Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_multiarm_DicerNOK (112 loci)

sblock8936 [novel_multiarm_DicerNOK]

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	0.174	no	no	0.65/0.81	20/21/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	6 6	2 2	5arm 3arm	1 1	nd nd	0.15 0.24	1 3	2	2	0	-1

		reads	miRBase family seed
seed	------------------------------------------GGUGCUU-------------------	1	novel
seed	-------GGCGGAG------------------------------------------------------	1	miR-25*
		len	cloning frequencies
			T1S1	T2S2
	-----------------------------------------CGGTGCTTCCCGCGCGTCCCC------	21	1	-
	------TGGCGGAGCAGGAAGTGCAG------------------------------------------	20	-	1
rat	gtcatcTGGCGGAGCAGGAAGTGCAGgcagagtccggaggcCGGTGCTTCCCGCGCGTCCCCaggact
	********************************************************************
rat	(((..((((.(((((.((((((((.(((...........))).)))))))).))...)))))))))).	1.000 -29.50

rat

chromosome:4:82407629:82407696:1

intergenic ## {SimpF: 1 Eponine}

sblock903 [novel_multiarm_DicerNOK]

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	0.465	no	no	0.57/0.65	20/21/1.00	0.0 0.7	0.0 0.3	1 3	0 0	1 2	0 0	8 9	16 13	5arm 3arm	1 1	nd nd	0.35 0.29	3 2	4	3	-2	1

		reads	miRBase family seed
seed	----------------------------------------------------------------GGCCUCU---------------------	2	novel
seed	--------------------------------------------------------------CAGGCCU-----------------------	1	novel
seed	---------CUGGGGU----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T5S1	T5S2
	---------------------------------------------------------------AGGCCTCTGAAGCAAGGACC---------	20	-	2	-
	-------------------------------------------------------------TCAGGCCTCTGAAGCAAGGAC----------	21	1	-	-
	--------GCTGGGGTGGTAGTGGTCCT----------------------------------------------------------------	20	-	-	1
rat	ggcggtggGCTGGGGTGGTAGTGGTCCTggtacatgagtgtacgcacgcgcagtctctcctTCAGGCCTCTGAAGCAAGGACCtacctagtc
	********************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041526 ENSRNOG00000016416 Rnh1
rat	...((((((((...((..(((.((.(((((.....(((....((....))....)))....))))))).)))..))..)).)))))).....	0.950 -31.50

rat

chromosome:1:201370740:201370831:-1

Same_strand|Intronic_non-coding|ENSRNOT00000041526|ENSRNOG00000016416 ## Same_strand|Boundary_non-coding|ENSRNOT00000022241|ENSRNOG00000016416 ## ENSRNOG00000016416|protein_coding|Rnh1|Ribonuclease inhibitor (Ribonuclease/angiogenin inhibitor 1). [Source:UniProtKB/Swiss-Prot;Acc:P29315]

sblock9051 [novel_multiarm_DicerNOK]

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	0.237	no	no	0.52/0.55	21/22/1.00	0.0 0.0	0.0 0.0	2 1	0 0	1 1	0 0	8 1	21 28	5arm 3arm	3 3	nd nd	0.32 0.19	3 1	3	1	5	5

		reads	miRBase family seed
seed	---------GAGCCUA---------------------------------------------------------------------------------------------	2	novel
seed	----------------------------------------------------------------------------------------GGUGUCG--------------	1	novel
		len	cloning frequencies
			T2S1
	--------GGAGCCTACCAATACCGTCATG-------------------------------------------------------------------------------	22	2
	---------------------------------------------------------------------------------------TGGTGTCGGTATGGACTGTGA-	21	1
rat	tcagactaGGAGCCTACCAATACCGTCATGattacgtcaacccatgtcaaagccgttaatttaacacacttgggtttgtcaaaatgcTGGTGTCGGTATGGACTGTGAt
	*************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000041957 ENSRNOG00000005599 LOC297568
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000036555 ENSRNOG00000005599 LOC297568
rat	(((...(((...((((((.((((((.(((....(((..(((((((((.(((........))).)))....)))))))))....))).)))))).)))).)).)))))).	0.930 -26.00

rat

chromosome:4:158240809:158240917:1

Same_strand|Intronic_non-coding|ENSRNOT00000036555|ENSRNOG00000005599 ## Same_strand|Boundary_non-coding|ENSRNOT00000044408|ENSRNOG00000005599 ## Same_strand|Intronic_coding|ENSRNOT00000041957|ENSRNOG00000005599 ## ENSRNOG00000005599|protein_coding|LOC297568|Alpha-1-inhibitor 3 precursor (Alpha-1-inhibitor III) (Alpha-1- inhibitor 3 variant II). [Source:UniProtKB/Swiss-Prot;Acc:P14046]

sblock9169 [novel_multiarm_DicerNOK]

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	0.062	no	no	0.43/0.54	22/24/1.00	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	13 35 19	19 0 15	5arm 3arm 3arm	1 1 1	nd nd nd	0.21 0.32 0.17	2 3 3	3	1	-18	-20

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------GGCUUUU----------------------------------	1	novel
seed	--------------GUUGCUU---------------------------------------------------------------------------------------------------	1	novel
seed	----------------------------------------------------------------GGAUGUG-------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------CGTTGCTTTGGGAACAAGGAGCAG-----------------------------------------------------------------------------------	24	1
	------------------------------------------------------------------------------TGGCTTTTGTACCTGTTTCCAAC-------------------	23	1
	---------------------------------------------------------------TGGATGTGAGATGGATGGCTTT-----------------------------------	22	1
rat	tggctgcattttcCGTTGCTTTGGGAACAAGGAGCAGcttcccgacctttcgtccatttcttcTGGATGTGAGATGGATGGCTTTTGTACCTGTTTCCAACgaggtcccttctggagcta
	************************************************************************************************************************
rat	(((((.((....((.(((..((((((((.(((.((((((..(((..(((.((((((.......)))))).))).)))..))))...)).)))))))))))))))).......)).)))))	0.550 -37.30

rat

chromosome:4:164297936:164298055:1

intergenic

sblock9313 [novel_multiarm_DicerNOK]

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	0.292	no	no	0.52/0.55	21/22/1.00	0.0 0.0	0.0 0.0	1 2	0 0	1 1	0 0	9 27	20 8	5arm 3arm	1 1	nd nd	0.19 0.32	2 2	3	1	-12	-13

		reads	miRBase family seed
seed	----------------------------------------------------------------CCGGCGU-----------------------------------------	2	novel
seed	----------GGCUAAG-----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	---------------------------------------------------------------TCCGGCGTAGTGCAGAAGTAGT---------------------------	22	2
	---------AGGCTAAGGAGAGACAACCTG----------------------------------------------------------------------------------	21	1
rat	ttgggcttcAGGCTAAGGAGAGACAACCTGgccgcgttgtctggctcctctggccgaggagcgTCCGGCGTAGTGCAGAAGTAGTttcttgcgattagggtgaaggcaccgg
	****************************************************************************************************************
rat	.(((((((((..((((.(((((((.(((((((..(((((....(((((((.....)))))))...)))))..)).)))..)).)))))))....))))..)))).)).))).	0.810 -41.50

rat

chromosome:5:59501697:59501808:-1

intergenic

sblock9481 [novel_multiarm_DicerNOK]

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	0.731	no	no	0.38/0.47	19/21/0.75	0.0 0.0	0.0 0.0	1 3	0 0	1 1	0 0	5 3	28 19	5arm 3arm	2 7	nd nd	0.42 0.24	4 2	4	2	-2	3

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------AAGUUCU----------------	3	miR-148b
seed	------CGCUUUU---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T4S1
	----------------------------------------------------------------------------AAAGTTCTACAATGTGGCTGA---	21	-	3
	-----GCGCTTTTGACTCAGGATT----------------------------------------------------------------------------	19	1	-
rat	ttttgGCGCTTTTGACTCAGGATTtaaaatttggaacggtgaaggcgacagcagctggttggagcaaacatcccccAAAGTTCTACAATGTGGCTGAgga
	****************************************************************************************************
rat	(((..((((..(((....(((((......(((((...((((...((..((((.....))))..))...))))..)))))))))).))).)).))..))).	0.450 -21.40

rat

chromosome:5:126881568:126881667:-1

intergenic

novel_lenNOK_cloningOK_bulgeHIGH (110 loci)

block9543 [novel_lenNOK_cloningOK_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	0.082	no	no	0.56/0.56	18/18/0.00	0.0 0.0	0.0 0.0	1 16	0 0	1 6	0 0	16 10	-2 4	3arm_loop 3arm	1 1	nd nd	0.44 0.28	4 4	19	6	na	na

		reads	miRBase family seed
seed	-----------------------------------------------CCCUGUC--------------------	18	miR-339
seed	-----------------------------------------GCUAUUC--------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S1	T3S2	T4S1	T4S2	T5S2
	----------------------------------------------TCCCTGTCCTCCAAGAAC----------	18	4	3	5	1	1	4
	----------------------------------------TGCTATTCCCTGTCCTCC----------------	18	-	-	-	-	1	-
rat	tctctagggaagtgtggtctgaaggaggaaactgacagtgtgctatTCCCTGTCCTCCAAGAACacccttgggg
	**************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000009524 ENSRNOG00000006932 Q3MIE5_RAT
rat	.((((((((..((((..(((...((((((....((.((....))..))....)))))).)))))))))))))))	0.800 -23.90

rat

chromosome:10:19282960:19283033:-1

Same_strand|Intronic_coding|ENSRNOT00000009524|ENSRNOG00000006932 ## Same_strand|Boundary_non-coding|ENSRNOT00000059810|ENSRNOG00000006932 ## ENSRNOG00000006932|protein_coding|Q3MIE5_RAT|Dock2 protein. [Source:UniProtKB/TrEMBL;Acc:Q3MIE5]

block35589 [novel_lenNOK_cloningOK_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	0.411	no	no	0.48/0.61	18/21/0.06	0.6	0.6	20	0	8	0	10	1	5arm	1	nd	0.21	4	32	8	na	na

		reads	miRBase family seed
seed	------------GCCAGUG--------------------------------------------	19	novel
seed	-----------GGCCAGU---------------------------------------------	13	novel
		len	cloning frequencies
			T1S1	T1S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------GGCCAGTGATGTGTCTCTT---------------------------------	19	1	1	7	1	1	1	4	1
	----------CGGCCAGTGATGTGTCTCT----------------------------------	19	1	-	9	-	1	-	-	1
	-----------GGCCAGTGATGTGTCTCTTTA-------------------------------	21	-	-	-	2	-	-	-	-
	----------CGGCCAGTGATGTGTCTC-----------------------------------	18	-	-	1	-	-	-	-	-
rat	ctagatgagaCGGCCAGTGATGTGTCTCTTtaagggaaggtgacagctgaggccttgaaatag
	***************************************************************
rat	...........(((((((....(((((((((....))))).)))))))..)))).........	0.590 -14.00

rat

chromosome:10:76778081:76778143:-1

intergenic

block69667 [novel_lenNOK_cloningOK_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	0.196	no	no	0.44/0.44	18/18/0.00	0.0	0.0	20	0	2	0	26	6	5arm	1	nd	0.28	4	20	2	na	na

		reads	miRBase family seed
seed	---------------------------GGAGUGU-------------------------------------------------------------------------------	20	miR-122
		len	cloning frequencies
			T2S1	T2S2
	--------------------------TGGAGTGTGACAAAGTAC---------------------------------------------------------------------	18	15	5
rat	acttctcctaagtgctctgactcttgTGGAGTGTGACAAAGTACgacctgaatctggccaggttgaatttagaacactgagtgtctgtgagggcagaggctggcggcaggcgt
	*****************************************************************************************************************
rat	((.(((((..(((.(((((.((((..((((((((....((((.(((((((........))))))).))))...))))......))))..))))))))))))...)).))).))	0.860 -35.90

rat

chromosome:10:37499648:37499760:1

intergenic

block88043 [novel_lenNOK_cloningOK_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	0.037	no	no	0.22/0.30	18/20/0.18	0.0	0.7	11	0	3	0	16	3	3arm	1	nd	0.28	4	11	3	na	na

		reads	miRBase family seed
seed	------------------------------------------------AAGGCAU----------------------------	11	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1
	-----------------------------------------------TAAGGCATTATTGAAATA------------------	18	1	3	1
	-----------------------------------------------TAAGGCATTATTGAAATAG-----------------	19	2	1	1
	-----------------------------------------------TAAGGCATTATTGAAATAGG----------------	20	2	-	-
rat	ctatatataattttccacagtattttatgccaaattatttaaaaaaaTAAGGCATTATTGAAATAGGacagagatttgtatag
	***********************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055776 ENSRNOG00000006248 NP_001101758.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000008298 ENSRNOG00000006248 NP_001101758.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055775 ENSRNOG00000006248 NP_001101758.1
rat	...(((((((.((((.....(((((((((((...((((((....)))))))))))....)))))).....)))).))))))).	1.000 -14.60

rat

chromosome:10:75477007:75477089:1

Same_strand|Intronic_non-coding|ENSRNOT00000055776|ENSRNOG00000006248 ## Same_strand|Intronic_coding|ENSRNOT00000008298|ENSRNOG00000006248 ## ENSRNOG00000006248|protein_coding|NP_001101758.1|tripartite motif protein 37 [Source:RefSeq_peptide;Acc:NP_001101758]

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