miR-Intess: classification

other hairpins

novel_loopOverlap_randfoldOK_bulgeHIGH (48 loci)

block2330848 [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	0.008	no	no	0.52/0.52	23/23/1.00	0.0	0.0	1	0	1	0	19	-4	3arm_loop	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------UCCCGGU----------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------------------------------------------CTCCCGGTTTCAGTTACAGGTTC-------------------	23	1
rat	tccagccaagttgggtctgcctgaaccctgtaactcattttgtttCTCCCGGTTTCAGTTACAGGTTCagatcttttcctggtggac
	***************************************************************************************
rat	((((.(((....(((((....((((.(((((((((....(((.......)))....)))))))))))))))))).....))))))).	0.880 -25.30

rat

chromosome:8:79444287:79444373:-1

intergenic

block2331473 [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	0.001	no	no	0.46/0.48	21/24/1.00	0.0	1.5	2	0	1	0	26	-1	5arm_loop	1	nd	0.24	4	2	1	na	na

		reads	miRBase family seed
seed	---------------------------GGGAGUU---------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S2
	--------------------------TGGGAGTTGGGGGGTTTTTTTGTT-----------------------------------------------------------	24	1
	--------------------------TGGGAGTTGGGGGGTTTTTTT--------------------------------------------------------------	21	1
rat	tgttaccagtttgggatgaattcttcTGGGAGTTGGGGGGTTTTTTTGTTtgtttttgttttttgctttttaaatccagcccagctcctgggtcctcctctggctgcag
	*************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000013053 ENSRNOG00000009381 Mapk6
rat	(((..((((...((((.((.....((..(((((((((((((((....((...............)).....))))))..)))))))))..)))).))))))))..))).	0.990 -36.46

rat

chromosome:8:80229239:80229347:-1

Same_strand|Intronic_non-coding|ENSRNOT00000013053|ENSRNOG00000009381 ## Same_strand|Boundary_non-coding|ENSRNOT00000033049|ENSRNOG00000009381 ## ENSRNOG00000009381|protein_coding|Mapk6|Mitogen-activated protein kinase 6 (EC 2.7.11.24) (Extracellular signal-regulated kinase 3) (ERK-3) (p55-MAPK). [Source:UniProtKB/Swiss-Prot;Acc:P27704] ## {Repeats: dust 80229298 80229307 0 class=dust}

block2376706 [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	0.002	no	no	0.42/0.42	24/24/1.00	0.0	0.0	1	0	1	0	14	-1	5arm_loop	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	---------------ACUCUUU----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--------------AACTCTTTCTCCTATTGCGATGAC------------------------------------------------------------	24	1
rat	cttaggttaaaaccAACTCTTTCTCCTATTGCGATGACatgtaattaactcatccaataggtcagcttagagtccagcttctggtttacctcttaagc
	**************************************************************************************************
rat	((((((...(((((((((((....(((((((.(((((............)))))))))))).......)))))........))))))....)))))).	0.800 -25.60

rat

chromosome:8:11043753:11043850:1

intergenic

block2465733 [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	0.010	no	no	0.15/0.15	20/20/1.00	0.0	0.0	1	0	1	0	14	-4	5arm_loop_3arm	2	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	---------------AUUUUGU--------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	--------------TATTTTGTTTTCTTTTTAAG--------------------------	20	1
rat	cgcttttatattttTATTTTGTTTTCTTTTTAAGagagggaaagaatatgaattggaagt
	************************************************************
rat	.(((((((....(((((.((.(((((((((....))))))))).)).))))).)))))))	1.000 -13.00

rat

chromosome:9:540823:540882:-1

intergenic ## {Repeats: dust 540851 540869 0 class=dust}

block2564108 [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	0.008	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	12	-3	5arm_loop	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-------------CUGAUGU----------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------ACTGATGTACTTCTGCCTGG----------------------------------	20	1
rat	gcattgtcccagACTGATGTACTTCTGCCTGGctggaagggaagctgacatcggagctgggaggca
	******************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000061714 ENSRNOG00000023351 Daam2
rat	((....((((((.(((((((.(((((.((.....))...)))))...)))))))..)))))).)).	1.000 -27.70

rat

chromosome:9:6684269:6684334:1

block2607725 [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	0.010	no	no	0.25/0.25	20/20/1.00	0.0	0.0	1	0	1	0	22	-3	3arm_loop	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------AAACUAC----------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-----------------------------------------------------TAAACTACAGTAGTAATAAC----------------------	20	1
rat	ctcaaacatccatcccaaaatgtgtgcctgtgcattttattactgtacagtaaTAAACTACAGTAGTAATAACtacagtgccccattgtttcagc
	***********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040778 ENSRNOG00000024345 LOC301455
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000038688 ENSRNOG00000024345 LOC301455
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000039122 ENSRNOG00000024345 LOC301455
rat	..................((((...(((((((....((((((((((..(((.....)))))))))))))....))))).))..))))........	0.440 -19.10

rat

chromosome:9:61004354:61004448:1

Same_strand|Intronic_coding|ENSRNOT00000040778|ENSRNOG00000024345 ## ENSRNOG00000024345|protein_coding|LOC301455| ## {Repeats: trf 7 27 0 class=trf}

novel_lenNOK_gcHIGH_shortStem (46 loci)

block50633 [novel_lenNOK_gcHIGH_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	0.016	no	no	1.00/1.00	19/19/0.00	0.0	0.0	1	0	1	0	3	15	3arm	1	nd	0.21	1	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------CGGCGGC--------------	1	novel
		len	cloning frequencies
			T1S1
	------------------------------------------------------GCGGCGGCGGCGGCCGCCG---	19	1
rat	gggggaggccgcggctcggcgcagcctgagtcattaggggagggggaggaggcgGCGGCGGCGGCGGCCGCCGcca
	****************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000050223 ENSRNOG00000006532 H3f3b
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...............................................	ENSRNOT00000009733 ENSRNOG00000006600 NP_001101776.1
rat	((.((.((((((.((.((.(((.((((...((.((....))...))...)))).))).)))).)))))).)).)).	1.000 -43.20

rat

chromosome:10:106132112:106132187:-1

Same_strand|Intronic_non-coding|ENSRNOT00000050223|ENSRNOG00000006532 ## ENSRNOG00000006532|protein_coding|H3f3b|H3 histone, family 3B (H3f3b), mRNA [Source:RefSeq_dna;Acc:NM_053985] ## {Repeats: GC_rich 3 22 -1 class=Low_complexity,GC_rich 1 25 -1 class=Low_complexity}

block52237 [novel_lenNOK_gcHIGH_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	0.637	no	no	0.94/0.94	18/18/0.00	0.0	0.0	1	0	1	0	2	24	5arm	1	nd	0.17	1	1	1	na	na

		reads	miRBase family seed
seed	---CCCGCGC---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	--CCCCGCGCCGCCGCCCAC-----------------------------------------------------------------------------	18	1
rat	cgCCCCGCGCCGCCGCCCACgccccgcacttggccgcctccgcgccgccgctggtggccccgcggctctccacgcgtcatggcgcccgggctggggt
	*************************************************************************************************
rat	.(((((((.(((.((((.((((.((((....(((((((...(((....))).)))))))..))))........))))...))))..))))).)))))	0.770 -47.40

rat

chromosome:10:108574893:108574989:-1

intergenic ## {Repeats: GC_rich 8 26 -1 class=Low_complexity,trf 2 20 0 class=trf,GC_rich 1 66 -1 class=Low_complexity,dust 108574970 108574988 0 class=dust} ## {SimpF: oe = 0.84 -1 CpG}

block167674 [novel_lenNOK_gcHIGH_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	0.607	no	no	0.94/0.94	18/18/0.00	0.0	0.0	1	0	1	0	4	8	5arm	1	nd	0.22	3	1	1	na	na

		reads	miRBase family seed
seed	-----CCUCCCG------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	----CCCTCCCGGGCCCCGGCC--------------------------------------------	18	1
rat	cccgCCCTCCCGGGCCCCGGCCtgccaggccgagcgtttaccgcgggctggcgccgaggcgcgcgg
	******************************************************************
	----------------------------------------------------------------------------	ENSRNOT00000002435 ENSRNOG00000001789 Zfp148
	----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000039996 ENSRNOG00000001789 Zfp148
rat	(((((((((...(((.(((((((((.((((.....))))...))))))))).))))))).))).))	0.600 -34.80

rat

chromosome:11:69207175:69207240:1

Opposite_strand|Intronic_non-coding|ENSRNOT00000039996|ENSRNOG00000001789 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000002436|ENSRNOG00000001789 ## ENSRNOG00000001789|protein_coding|Zfp148|Zinc finger protein 148 (Zinc finger DNA-binding protein 89) (Transcription factor ZBP-89). [Source:UniProtKB/Swiss-Prot;Acc:Q62806] ## {Repeats: dust 69207139 69207153 0 class=dust,C-rich 165 163 1 class=Low_complexity,C-rich 2 163 1 class=Low_complexity} ## {SimpF: -1 Eponine}

block197621 [novel_lenNOK_gcHIGH_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	0.629	no	no	0.94/0.94	18/18/0.00	0.0	0.0	1	0	1	0	3	13	5arm	3	nd	0.06	1	1	1	na	na

		reads	miRBase family seed
seed	----CCGCGGC------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	---GCCGCGGCCGCCGCCTCC--------------------------------------------------------------	18	1
rat	gccGCCGCGGCCGCCGCCTCCcgcctccccggctcttcggctcggggcggggaagagaacgtgacgcgccgccgccgcggggc
	***********************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000057775 ENSRNOG00000037978
	<<<<<<<<<<<<<<<<<<<<.........................................................................	ENSRNOT00000001683 ENSRNOG00000001247 Rsn
rat	(((.(((((((.((((((((((.((.((((((((....))).))))).))))..)))........)))..)).))))))))))	0.540 -45.30

rat

chromosome:12:34049705:34049787:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000001683|ENSRNOG00000001247 ## Same_strand|Boundary_non-coding|ENSRNOT00000001672|ENSRNOG00000037978 ## Same_strand|Intronic_coding|ENSRNOT00000057775|ENSRNOG00000037978 ## ENSRNOG00000001247|protein_coding|Rsn|restin [Source:RefSeq_peptide;Acc:NP_113933] ## ENSRNOG00000037978|protein_coding|| ## {SimpF: oe = 0.95 -1 CpG}

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miR-Intess™