Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_randfoldOK (15 loci)

sblock7275 [novel_lenNOK_multiarm_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
no	0.002	no	no	0.62/0.79	19/21/0.67	0.0 0.0	0.0 0.0	1 2	0 0	1 1	0 0	3 28	20 3	5arm 3arm	2 2	nd nd	0.16 0.29	2 2	3	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------CGGUCCA-----------------------------------------	2	novel
seed	----GGCUCGG---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------------------------TCGGTCCAGGAAGATGGCAGG----------------------------	21	2
	---CGGCTCGGGAGCCAGGCTG----------------------------------------------------------------------------	19	1
rat	gctCGGCTCGGGAGCCAGGCTGcctacccttctagagcgtcctgtgggcTCGGTCCAGGAAGATGGCAGGcacagcaagcctggctccgtggcgggca
	**************************************************************************************************
rat	((((.(((..(((((((((((((((.(((((((.((.((.((....))..)).))..)))))..)).)))))......))))))))))..))))))).	0.990 -50.10

rat

chromosome:20:13678609:13678706:1

intergenic

sblock7276 [novel_lenNOK_multiarm_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
no	0.002	no	no	0.62/0.79	19/21/0.67	0.0 0.0	0.0 0.0	1 2	0 0	1 1	0 0	3 28	20 3	5arm 3arm	2 2	nd nd	0.16 0.29	2 2	3	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------CGGUCCA-----------------------------------------	2	novel
seed	----GGCUCGG---------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------------------------TCGGTCCAGGAAGATGGCAGG----------------------------	21	2
	---CGGCTCGGGAGCCAGGCTG----------------------------------------------------------------------------	19	1
rat	gctCGGCTCGGGAGCCAGGCTGcctacccttctagagcgtcctgtgggcTCGGTCCAGGAAGATGGCAGGcacagcaagcctggctccgtggcgggca
	**************************************************************************************************
	------------------------------------------------------------------------------------------------------------	ENSRNOT00000058237 ENSRNOG00000038258 Upb1
rat	((((.(((..(((((((((((((((.(((((((.((.((.((....))..)).))..)))))..)).)))))......))))))))))..))))))).	0.990 -50.10

rat

chromosome:20:13738731:13738828:1

Opposite_strand|Intronic_coding|ENSRNOT00000058237|ENSRNOG00000038258 ## ENSRNOG00000038258|protein_coding|Upb1|ureidopropionase, beta Gene [Source:MGI (curated);Acc:Upb1-001]

sblock7459 [novel_lenNOK_multiarm_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
no	0.002	no	no	0.64/0.68	19/22/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	25 0	3 29	5arm 3arm	1 2	nd nd	0.32 0.28	2 3	2	1	na	na

		reads	miRBase family seed
seed	--------------------------AGCUGGG---------------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------------------CCGCUGA-----------	1	novel
		len	cloning frequencies
			T1S1
	-----------------------------------------------------------------------------------ACCGCTGAGCTGGAGGTCC	19	1
	-------------------------GAGCTGGGCAGTGGCTACCGTT-------------------------------------------------------	22	1
rat	ggtagcttttggaggcggagagcgcGAGCTGGGCAGTGGCTACCGTTgtgaccccgtgacggaagcacagtgcctggttgctaACCGCTGAGCTGGAGGTCC
	******************************************************************************************************
rat	((..((((..((.(((((..((((...((..((((.(((((.((((..((....))..)))).))).)).))))..))))))..)))))...))..))))))	1.000 -50.10

rat

chromosome:3:9461256:9461357:-1

intergenic ## {SimpF: oe = 0.71 -1 CpG}

sblock9863 [novel_lenNOK_multiarm_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
no	0.001	no	no	0.47/0.53	19/19/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	1 32	29 3	5arm 3arm	1 1	nd nd	0.16 0.26	2 4	2	1	na	na

		reads	miRBase family seed
seed	--CCUGAGU---------------------------------------------------------------------------------------------------------	1	novel
seed	----------------------------------------------------------------GUACCAA-------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-GCCTGAGTTGTTGCAGCTA----------------------------------------------------------------------------------------------	19	1
	---------------------------------------------------------------TGTACCAAGAATGGATGCC--------------------------------	19	1
rat	aGCCTGAGTTGTTGCAGCTAtgaggttaatggcatctattcctgcacacatacagacccagtgTGTACCAAGAATGGATGCCtgcttggggacccatagactgtaaacctaggc
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000020069 ENSRNOG00000014909 Sh2d5
rat	.(((((.((..(((((((((((.((((...(((((((((((.(((((((...........)))))))....)))))))))))........))))))))).)))))))).)))))	1.000 -47.20

rat

chromosome:5:157031572:157031685:1

Same_strand|Intronic_coding|ENSRNOT00000020069|ENSRNOG00000014909 ## ENSRNOG00000014909|protein_coding|Sh2d5|SH2 domain containing 5 Gene [Source:MGI (curated);Acc:Sh2d5-002]

novel_lenNOK_shortStem_5varHIGH_bulgeHIGH (15 loci)

block91159 [novel_lenNOK_shortStem_5varHIGH_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	0.065	no	no	0.57/0.58	19/21/0.50	1.5	2.5	2	0	2	0	1	28	3arm	1	nd	0.26	4	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------GGAAGUG--------------	1	novel
seed	------------------------------------------------------------------------------------CUGGGAA-----------------	1	miR-204*
		len	cloning frequencies
			T3S2	T4S1
	-----------------------------------------------------------------------------------TCTGGGAAGTGCAGAGGAC------	19	1	-
	--------------------------------------------------------------------------------------GGGAAGTGCAGAGGACACTTC-	21	-	1
rat	tgaatattctcattttttagattaatttcacccattttcatactgacatttaagaaatgtattatctgaagtttaggaaatatTCTGGGAAGTGCAGAGGACACTTCa
	************************************************************************************************************
rat	.(((..(((((((((((((((...(((((......(((((.....(((((.....)))))......))))).....)))))..))))))))))).)))).....))).	0.970 -21.40

rat

chromosome:10:82760298:82760405:1

intergenic

block178885 [novel_lenNOK_shortStem_5varHIGH_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	0.100	no	no	0.56/0.57	18/21/0.33	1.7	0.7	3	0	2	0	4	29	5arm	7	nd	0.29	4	3	2	na	na

		reads	miRBase family seed
seed	----------CUGAGCA----------------------------------------------------------------------------------------------	2	novel
seed	-----UGCAGCU---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	---------GCTGAGCAGGCTTGAATG------------------------------------------------------------------------------------	18	2	-
	----CTGCAGCTGAGCAGGCTTGAA--------------------------------------------------------------------------------------	21	-	1
rat	agctCTGCAGCTGAGCAGGCTTGAATGgttccgtgtgatgtgctctgtgcgctgcagtttggtgcggcgagggagctcaggcgaggtctgcagtcacggcatggtgagagc
	***************************************************************************************************************
rat	.(((((((.((((.((((((((.........(((.(((...(((((...(((((((......)))))))..)))))))).))))))))))).....))))...)).)))))	0.460 -44.00

rat

chromosome:12:4832089:4832199:-1

intergenic

block785965 [novel_lenNOK_shortStem_5varHIGH_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	0.135	no	no	0.44/0.48	18/21/0.50	2.0	0.5	2	0	2	0	0	27	3arm	1	nd	0.29	4	2	2	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------UCCCCCC--------------	1	novel
seed	----------------------------------------------------------------------------CCCAAAC----------	1	novel
		len	cloning frequencies
			T1S2	T2S2
	-----------------------------------------------------------------------TTCCCCCCAAACCAAGTTGAA-	21	1	-
	---------------------------------------------------------------------------CCCCAAACCAAGTTGAAT	18	-	1
rat	ttcagggtagtggggagggaggcggggacacagaacgactcactagtctgttgcagttaccgtacacgaatTTCCCCCCAAACCAAGTTGAAT
	*********************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000016577 ENSRNOG00000012428 Maf
rat	((((.(((..(((((.(((((((((..((.(((...((((....))))..)))..))..)))).......)))))))))).)))....)))).	1.000 -28.71

rat

chromosome:19:45848319:45848411:-1

Same_strand|Intronic_coding|ENSRNOT00000016577|ENSRNOG00000012428 ## ENSRNOG00000012428|protein_coding|Maf|Transcription factor Maf (Proto-oncogene c-maf). [Source:UniProtKB/Swiss-Prot;Acc:P54844]

block1084265 [novel_lenNOK_shortStem_5varHIGH_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	0.871	no	no	0.58/0.63	19/19/0.00	1.5	1.5	2	0	2	0	2	19	5arm	5	nd	0.26	5	2	2	na	na

		reads	miRBase family seed
seed	------UGGGCUA---------------------------------------------------------------------------------	1	novel
seed	---UUGUGGG------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T3S1
	--GTTGTGGGCTAGTCACCTC-------------------------------------------------------------------------	19	-	1
	-----GTGGGCTAGTCACCTCTGC----------------------------------------------------------------------	19	1	-
rat	tgGTTGTGGGCTAGTCACCTCTGCtggtcggagaagctggggacgcgtccttagacgccgagagttgtccttgaccgtagccccgccgctgccg
	**********************************************************************************************
rat	.(((.((((((((((((.....(((..((((.....(((((((....)))))))...)))).)))......))))..))))))....)).))).	0.510 -33.00

rat

chromosome:20:44514995:44515088:-1

intergenic

block1095767 [novel_lenNOK_shortStem_5varHIGH_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	0.60/0.61	18/20/0.50	2.0	1.0	2	0	2	0	2	22	3arm	1	nd	0.30	4	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------GCCUUGA------------	1	novel
seed	-----------------------------------------------------------------------------------UCAUGCC----------------	1	novel
		len	cloning frequencies
			T3S1	T3S2
	----------------------------------------------------------------------------------GTCATGCCTTGAGCGGTCTG----	20	1	-
	--------------------------------------------------------------------------------------TGCCTTGAGCGGTCTGTG--	18	-	1
rat	aagttttaacctcttgaaaagcgatgaatgactccctacaaggaagtcctcccggaacaagggaagagagctccttctgttaGTCATGCCTTGAGCGGTCTGTGct
	**********************************************************************************************************
rat	.(((....(((.(((((...((.((((.((((.......(((((..(((((((.......))).)).))..)))))..)))).)))))).))))).)))....)))	0.920 -25.40

rat

chromosome:20:7292636:7292741:1

intergenic

block1162377 [novel_lenNOK_shortStem_5varHIGH_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	0.544	no	no	0.19/0.22	18/21/0.22	2.3	0.0	9	0	6	0	4	9	5arm	1	nd	0.28	4	9	6	na	na

		reads	miRBase family seed
seed	--------UGUUAAA-----------------------------------------------------------	7	novel
seed	-----UUUUGUU--------------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S1	T4S1	T5S2
	-------TTGTTAAAGTACTTAGTT-------------------------------------------------	18	1	1	1	1	1	2
	----ATTTTGTTAAAGTACTTAGTT-------------------------------------------------	21	-	-	-	-	2	-
rat	aagaATTTTGTTAAAGTACTTAGTTattgactagatggatactttcagtggcaggtgaacattgtaattgcttg
	**************************************************************************
rat	(((((((.((((....(((((.((((((((..((.......)).)))))))))))))))))....)))).))).	0.970 -11.20

rat

chromosome:2:93070585:93070658:-1

intergenic

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