Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_randfoldOK_nonpairedHIGH_bulgeHIGH (390 loci)

block1600685 [novel_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	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	28	5	5arm	1	nd	0.48	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------UGACUGU------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------ATGACTGTCACTCTGGGCAGA-----------------------------------------------------------------	21	1
rat	gtgttctggttctgacccctggaaagacATGACTGTCACTCTGGGCAGAagcagcttctctgctgtacccagtggacttctttccttgtcttcccagctctcagtgctccatac
	******************************************************************************************************************
rat	((((...(((.((((...((((.((((((.((..(((...(((((....(((((.....)))))...)))))..))).....))..)))))).))))...)))).)))..))))	0.990 -38.20

rat

chromosome:4:164269264:164269377:-1

intergenic

block1634810 [novel_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	0.001	no	no	0.65/0.65	20/20/1.00	0.0	0.0	1	0	1	0	13	26	5arm	1	nd	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	--------------CUGUGAG-------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	-------------CCTGTGAGCCTCCCTGGCAA-------------------------------------------------------------------------------	20	1
rat	cacagcacaaagtCCTGTGAGCCTCCCTGGCAAgtcttgtctcatttctacttctgtggatatcctgaagtagactgaaaaggaagggcagagtatcactggaaaagctgtg
	****************************************************************************************************************
rat	((((((......(((.((((..(((....((...((((...(((..((((((((...((....)).)))))))).)))..))))...)).)))..)))).)))...))))))	0.690 -40.10

rat

chromosome:4:43608175:43608286:1

intergenic

block1644920 [novel_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	0.62/0.62	21/21/1.00	0.0	0.0	1	0	1	0	26	9	3arm	1	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------AAGCUCC---------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------------------------------------------GAAGCTCCAGTGCCAAGCCCA--------------------------	21	1
rat	tcattcatgtccagaccttgggctctgcacactgctttggcaatactggtgaaatcacatttctGAAGCTCCAGTGCCAAGCCCAgagagcatagatggaatgctgaatga
	***************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000017675 ENSRNOG00000013004 Akr1d1
rat	(((((((..((((...((((((((..((((...(((((((.((.....(((....)))..)))))))))....))))..)))))).))........))))....)))))))	0.600 -35.00

rat

chromosome:4:64974866:64974976:1

Same_strand|Intronic_coding|ENSRNOT00000017675|ENSRNOG00000013004 ## ENSRNOG00000013004|protein_coding|Akr1d1|3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.1.3) (Delta(4)-3- ketosteroid 5-beta-reductase) (Aldo-keto reductase family 1 member D1). [Source:UniProtKB/Swiss-Prot;Acc:P31210]

block1766932 [novel_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	0.007	no	no	0.33/0.33	21/21/1.00	0.0	0.0	1	0	1	0	23	1	3arm	1	nd	0.33	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------CCACUUU------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-----------------------------------------------TCCACTTTAGAATCACAATCT-----------------------	21	1
rat	gagcttcttgttctttggtgattggagtgggaaagtggaaagtcaatTCCACTTTAGAATCACAATCTtattaattgccttgagaaggctc
	*******************************************************************************************
rat	(((((.....(((((.((..((((((((((.(((((((((......)))))))))....))))..)))....)))..))..))))))))))	0.990 -28.50

rat

chromosome:5:114552955:114553045:-1

intergenic

block1789525 [novel_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	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	26	9	3arm	1	nd	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------UGCAGAU---------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------------------------------------------------GTGCAGATGAAGGAGTAGGGA--------------------------	21	1
rat	tcggtgccctactcccaagggctgtcgggatgccttggatttttctttaccccctggctttgcagaggggGTGCAGATGAAGGAGTAGGGAgagacagactagggatgggcagcgac
	*********************************************************************************************************************
rat	(((.(((((...((((.((..(((((......(((((..(((.(((.((((((((.((...))..)))))))).))).)))....)))))...))))).)).)))).))))).))).	1.000 -53.50

rat

chromosome:5:150945625:150945741:-1

intergenic

block1886262 [novel_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	0.001	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	31	6	3arm	1	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------UGGUUGA-------------------------------------------	1	miR-380
		len	cloning frequencies
			T3S1
	-------------------------------------------------------------------ATGGTTGAATGAGTAAGTTG-------------------------------	20	1
rat	gcgtggcttcctgggtcgctgcttccgtttaatctgctaacagtctggtgcaccgtaagtcgtgcccATGGTTGAATGAGTAAGTTGgaggaagcagtttaggagaaggaggccctgt
	**********************************************************************************************************************
rat	(((.((((((((...(((((((((((.(((((..((((..((((((((.((((........))))))).)))))....))))..))))))))))))))...))...)))))))).)))	1.000 -48.80

rat

chromosome:5:150945787:150945904:1

intergenic

novel_lenNOK_Multihit_loopOverlap_nonpairedHIGH_bulgeHIGH (387 loci)

block60035 [novel_lenNOK_Multihit_loopOverlap_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	0.020	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	36	-4	5arm_loop	40	nd	0.47	5	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------AGCCUCA---------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------------------AAGCCTCAGGCCATCAAGC----------------------------------------------------	19	1
rat	ggcctgaagaagatgcaggccatcaaggcccctgtgAAGCCTCAGGCCATCAAGCccaagatgccaaaaggccccagctgcaaactctggccttcatcactcaaccg
	***********************************************************************************************************
rat	((..(((....((((.((((((.....((..(((....((((..((.((((........))))))...))))..)))..))......)))))).))))..))).)).	0.500 -32.90

rat

chromosome:10:13790837:13790943:1

intergenic

block73413 [novel_lenNOK_Multihit_loopOverlap_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	0.098	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	10	-4	5arm_loop	40	nd	0.53	5	1	1	na	na

		reads	miRBase family seed
seed	-----------AGCCUCA------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------AAGCCTCAGGCCATCAAGC-------------------------	19	1
rat	ggcccctgccAAGCCTCAGGCCATCAAGCccaagatgccaaaggaccccagcca
	******************************************************
rat	(((...((.....(((..((.((((........))))))..)))....))))).	0.600 -13.20

rat

chromosome:10:45511538:45511591:1

intergenic

block105274 [novel_lenNOK_Multihit_loopOverlap_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	0.109	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	10	-3	5arm_loop	13	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-----------CCUGACC------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----------ACCTGACCCCAGCTTTTCT-------------------------------------------------------------	19	1
rat	tgcacagtgcACCTGACCCCAGCTTTTCTatctacacctccgtttttcatcccctgaagccccagttaggtcgctccctgggctgtgtag
	******************************************************************************************
	----------------------------------------------------------------------------------------------------	ENSRNOT00000004035 ENSRNOG00000003028 Q63172_RAT
rat	(((((((((((((((((....(((((.............................)))))....))))))).)).......)))))))).	0.890 -22.06

rat

chromosome:10:108096383:108096472:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000054991|ENSRNOG00000003028 ## Opposite_strand|Intronic_coding|ENSRNOT00000004035|ENSRNOG00000003028 ## ENSRNOG00000003028|protein_coding|Q63172_RAT|Dynein-like protein 9B (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q63172]

block188355 [novel_lenNOK_Multihit_loopOverlap_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	0.265	no	no	0.53/0.55	19/20/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	25 30	2 -4	5arm 5arm_loop	18 18	nd nd	0.37 0.45	4 5	2	2	na	na

		reads	miRBase family seed
seed	--------------------------UGAUUCU------------------------------------------------------------	1	novel
seed	-------------------------------CUCUCUG-------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T5S2
	-------------------------CTGATTCTCTCTGGACTGC-------------------------------------------------	19	1	-
	------------------------------TCTCTCTGGACTGCTGAGTG-------------------------------------------	20	-	1
rat	gtctgagcatgtggttttatttaccCTGATTCTCTCTGGACTGCTGAGTGccccagtgtccctagacagggcaaccttgactgcctgatggcc
	*********************************************************************************************
rat	(((....((.((((((.......(((((....(((..((((.((((.......))))))))..)))))))).......)))))).))..))).	0.950 -26.74

rat

chromosome:12:19963746:19963838:-1

intergenic

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