattgagggagccttgttgggtgttCAAGCCTTGTGGTCTCCCTTGCAGcctg
	***********************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>	ENSRNOT00000008679 ENSRNOG00000006612 Map2k3
rat	(((.((...((((((((((.....((((......))))...)).)))))))).))))).	1.000 -21.00