miR-Intess: classification

other hairpins

novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_bulgeHIGH (48 loci)

block2151141 [novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_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	0.076	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	34	-4	5arm_loop	1	1	0.32	5	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------UAGGCCG------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------------GTAGGCCGTGTCTCCTGAA-------------------------------------------------------------	19	1
rat	gctctatgtgtaccgcctgaaccgcgacgctgagGTAGGCCGTGTCTCCTGAAcggagatgcccaggccgtaccgtagtcacctcggcaggttccccagtgcagaaactgagcc
	******************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042595 ENSRNOG00000030705 Cpsf1
rat	((((....(((((.....(((((.....((((((((.((((((((((((.....))))))))...))))...........)))))))).)))))....)))))......)))).	0.560 -44.00

rat

chromosome:7:114658212:114658325:-1

block2256544 [novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_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	0.061	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	44	-2	3arm_loop	1	2	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------CAUUCUA------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------------------------TCATTCTATCTCCGATTT--------------------------------------------	18	1
rat	gctacaaggcctgctttggtttgaggagtggtagctgtccctgtcttttatagagttgTCATTCTATCTCCGATTTagctacaaaggcatttaccgggagctggagcagagcatcaaagc
	************************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000013398 ENSRNOG00000009756 Pacsin2
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000013428 ENSRNOG00000009756 Pacsin2
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000042978 ENSRNOG00000009756 Pacsin2
rat	(((.....((((((((..((((..(((((((((((((.....(((....(((((((....)))))))....))).))))))).....))))..))..))))..)))))).)).....)))	0.780 -37.20

rat

chromosome:7:121536706:121536825:1

Same_strand|Intronic_coding|ENSRNOT00000013428|ENSRNOG00000009756 ## ENSRNOG00000009756|protein_coding|Pacsin2|Protein kinase C and casein kinase substrate in neurons 2 protein (Synaptic dynamin-associated protein II) (Syndapin 2) (Syndapin-II) (SdpII). [Source:UniProtKB/Swiss-Prot;Acc:Q9QY17]

block2260284 [novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_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	0.551	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	19	-3	3arm_loop	1	2	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------UGUUCAG------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--------------------------------------------TTGTTCAGTGTTCTCCCCC-------------------	19	1
rat	tcagaggccctgatggaggcagactgagagctaatgaaggcccgTTGTTCAGTGTTCTCCCCCagtgtgtatacatcctgat
	**********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000048501 ENSRNOG00000033627 Panx2
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000043461 ENSRNOG00000029698
rat	((((.......((((...(((.(((((((((...((((.........))))..))))))....))).)))...)))))))).	0.470 -20.41

rat

chromosome:7:127170502:127170583:1

Same_strand|Intronic_coding|ENSRNOT00000043461|ENSRNOG00000029698 ## Same_strand|Intronic_non-coding|ENSRNOT00000048501|ENSRNOG00000033627 ## Same_strand|Boundary_non-coding|ENSRNOT00000046957|ENSRNOG00000033627 ## ENSRNOG00000033627|protein_coding|Panx2|Pannexin-2. [Source:UniProtKB/Swiss-Prot;Acc:P60571] ## ENSRNOG00000029698|protein_coding||

block2464053 [novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_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	0.525	no	no	0.61/0.63	18/19/0.00	0.0	0.4	9	0	8	0	16	-5	5arm_loop	1	3	0.39	5	9	8	na	na

		reads	miRBase family seed
seed	-----------------AGGGUGA----------------------------------------------	9	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T3S1	T3S2	T4S2	T5S1	T5S2
	----------------AAGGGTGAGGACTGTGGG------------------------------------	18	1	-	-	1	1	-	1	1
	----------------AAGGGTGAGGACTGTGGGG-----------------------------------	19	1	1	1	-	-	1	-	-
rat	ccaggagaaagcattcAAGGGTGAGGACTGTGGGGaggtgcttagttatcattcaagcctgcttgtactg
	**********************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043784 ENSRNOG00000004104
rat	.(((....(((((.....((((((.(((((............))))).)))))).....)))))...)))	0.970 -15.80

rat

chromosome:8:127654090:127654159:1

Same_strand|Boundary_coding|ENSRNOT00000043784|ENSRNOG00000004104 ## ENSRNOG00000004104|protein_coding||

block2523213 [novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_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	0.176	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	40	-4	3arm_loop	1	4	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------CCUGGAC---------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	-------------------------------------------------------------ACCTGGACCCATTGTCTAC----------------------------------------	19	1
rat	ctattaggaacttgcgcctgactaactgggtattagagacggggttggattcctggttctgACCTGGACCCATTGTCTACccagtctctctagaaacctgagtgtgagccgagccatgga
	************************************************************************************************************************
	......................................................................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000035277 ENSRNOG00000014182 Tns
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000019092 ENSRNOG00000014182 Tns
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057515 ENSRNOG00000037862
rat	((((..((......((.((.((..(((((((.((((((((.(((.(((((....(((((......)))))....)))))))).))))))...)).)))).))))).)).))..)))))).	0.920 -36.40

rat

chromosome:9:73315361:73315480:-1

Same_strand|Boundary_non-coding|ENSRNOT00000035277|ENSRNOG00000014182 ## Same_strand|Intronic_coding|ENSRNOT00000057515|ENSRNOG00000037862 ## ENSRNOG00000014182|protein_coding|Tns|Tensin (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q62783] ## ENSRNOG00000037862|protein_coding||

block2538226 [novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_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	0.626	no	no	0.50/0.50	18/18/0.00	0.0	0.0	2	0	1	0	26	-4	3arm_loop	1	1	0.44	4	2	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------AGGGAGG------------------------------------	2	novel
		len	cloning frequencies
			T1S2
	-----------------------------------------------------AAGGGAGGGTTTTGAAGG--------------------------	18	2
rat	tcctttcctattgtggcccctaaacagccctcaacaggaagtgaagtgaagagAAGGGAGGGTTTTGAAGGactgccactgtcaggtgctcaagggc
	*************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056696 ENSRNOG00000019887 NP_001102833.1
	-----------------------------------------------------------------------------------------------------------	ENSRNOT00000038536 ENSRNOG00000024878 RGD1566074_predicted
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056678 ENSRNOG00000037445
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056677 ENSRNOG00000037445
rat	(((((.(((((.(((((.(((....(((((((.........................)))))))....)))...))))).)).))).....))))).	0.960 -25.11

rat

chromosome:9:90390938:90391034:-1

Same_strand|Boundary_non-coding|ENSRNOT00000026918|ENSRNOG00000019887 ## Same_strand|Intronic_coding|ENSRNOT00000056678|ENSRNOG00000037445 ## Same_strand|Boundary_coding|ENSRNOT00000056696|ENSRNOG00000019887 ## Opposite_strand|Intronic_coding|ENSRNOT00000038536|ENSRNOG00000024878 ## ENSRNOG00000019887|protein_coding|NP_001102833.1|similar to RAB17, member RAS oncogene family (predicted) (RGD1562478_predicted), mRNA [Source:RefSeq_dna;Acc:NM_001109363] ## ENSRNOG00000024878|protein_coding|RGD1566074_predicted| ## ENSRNOG00000037445|protein_coding||

block2957564 [novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_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	0.209	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	19	-3	5arm_loop	1	3	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------CCUUGUU----------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-------------------TCCTTGTTTCCACAGGAA------------------------------------	18	1
rat	gccgacatttatgcctctgTCCTTGTTTCCACAGGAAcctgtagacttggctgggcctattactgtgctggtg
	*************************************************************************
	+++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000030400 ENSRNOG00000027601 Lhfpl1
rat	((((.(((.((.((((..(((...((((..((((....))))))))..))).)))).)).....))).)))).	1.000 -19.10

rat

chromosome:X:33220620:33220692:1

block3017312 [novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_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	0.206	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	20	-2	5arm_loop	1	4	0.61	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------CCGACCU------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	--------------------GCCGACCTTGTGCACTAA--------------------------------------	18	1
rat	agtatccatggagaaaggtaGCCGACCTTGTGCACTAAggaaagaggccatgagctgctatctgcctcagtttact
	****************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000048521 ENSRNOG00000033316 NP_001100413.1
	++++++++++++++++++>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040296 ENSRNOG00000033316 NP_001100413.1
rat	((((......(((..(((((((....((..((..((........))..))..))..)))))))..)))....))))	0.610 -18.80

rat

chromosome:X:89333527:89333602:1

novel_loopOverlap_randfoldOK_bulgeHIGH (48 loci)

block28108 [novel_loopOverlap_randfoldOK_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	0.006	no	no	0.62/0.62	24/24/1.00	0.0	0.0	1	0	1	0	16	-4	5arm_loop	1	nd	0.29	5	1	1	na	na

		reads	miRBase family seed
seed	-----------------GUUCCCA--------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	----------------AGTTCCCAGCACCCAGCTCCAGTG----------------------------------------	24	1
rat	cagatttctccctggaAGTTCCCAGCACCCAGCTCCAGTGcccaggagcatctgggtctgggacaaataggctaacctgg
	********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004143 ENSRNOG00000003096 Hic1
rat	(((.((....((((...((.(((((.((((((((((........)))))...))))))))))))...))))..)).))).	0.710 -31.60

rat

chromosome:10:62474419:62474498:-1

block207302 [novel_loopOverlap_randfoldOK_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	0.005	no	no	0.64/0.64	22/22/1.00	0.0	0.0	1	0	1	0	13	-2	3arm_loop	1	nd	0.23	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------UCCCAAG---------------------------	1	novel
		len	cloning frequencies
			T3S1
	-----------------------------------------------TTCCCAAGCCTTCCTCCCTCCC-------------	22	1
rat	taaggtctgtttcctgacagtgggcctgaagggaaggctctgggatcTTCCCAAGCCTTCCTCCCTCCCaacgcagacagtg
	**********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000001446 ENSRNOG00000001090 NP_001102530.1
rat	....((((((..........((((......(((((((((.((((.....)))))))))))))....))))..))))))....	0.860 -33.40