miR-Intess: classification

other hairpins

novel_lenNOK_gcHIGH_multiarm_DicerNOK_loopOverlap_bulgeHIGH (1 loci)

novel_lenNOK_gcHIGH_multiarm_DicerNOK_loopOverlap_randfoldOK (1 loci)

sblock6032 [novel_lenNOK_gcHIGH_multiarm_DicerNOK_loopOverlap_randfoldOK]

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	0.001	no	no	0.83/0.95	18/23/0.33	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	32 6 3	-5 -1 7	5arm_loop 3arm 3arm	1 1 1	nd nd nd	0.58 0.30 0.33	6 3 3	3	3	0	8

		reads	miRBase family seed
seed	---------------------------------CGCCCGC----------------------------------------	1	novel
seed	----------------------------------------------------GUCCCCG---------------------	1	novel
seed	------------------------------------------------------------AGCCGGC-------------	1	novel
		len	cloning frequencies
			T1S1	T3S2	T4S2
	--------------------------------CCGCCCGCGCAGGCCCCGC-----------------------------	19	-	1	-
	-----------------------------------------------------------CAGCCGGCCGCCGAGCGC---	18	-	-	1
	---------------------------------------------------AGTCCCCGCAGCCGGCCGCCGAG------	23	1	-	-
rat	nnnnnnnnnnnnnnnnnnncagtcgccggccgCCGCCCGCGCAGGCCCCGCAGTCCCCGCAGCCGGCCGCCGAGCGCact
	********************************************************************************
rat	....................((((((((((.((((...(((..(((......)))..)))...)))).)))).))).)))	1.000 -28.20

rat

chromosome:2:54327323:54327402:-1

intergenic ## {Repeats: GC_rich 1 20 -1 class=Low_complexity,GC_rich 1 28 -1 class=Low_complexity} ## {SimpF: oe = 0.91 0 CpG}

novel_lenNOK_gcHIGH_multiarm_DicerNOK_mirtron (1 loci)

sblock4285 [novel_lenNOK_gcHIGH_multiarm_DicerNOK_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	0.162	no	no	0.67/0.95	18/19/0.00	0.0 0.3	0.0 1.0	1 3	0 0	1 2	0 0	12 18	4 3	5arm 3arm	1 1	35 4	0.16 0.26	2 2	4	3	-2	-4

		reads	miRBase family seed
seed	-------------------------------------------UGACCGC------------------------------	2	novel
seed	-------------GGUGGGC------------------------------------------------------------	1	novel
seed	--------------------------------------------GACCGCA-----------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1	T4S1
	-------------------------------------------TGACCGCACCGTCTGTCCC------------------	19	1	-	-
	------------GGGTGGGCGGCGGGCGGGC-------------------------------------------------	19	-	-	1
	------------------------------------------CTGACCGCACCGTCTGTCC-------------------	19	1	-	-
	------------------------------------------CTGACCGCACCGTCTGTC--------------------	18	-	1	-
rat	ttgtgccagggtGGGTGGGCGGCGGGCGGGCgcagggggctgCTGACCGCACCGTCTGTCCCgcagaggccgagcacggc
	********************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>	ENSRNOT00000020247 ENSRNOG00000015033 Mxd4
rat	.(((((..((....(((((((((((((((..((((....))))...)))).))).))).))))).....))..)))))..	1.000 -40.60

rat

chromosome:14:82253576:82253655:1

Same_strand|Intronic_coding|ENSRNOT00000020247|ENSRNOG00000015033 ## ENSRNOG00000015033|protein_coding|Mxd4|Max dimerization protein 4 Gene [Source:MGI (curated);Acc:Mxd4-002] ## {SimpF: oe = 0.81 1 CpG}

novel_lenNOK_gcHIGH_multiarm_DicerNOK_nonpairedHIGH (1 loci)

sblock7528 [novel_lenNOK_gcHIGH_multiarm_DicerNOK_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	0.798	no	no	0.83/0.94	18/23/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	25 25	12 0	5arm 3arm	1 1	22 15	0.33 0.35	3 7	2	2	-9	-8

		reads	miRBase family seed
seed	--------------------------GCCGGGA-------------------------------------------------------------------------	1	novel
seed	-----------------------------------------------------------CCGCGGC----------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T3S2
	----------------------------------------------------------CCCGCGGCCCTCGCTGAGCCCCT-------------------------	23	-	1
	-------------------------GGCCGGGAGCGGGCCCCG---------------------------------------------------------------	18	1	-
rat	ccgggtgagagagaccggcgggccgGGCCGGGAGCGGGCCCCGggcctcggcgggcgcCCCGCGGCCCTCGCTGAGCCCCTtctttgcctcggcagctggtactgg
	**********************************************************************************************************
	>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>	ENSRNOT00000013584 ENSRNOG00000009723 PTPM1_RAT
rat	((((.........((((((..(((((((..((((.((((...(((((...(((((...)))))))))).......)))).))))..))).)))).)))))).))))	0.670 -56.10

rat

chromosome:3:75279001:75279106:-1

Same_strand|Intronic_coding|ENSRNOT00000013584|ENSRNOG00000009723 ## ENSRNOG00000009723|protein_coding|PTPM1_RAT|Protein-tyrosine phosphatase mitochondrial 1, mitochondrial precursor (EC 3.1.3.48) (EC 3.1.3.16). [Source:UniProtKB/Swiss-Prot;Acc:P0C089] ## {Repeats: GC_rich 1 11 -1 class=Low_complexity,GC_rich 1 54 -1 class=Low_complexity,dust 75279064 75279082 0 class=dust,GC_rich 26 44 -1 class=Low_complexity,dust 75279041 75279049 0 class=dust}

novel_lenNOK_gcHIGH_multiarm_DicerNOK_shortStem (1 loci)

sblock12178 [novel_lenNOK_gcHIGH_multiarm_DicerNOK_shortStem]

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	0.698	no	no	0.89/0.95	18/20/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	0 4	14 10	5arm 3arm	1 1	nd nd	0.25 0.22	2 2	2	2	-3	-4

		reads	miRBase family seed
seed	-CCGCAGC--------------------------------------------------------------	1	novel
seed	-------------------------------------------------GGGCGCC--------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	------------------------------------------------AGGGCGCCCGCCCGGGTG----	18	1	-
	GCCGCAGCCGCCCGGCGCGC--------------------------------------------------	20	-	1
rat	GCCGCAGCCGCCCGGCGCGCcccagccccgcgccctggggaggaagggAGGGCGCCCGCCCGGGTGgggt
	**********************************************************************
rat	(((.((.(((..(((.((((((...(((....((....)).....))).)))))))))..))).)).)))	0.980 -39.60

rat

chromosome:9:8719604:8719673:-1

intergenic ## {Repeats: GC_rich 16 36 -1 class=Low_complexity,GC_rich 1 38 -1 class=Low_complexity} ## {SimpF: oe = 0.78 1 CpG}

novel_lenNOK_gcHIGH_multiarm_DicerOK_loopOverlap (1 loci)

sblock634 [novel_lenNOK_gcHIGH_multiarm_DicerOK_loopOverlap]

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	0.133	no	no	0.83/0.95	18/19/0.00	0.0 0.0	0.0 0.0	1 2	0 0	1 1	0 0	8 7	-1 0	5arm_loop 3arm	2 2	nd nd	0.33 0.26	2 2	3	2	1	1

		reads	miRBase family seed
seed	----------------------------------CCGGGGG------------------	2	novel
seed	---------GGGCGGG-------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2
	---------------------------------CCCGGGGGCCGGGCCACCG-------	19	2	-
	--------GGGGCGGGGGTTTGGGGG---------------------------------	18	-	1
rat	ggtgagtcGGGGCGGGGGTTTGGGGGttcgggaCCCGGGGGCCGGGCCACCGgagtgcc
	***********************************************************
	---------------------------------------------------------------------	ENSRNOT00000016376 ENSRNOG00000011945 NP_001100987.1
rat	((((..(((((((..((.(((.(((........))).))).))..))).))))..))))	1.000 -27.50

rat

chromosome:1:107246358:107246416:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000016376|ENSRNOG00000011945 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000016256|ENSRNOG00000011945 ## ENSRNOG00000011945|protein_coding|NP_001100987.1|cytoplasmic FMR1 interacting protein 1 [Source:RefSeq_peptide;Acc:NP_001100987] ## {Repeats: dust 107246370 107246384 0 class=dust,dust 107246391 107246409 0 class=dust}

novel_lenNOK_gcHIGH_multiarm_Multihit (1 loci)

sblock2086 [novel_lenNOK_gcHIGH_multiarm_Multihit]

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	no	0.59/0.95	19/22/0.25	0.0 0.0 0.0	0.0 0.0 0.0	2 1 1	0 0 0	1 1 1	0 0 0	0 26 1	27 4 26	5arm 3arm 3arm	1 12 12	nd nd nd	0.26 0.26 0.32	3 3 3	4	2	na	na

		reads	miRBase family seed
seed	-UCGUCUG------------------------------------------------------------------------------------------	2	novel
seed	------------------------------------------------------CGGGCAG-------------------------------------	1	novel
seed	----------------------------------------------------------------------------CCGAGGU---------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	CTCGTCTGGGCTCATCTGC-------------------------------------------------------------------------------	19	-	2
	-----------------------------------------------------GCGGGCAGGCGGGCGGGCG--------------------------	19	1	-
	---------------------------------------------------------------------------GCCGAGGTACGGTATCTCAGTC-	22	1	-
rat	CTCGTCTGGGCTCATCTGCcgccatcgggcctcccgcctcgcggggcgcccccGCGGGCAGGCGGGCGGGCGcggGCCGAGGTACGGTATCTCAGTCg
	**************************************************************************************************
rat	..((.(((((...((((((((((..((.((((((((((((((((((...)))))))...))))))).)))).)))))...)))).)))..))))).))	0.730 -53.80

rat

chromosome:1:185499663:185499760:1

intergenic ## {Repeats: GC_rich 14 33 1 class=Low_complexity,GC_rich 36 40 1 class=Low_complexity,GC_rich 1 40 1 class=Low_complexity} ## {SimpF: -1 Eponine}

novel_lenNOK_gcHIGH_multiarm_loopOverlap_bulgeHIGH (1 loci)

block39103 [novel_lenNOK_gcHIGH_multiarm_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	0.161	no	no	0.94/0.95	18/21/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	36 14	-16 -1	5arm_loop_3arm 3arm	1 1	nd nd	0.44 0.19	4 4	2	2	na	na

		reads	miRBase family seed
seed	-------------------------------------CCGCCGC--------------------------------	1	novel
seed	------------------------------------------GCCCCCC---------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1
	-----------------------------------------CGCCCCCCCCCCTCCCCCCCC--------------	21	1	-
	------------------------------------GCCGCCGCCCCCCCCCCT----------------------	18	-	1
rat	gatggagatgcggtgggacaaggagaggggaccctgGCCGCCGCCCCCCCCCCTCCCCCCCCgcacactagcattg
	****************************************************************************
rat	((((.((.(((((.(((....((.((((((.....(((....)))....))))))))))))))))..))..)))).	1.000 -32.30

rat

chromosome:10:84983369:84983444:-1

intergenic ## {Repeats: dust 84983383 84983401 0 class=dust,GC_rich 3 29 -1 class=Low_complexity,GC_rich 1 29 -1 class=Low_complexity}

novel_lenNOK_gcHIGH_multiarm_randfoldOK (1 loci)

sblock4085 [novel_lenNOK_gcHIGH_multiarm_randfoldOK]

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	0.007	no	no	0.50/0.91	18/22/0.33	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	10 32 10	30 1 27	5arm 3arm 3arm	9 9 9	nd nd nd	0.50 0.18 0.33	5 2 3	3	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------CCAGAAC--------------------	1	novel
seed	-----------ACCCAAU------------------------------------------------------------------------------------------------------	1	novel
seed	-------------------------------------------------------------------GGAAGGG----------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1
	--------------------------------------------------------------------------------------------GCCAGAACCAGCCAAGGA----------	18	1	-
	----------TACCCAATGGGCTCACTT--------------------------------------------------------------------------------------------	18	1	-
	------------------------------------------------------------------GGGAAGGGGGGCGGGGGGGGGG--------------------------------	22	-	1
rat	tcccttccccTACCCAATGGGCTCACTTtgcattgcctccttctgccactgctttcccaggacaggGGGAAGGGGGGCGGGGGGGGGGcaggGCCAGAACCAGCCAAGGAgggacgaggg
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000045975 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000059076 ENSRNOG00000032207 LOC690700
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000041734 ENSRNOG00000032207 LOC690700
rat	.(((((.((((.((.....((((...(((((.((((((((..(((((.((.(((((((.......))))))).)))))))..))))).))).)).)))...))))..))))))..)))))	0.990 -60.30

rat

chromosome:14:49591024:49591143:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000050021|ENSRNOG00000032207 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000043791|ENSRNOG00000032207 ## Opposite_strand|Intronic_coding|ENSRNOT00000045975|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7] ## {Repeats: dust 49591056 49591078 0 class=dust}

novel_lenNOK_gcHIGH_shortStem_loopOverlap_bulgeHIGH (1 loci)

block469254 [novel_lenNOK_gcHIGH_shortStem_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	0.327	no	no	1.00/1.00	18/18/0.00	0.0	0.0	1	0	1	0	0	-1	3arm	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------CCGGCGC----------	1	novel
		len	cloning frequencies
			T1S2
	--------------------------CCCGGCGCGGGGGGGGGG	18	1
rat	accccatactcccaatctcatggtagCCCGGCGCGGGGGGGGGG
	********************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000034723 ENSRNOG00000011511 RGD1561742_predicted
rat	.((((...(((((.......(((....)))....))))).))))	0.460 -16.50

rat

chromosome:15:106285263:106285306:-1

novel_lenNOK_gcHIGH_shortStem_mirtron_bulgeHIGH (1 loci)

block836193 [novel_lenNOK_gcHIGH_shortStem_mirtron_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	0.662	no	no	1.00/1.00	19/19/0.00	0.0	0.0	1	0	1	0	1	28	3arm	1	2	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------CCGCCGC------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------------------------------------------GCCGCCGCCGCCGGGGGGG-	19	1
rat	gtcccatattgaactcgagttggaagaggcgagtccggtctcaaaatggaggtaaaaccgccgccaggtcgcccccagcctgactccggccgtcGCCGCCGCCGCCGGGGGGGa
	******************************************************************************************************************
	..................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++>>>>	ENSRNOT00000021852 ENSRNOG00000039654 RGD1561108_predicted
rat	.((((........((((.((.((....(((((..((((..(((...(((.(((...(((.......))).))).)))...)))..))))...)))))....)))))))).))))	0.660 -41.80

rat

chromosome:1:33798691:33798804:-1

Same_strand|Boundary_coding|ENSRNOT00000021852|ENSRNOG00000039654 ## ENSRNOG00000039654|protein_coding|RGD1561108_predicted|Heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3). [Source:UniProtKB/Swiss-Prot;Acc:Q6URK4] ## {Repeats: GC_rich 1 20 -1 class=Low_complexity,GC_rich 1 28 -1 class=Low_complexity}

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miR-Intess™