miR-Intess: classification

other hairpins

novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH (9 loci)

block276351 [novel_lenNOK_cloningOK_shortStem_randfoldOK_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	0.005	no	no	0.56/0.58	18/19/0.00	0.0	0.0	15	0	8	0	2	21	3arm	1	nd	0.33	4	20	8	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------GGCCACA------------	20	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T3S2	T4S2	T5S1	T5S2
	---------------------------------------------------------------------TGGCCACATCCTACACTC--	18	3	5	4	-	1	1	1	3
	---------------------------------------------------------------------TGGCCACATCCTACACTCC-	19	1	-	-	1	-	-	-	-
rat	ggacttttcaggagatgcactgccatccgggattgacgtttccaccatgtggaaaagccagtctttcccTGGCCACATCCTACACTCca
	*****************************************************************************************
rat	(((......((((..((....((((...((((..(((.(((((((...))))))).....)))..))))))))))..))))....))).	0.980 -29.70

rat

chromosome:13:90531520:90531608:-1

intergenic

block469550 [novel_lenNOK_cloningOK_shortStem_randfoldOK_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	0.002	no	no	0.39/0.45	18/20/0.14	0.0	0.3	10	0	2	0	1	6	5arm	1	nd	0.32	4	14	2	na	na

		reads	miRBase family seed
seed	--CCUUACA------------------------------------------------------------	14	novel
		len	cloning frequencies
			T4S1	T4S2
	-TCCTTACATTTCCCTACTG-------------------------------------------------	19	2	7
	-TCCTTACATTTCCCTACT--------------------------------------------------	18	-	3
	-TCCTTACATTTCCCTACTGG------------------------------------------------	20	1	1
rat	gTCCTTACATTTCCCTACTGggctgggccccctcctcaggaagtgtttttttttttttttttttggaca
	*********************************************************************
rat	((((..((((((((....((((..((....))..))))))))))))..................)))).	1.000 -18.85

rat

chromosome:15:106874295:106874363:-1

intergenic

block497098 [novel_lenNOK_cloningOK_shortStem_randfoldOK_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	0.004	no	no	0.39/0.42	18/19/0.00	0.0	0.0	7	0	5	0	1	20	5arm	1	nd	0.50	4	12	5	na	na

		reads	miRBase family seed
seed	--AAUGUUG--------------------------------------------------------------------------	12	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1	T4S2	T5S2
	-TAATGTTGAGAAGGGCTA----------------------------------------------------------------	18	7	1	-	1	1
	-TAATGTTGAGAAGGGCTAG---------------------------------------------------------------	19	1	-	1	-	-
rat	gTAATGTTGAGAAGGGCTAgaaactagggcttggggcccagttgggccagaagtccctgggggtgtgccttggagggcagaac
	***********************************************************************************
rat	((..((((....(((((......(((((((((..(((((....)))))..))).))))))......)))))....))))..))	0.990 -35.20

rat

chromosome:15:58765100:58765182:1

intergenic

block911789 [novel_lenNOK_cloningOK_shortStem_randfoldOK_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	0.002	no	no	0.53/0.56	18/19/0.00	0.0	0.0	8	0	5	0	4	13	5arm	2	nd	0.33	4	12	5	na	na

		reads	miRBase family seed
seed	-----AGCACCA------------------------------------------------------------	12	miR-29a/29b/29c
		len	cloning frequencies
			T1S2	T3S2	T4S1	T4S2	T5S1
	----TAGCACCAGAGTAGGCTG--------------------------------------------------	18	-	1	3	1	5
	----TAGCACCAGAGTAGGCTGA-------------------------------------------------	19	1	-	1	-	-
rat	gccaTAGCACCAGAGTAGGCTGagggcagaatggccctgctgcaactctgccagcctgctcaggcttcggct
	************************************************************************
rat	(((..(((....(((((((((...((((((...((......))...)))))))))))))))..)))..))).	0.590 -35.70

rat

chromosome:1:204423827:204423898:-1

intergenic

block1052280 [novel_lenNOK_cloningOK_shortStem_randfoldOK_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	0.004	no	no	0.28/0.28	18/18/0.00	0.0	0.0	11	0	8	0	1	33	5arm	1	nd	0.39	4	15	8	na	na

		reads	miRBase family seed
seed	--GGAAUAU------------------------------------------------------------------------------------------------	15	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S2	T4S1	T4S2	T5S2
	-TGGAATATGTTTGTAAAG--------------------------------------------------------------------------------------	18	4	3	2	2	1	1	1	1
rat	gTGGAATATGTTTGTAAAGagctcctcaggcctcactgactctctcgccatgccctcaaggtgaatgtagcctgaggtatcctctagagaaacaccttatccatt
	*********************************************************************************************************
rat	(((((...(((((....((((..((((((((..((.........(((((.((....)).))))).))..))))))))....))))....))))).....))))).	0.750 -30.40

rat

chromosome:1:257849363:257849467:1

intergenic

block2170444 [novel_lenNOK_cloningOK_shortStem_randfoldOK_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	0.004	no	no	0.56/0.56	18/18/0.00	0.0	0.0	6	0	5	0	2	17	5arm	1	nd	0.33	4	10	5	na	na

		reads	miRBase family seed
seed	---GCCCUGA-------------------------------------------------------------------	9	novel
seed	--AGCCCUG--------------------------------------------------------------------	1	miR-349
		len	cloning frequencies
			T2S2	T3S1	T4S1	T4S2	T5S1
	--AGCCCTGAAAATGGGCAG---------------------------------------------------------	18	1	1	4	1	2
	-CAGCCCTGAAAATGGGCA----------------------------------------------------------	18	-	-	-	-	1
rat	gcAGCCCTGAAAATGGGCAGcccttgcaaatgcaggcccacgcctgtggcttctgtccaacctttctcttctctgca
	*****************************************************************************
	---------------------------------------------------------------------------------------	ENSRNOT00000045515 ENSRNOG00000032075 Kcnh3
rat	((((....((((.(((((((.....((....((((((....)))))).))..)))))))...))))......)))).	0.910 -26.40

rat

chromosome:7:137992146:137992222:-1

Opposite_strand|Intronic_coding|ENSRNOT00000045515|ENSRNOG00000032075 ## ENSRNOG00000032075|protein_coding|Kcnh3|Potassium voltage-gated channel subfamily H member 3 (Voltage-gated potassium channel subunit Kv12.2) (Ether-a-go-go-like potassium channel 2) (ELK channel 2) (rElk2) (Brain-specific eag-like channel 1) (BEC1). [Source:UniProtKB/Swiss-Prot;Acc:O89047]

block2221219 [novel_lenNOK_cloningOK_shortStem_randfoldOK_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	0.008	no	no	0.42/0.56	18/23/0.30	0.4	2.2	10	0	6	0	3	1	3arm	2	nd	0.50	4	10	6	na	na

		reads	miRBase family seed
seed	-------------------------------------CAAGGCG------------------	7	novel
seed	--------------------------------------AAGGCGG-----------------	2	novel
seed	---------------------------------------AGGCGGG----------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T4S1	T4S2
	------------------------------------CCAAGGCGGGGGAAAAAA--------	18	1	2	1	-	-	-
	------------------------------------CCAAGGCGGGGGAAAAAAAAAAA---	23	-	-	2	1	-	-
	-------------------------------------CAAGGCGGGGGAAAAAAAA------	19	-	-	-	-	1	1
	--------------------------------------AAGGCGGGGGAAAAAAAAA-----	19	-	-	-	-	-	1
rat	atgtgacccacatttccacagccagaagggaaaaacCCAAGGCGGGGGAAAAAAAAAAAgca
	**************************************************************
rat	.(((........(((((...(((....(((.....)))..)))...)))))........)))	0.420 -14.59

rat

chromosome:7:66345884:66345945:1

intergenic ## {Repeats: dust 66345932 66345942 0 class=dust}

block2511356 [novel_lenNOK_cloningOK_shortStem_randfoldOK_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	0.008	no	no	0.67/0.67	18/18/0.00	0.0	0.0	14	0	6	0	4	5	3arm	2	nd	0.33	4	15	6	na	na

		reads	miRBase family seed
seed	-------------------------------------CCCCCAA--------------	15	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T3S1	T3S2	T4S2
	------------------------------------TCCCCCAACCCCCAAAGG----	18	6	2	1	2	2	2
rat	ctgccatttggaaactgggtctggtgctaaaactctTCCCCCAACCCCCAAAGGcagc
	**********************************************************
rat	(((((.(((((....((((...(((......))).....))))....)))))))))).	1.000 -18.80

rat

chromosome:9:58019907:58019964:-1

intergenic

novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH_bulgeHIGH (9 loci)

block82226 [novel_lenNOK_mirtron_randfoldOK_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	0.002	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	13	24	5arm	1	0	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	--------------CAACGUU---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	-------------GCAACGTTTCTCTCCTCAG----------------------------------------------------------------------------------------	19	1
rat	tgcaggcctaatgGCAACGTTTCTCTCCTCAGgctgtggaggagctgctggagtccctagacctggaaaagagcagctgctgcatgggcctgagtcgggtaagttgcccacaggtgggca
	************************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++	ENSRNOT00000043448 ENSRNOG00000033101 LOC360570
	+++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++	ENSRNOT00000056257 ENSRNOG00000033101 LOC360570
	+++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++	ENSRNOT00000042166 ENSRNOG00000033101 LOC360570
rat	.((..((((...((((((....(((..(((((((((((.((.(((((((....(((........)))....))))))).)).))))).))))))..)))...))))))...))))..)).	1.000 -58.80

rat

chromosome:10:63877488:63877607:1

block116458 [novel_lenNOK_mirtron_randfoldOK_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	0.006	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	10	30	5arm	1	4	0.44	4	1	1	na	na

		reads	miRBase family seed
seed	-----------GCAGCAU---------------------------------------------------------------------------------------------------	1	miR-103/107
		len	cloning frequencies
			T3S1
	----------AGCAGCATCCGCAGACTG-----------------------------------------------------------------------------------------	18	1
rat	ctgtgggtgtAGCAGCATCCGCAGACTGggctatggctctggctttggaggctttggatatggttctggtttcggaggctacggatatggctctggcttcggaggctacggatatgg
	*********************************************************************************************************************
	+++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000061606 ENSRNOG00000040064 LOC685333
rat	(((((..((((((....((((.((...((((((((.((.(((((((.((((((..(((......))))))))).))))))).)).))))))))...)).)))).))))))..)))))	0.920 -48.40

rat

chromosome:11:28775085:28775201:-1

Page 31008

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Page 31204

miR-Intess™

block276351 [novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]

block469550 [novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]

block497098 [novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]

block911789 [novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]

block1052280 [novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]

block2170444 [novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]

block2221219 [novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]

block2511356 [novel_lenNOK_cloningOK_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]

block82226 [novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH_bulgeHIGH]

block116458 [novel_lenNOK_mirtron_randfoldOK_nonpairedHIGH_bulgeHIGH]