miR-Intess: classification

other hairpins

novel_shortStem_5varHIGH_loopOverlap (9 loci)

block884493 [novel_shortStem_5varHIGH_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	0.666	no	no	0.43/0.50	20/21/1.00	1.5	1.0	2	0	2	0	2	-3	5arm_loop	1	9	0.29	2	2	2	na	na

		reads	miRBase family seed
seed	---CAGAGCA--------------------------------------------	1	novel
seed	------AGCAAAG-----------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	-----GAGCAAAGGGGTATGAATGG-----------------------------	20	1	-
	--TCAGAGCAAAGGGGTATGAAT-------------------------------	21	-	1
rat	ctTCAGAGCAAAGGGGTATGAATGGtctttatgtctttacagcatcaggtgagg
	******************************************************
	>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000015065 ENSRNOG00000011213 NP_001100996.1
rat	(((((((((..((((..(((((.....)))))..))))...)).))...)))))	0.990 -9.00

rat

chromosome:1:136276019:136276072:-1

block1279263 [novel_shortStem_5varHIGH_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	0.243	no	no	0.46/0.56	18/24/0.88	2.4	2.8	8	0	3	0	2	-2	5arm_loop	1	nd	0.15	3	8	3	na	na

		reads	miRBase family seed
seed	------CAUGUCC-----------------------------------------------------	3	novel
seed	----AACAUGU-------------------------------------------------------	2	novel
seed	---UAACAUG--------------------------------------------------------	2	novel
seed	-----------CCUGAGA------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1
	-----ACATGTCCTGAGACAGACAC-----------------------------------------	20	2	-	-
	--CTAACATGTCCTGAGACAGAC-------------------------------------------	21	-	2	-
	---TAACATGTCCTGAGACAGACACAC---------------------------------------	24	-	2	-
	----------TCCTGAGACAGACACACC--------------------------------------	18	-	-	1
	-----ACATGTCCTGAGACAGACACACC--------------------------------------	23	1	-	-
rat	gaCTAACATGTCCTGAGACAGACACACCctttgctgatgtttggagcagcaggtgatatgagggtc
	******************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000016083 ENSRNOG00000011913 Cp
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000016914 ENSRNOG00000011913 Cp
rat	((((..(((((((((...((((((((........)).))))))...))).....))))))..))))	0.710 -17.40

rat

chromosome:2:105121885:105121950:1

block2153291 [novel_shortStem_5varHIGH_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	0.069	no	no	0.55/0.57	22/23/1.00	1.2	0.8	5	0	1	0	1	-1	3arm	1	nd	0.30	2	5	1	na	na

		reads	miRBase family seed
seed	------------------------------GCUUCCA------------------	3	novel
seed	---------------------------------UCCAUGA---------------	2	novel
		len	cloning frequencies
			T5S1
	-----------------------------TGCTTCCATGAGCTAGCCCACCT---	23	3
	--------------------------------TTCCATGAGCTAGCCCACCTCA-	22	2
rat	tgagagggagacagcacaaggtcagcggtTGCTTCCATGAGCTAGCCCACCTCAt
	*******************************************************
rat	((((.(((....(((.((.((..(((....))).)).)).)))..)))..)))).	0.680 -16.40

rat

chromosome:7:116622938:116622992:-1

intergenic

block2168408 [novel_shortStem_5varHIGH_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	0.049	no	no	0.50/0.54	20/24/1.00	2.7	3.3	3	0	3	0	0	-8	5arm_loop_3arm	5	nd	0.29	3	3	3	na	na

		reads	miRBase family seed
seed	------UCACCAU-------------------------------------	1	novel
seed	-AGCCGUC------------------------------------------	1	novel
seed	----CGUCACC---------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S1	T3S2
	-----GTCACCATGATCATCTACCGGGAC---------------------	24	-	-	1
	---CCGTCACCATGATCATCTAC---------------------------	20	1	-	-
	CAGCCGTCACCATGATCATCT-----------------------------	21	-	1	-
rat	CAGCCGTCACCATGATCATCTACCGGGACctcatcagccatgacgagctg
	**************************************************
	................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000003348 ENSRNOG00000002475 RGD1565798_predicted
rat	(((((((((...((((..(((....)))....))))....))))).))))	1.000 -13.90

rat

chromosome:7:136156050:136156099:-1

block209263 [novel_shortStem_5varHIGH_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	0.249	no	no	0.37/0.43	19/23/0.75	5.2	3.0	4	0	1	0	4	-4	5arm_loop_3arm	1	nd	0.26	2	4	1	na	na

		reads	miRBase family seed
seed	------------CCUGGCU----------------------------------------------	3	novel
seed	-----GACACUU-----------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-----------TCCTGGCTTTTGCAAATAAGT---------------------------------	21	1
	-----------TCCTGGCTTTTGCAAATAA-----------------------------------	19	1
	-----------TCCTGGCTTTTGCAAATAAG----------------------------------	20	1
	----TGACACTTCCTGGCTTTTGCAAA--------------------------------------	23	1
rat	caggTGACACTTCCTGGCTTTTGCAAATAAGTataggcagcagagaggacatagacgttagcctg
	*****************************************************************
rat	((((((((.((((((..((.((((..((....))..)))).))..))))...))..)))).))))	0.860 -15.30

rat

chromosome:12:5626066:5626130:1

intergenic

block1751026 [novel_shortStem_5varHIGH_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	0.153	no	no	0.33/0.50	21/24/1.00	4.0	5.2	5	0	3	0	3	-2	3arm	1	nd	0.23	3	5	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------UUCUCAU----------------------------	2	novel
seed	-------------------------------------------CUCAUUC--------------------------	1	novel
seed	------------------------------------------------UCAUUUG---------------------	1	novel
seed	----------------------------------------------------UUGACAG-----------------	1	novel
		len	cloning frequencies
			T1S1	T3S2	T5S1
	----------------------------------------TTTCTCATTCATTTGACAGAG---------------	21	-	-	1
	------------------------------------------TCTCATTCATTTGACAGAGGGT------------	22	1	-	-
	-----------------------------------------------TTCATTTGACAGAGGGTAGGAC-------	22	-	1	-
	----------------------------------------TTTCTCATTCATTTGACAGAGGGT------------	24	-	-	1
	---------------------------------------------------TTTGACAGAGGGTAGGACGAAG---	22	-	-	1
rat	gccagagtcagtctgaacccaagttagagtcagggattgtTTTCTCATTCATTTGACAGAGGGTAGGACGAAGgtg
	****************************************************************************
rat	(((....((.((((..((((..((((((....((((......)))).....))))))...)))).)))))).))).	0.990 -20.40

rat

chromosome:5:79197368:79197443:-1

intergenic

miRNAunknown_lenNOK_Multihit_randfoldOK (8 loci)

block893717 (miRNA) [miRNAunknown_lenNOK_Multihit_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
Ensembl miRNA	0.007	no	no	0.50/0.53	19/20/0.67	0.0	0.7	3	0	3	0	21	11	3arm	11	nd	0.25	2	3	3	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------UGGCUCU---------------------------------	3	novel
		len	cloning frequencies
			T2S2	T3S1	T5S2
	-------------------------------------------------------------------------------ATGGCTCTCACTGAAGACCA---------------------	20	1	-	1
	-------------------------------------------------------------------------------ATGGCTCTCACTGAAGACC----------------------	19	-	1	-
rat	aaacaggaaacatgcagtcagctggcttttaaaaacttgacaaggcaatgtgtatgtatgtattaagaatgcatatataATGGCTCTCACTGAAGACCAgcagttgtattgtagctgttg
	************************************************************************************************************************
	...................................................................................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063308 ENSRNOG00000041555
rat	.(((((...((((((((...(((((((((........(((..((.((.(((((((((((.........))))))))))).)).)).)))..)))).)))))..)))))).))..))))).	0.900 -32.50

rat

chromosome:1:161283689:161283808:-1

Same_strand|Exonic_non-coding|ENSRNOT00000063308|ENSRNOG00000041555 ## ENSRNOG00000041555|miRNA||

block2029349 (miRNA) [miRNAunknown_lenNOK_Multihit_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
Ensembl miRNA	0.004	no	no	0.50/0.53	19/20/0.67	0.0	0.7	3	0	3	0	12	5	5arm	11	nd	0.25	2	3	3	na	na

		reads	miRBase family seed
seed	-------------UGGCUCU--------------------------------------------------------------	3	novel
		len	cloning frequencies
			T2S2	T3S1	T5S2
	------------ATGGCTCTCACTGAAGACCA--------------------------------------------------	20	1	-	1
	------------ATGGCTCTCACTGAAGACC---------------------------------------------------	19	-	1	-
rat	cagacaggtgtcATGGCTCTCACTGAAGACCAgcagtcgtactgtagctgttggtttcaagcagacgcctagagaactgtct
	**********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049945 ENSRNOG00000032407 Npas3
	..................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000063231 ENSRNOG00000041478
rat	.((((((...((..((((((..((..(((((((((((.........)))))))))))..)).))).)))..))...))))))	1.000 -30.50

rat

chromosome:6:73866630:73866711:1

Same_strand|Intronic_coding|ENSRNOT00000049945|ENSRNOG00000032407 ## Same_strand|Boundary_non-coding|ENSRNOT00000063231|ENSRNOG00000041478 ## ENSRNOG00000041478|miRNA|| ## ENSRNOG00000032407|protein_coding|Npas3|neuronal PAS domain protein 3 Gene [Source:MGI Symbol;Acc:MGI:1351610]

block2575648 (miRNA) [miRNAunknown_lenNOK_Multihit_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
Ensembl miRNA	0.008	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	7	12	5arm	18	22	0.28	1	1	1	na	na

		reads	miRBase family seed
seed	--------GCGAGUA--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-------GGCGAGTATCTCTTTGAG----------------------------------------------------	18	1
rat	acctctgGGCGAGTATCTCTTTGAGcgcctcactttcaagcaggaataggaggccttccgagcgaagccgccttagg
	*****************************************************************************
	---------------------------------------------------------------------------------------	ENSRNOT00000018552 ENSRNOG00000013781 Kcnq5
	---------------------------------------------------------------------------------------	ENSRNOT00000040034 ENSRNOG00000013781 Kcnq5
	++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.................................	ENSRNOT00000048965 ENSRNOG00000030559
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...................	ENSRNOT00000054654 ENSRNOG00000036549
rat	.(((..(((((.((.((.(((.(((.(((((...(((......)))...))))).))).))).)).))))))).)))	1.000 -30.80

rat

chromosome:9:20293813:20293889:1

Opposite_strand|Intronic_coding|ENSRNOT00000018552|ENSRNOG00000013781 ## Same_strand|Exonic_coding|ENSRNOT00000048965|ENSRNOG00000030559 ## Same_strand|Exonic_non-coding|ENSRNOT00000054654|ENSRNOG00000036549 ## ENSRNOG00000036549|miRNA|| ## ENSRNOG00000013781|protein_coding|Kcnq5|Potassium voltage-gated channel KQT-like subfamily member 5 (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q8K3W7] ## ENSRNOG00000030559|protein_coding||

block2832336 (miRNA) [miRNAunknown_lenNOK_Multihit_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
Ensembl miRNA	0.008	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	32	0	5arm	18	nd	0.28	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------GCGAGUA------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--------------------------------GGCGAGTATCTCTTTGAG--------------------------------------------------------------	18	1
rat	cagagcagactggcgtggcccaggcatctctgGGCGAGTATCTCTTTGAGcacctcactctgaagcactactaggcctctgtgccttccaaggggctccctcctctgctctg
	****************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>............................	ENSRNOT00000054663 ENSRNOG00000036559
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.................................................	ENSRNOT00000049856 ENSRNOG00000034150
rat	(((((((((..((...(((((((((((....((((.((((...(((((((.......))).))))...))))..))))..))))))......))))).))...)))))))))	0.590 -43.10

rat

chromosome:X:139087857:139087968:-1

Same_strand|Exonic_coding|ENSRNOT00000049856|ENSRNOG00000034150 ## Same_strand|Exonic_non-coding|ENSRNOT00000054663|ENSRNOG00000036559 ## ENSRNOG00000034150|protein_coding|| ## ENSRNOG00000036559|miRNA||

Page 31019

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Page 31204

miR-Intess™

block884493 [novel_shortStem_5varHIGH_loopOverlap]

block1279263 [novel_shortStem_5varHIGH_loopOverlap]

block2153291 [novel_shortStem_5varHIGH_loopOverlap]

block2168408 [novel_shortStem_5varHIGH_loopOverlap]

block209263 [novel_shortStem_5varHIGH_loopOverlap]

block1751026 [novel_shortStem_5varHIGH_loopOverlap]

block893717 (miRNA) [miRNAunknown_lenNOK_Multihit_randfoldOK]

block2029349 (miRNA) [miRNAunknown_lenNOK_Multihit_randfoldOK]

block2575648 (miRNA) [miRNAunknown_lenNOK_Multihit_randfoldOK]

block2832336 (miRNA) [miRNAunknown_lenNOK_Multihit_randfoldOK]