Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_nonpairedHIGH_bulgeHIGH (34 loci)

novel_Multihit_shortStem_bulgeHIGH (33 loci)

block6847 [novel_Multihit_shortStem_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	0.051	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	4	25	5arm	18	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-----CCUCAUC--------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----ACCTCATCTTGTAACGGAAG--------------------------------------------------------------------------------------------	20	1
rat	acagACCTCATCTTGTAACGGAAGcccagtgtcacaacctttatcatgttctgaacatgactgcagatggttctgacagtggccagttcctttctgttaccgtttgtaaccgtttg
	********************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000022050 ENSRNOG00000024635 Cramp1l_predicted
rat	.(((((..((....((((((((((((((.(((((.(((((((.((((((.....))))))....))).)))).))))).)))...))....)))))))))....)).....)))))	0.920 -31.00

rat

chromosome:10:14247792:14247907:-1

Same_strand|Intronic_coding|ENSRNOT00000022050|ENSRNOG00000024635 ## ENSRNOG00000024635|protein_coding|Cramp1l_predicted|

block103956 [novel_Multihit_shortStem_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	0.493	no	no	0.39/0.39	23/23/1.00	0.0	0.0	1	0	1	0	3	22	3arm	30	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------GUCUAUA------------------	1	novel
		len	cloning frequencies
			T4S1
	-------------------------------------------------------------------------------TGTCTATAAAGCATTTAACCCCC---	23	1
rat	aggaggaagaagaggaagatgaagatgatgaagaagaagatgatgatgaataagttggttctagcgcagttttttttctTGTCTATAAAGCATTTAACCCCCctg
	*********************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000005035 ENSRNOG00000003673 Pcnt1
	-------------------------------------------------------------------------------------------------------------------	ENSRNOT00000005347 ENSRNOG00000003990 Grb2
	-------------------------------------------------------------------------------------------------------------------	ENSRNOT00000043473 ENSRNOG00000003990 Grb2
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.........................................................	ENSRNOT00000009330 ENSRNOG00000007121
rat	(((.((.......((.(((((...(((((((..((((((((..((..((((......))))...))..))))))))..))))).))....)))))..))))))).	0.950 -18.51

rat

chromosome:10:105805878:105805982:1

Opposite_strand|Intronic_coding|ENSRNOT00000043473|ENSRNOG00000003990 ## Same_strand|Intronic_non-coding|ENSRNOT00000005035|ENSRNOG00000003673 ## ENSRNOG00000003990|protein_coding|Grb2|Growth factor receptor-bound protein 2 (Adapter protein GRB2) (SH2/SH3 adapter GRB2) (Protein Ash). [Source:UniProtKB/Swiss-Prot;Acc:P62994] ## ENSRNOG00000003673|protein_coding|Pcnt1|pericentrin 1 [Source:RefSeq_peptide;Acc:NP_001020572]

block352557 [novel_Multihit_shortStem_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	0.502	no	no	0.59/0.59	22/22/1.00	0.0	0.0	1	0	1	0	3	3	3arm	112	nd	0.27	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------UCAGUUG-----------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------------------------CTCAGTTGCTGAGGAGTCCCCA---	22	1
rat	ggatcacccaccccagcccagcaaggatactgagagcaagagagaggccCTCAGTTGCTGAGGAGTCCCCAtcc
	**************************************************************************
rat	((((............(((((((.....((((((.((.........)).))))))))))).)).))))......	0.430 -19.02

rat

chromosome:14:47763784:47763857:-1

intergenic

block353647 [novel_Multihit_shortStem_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	0.025	no	no	0.43/0.43	21/21/1.00	0.0	0.0	1	0	1	0	1	39	5arm	25	nd	0.24	4	1	1	na	na

		reads	miRBase family seed
seed	--CUCCUUU---------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-GCTCCTTTTGCAGAATAGACT--------------------------------------------------------------------------------------------------	21	1
rat	tGCTCCTTTTGCAGAATAGACTtatagcctgtagcttgcctcggagacatagtagacaagcagttagtgatggtaataatcttttcaaggggagtggaagtaggtctgtattgttggagt
	************************************************************************************************************************
	----------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000049147 ENSRNOG00000032644
rat	.(((((....((((.((((((((((..((....((((.(((.(((((.((.((...((.((.....))..))...)).)).))))).))).))))))..)))))))))).)))).)))))	0.870 -35.30

rat

chromosome:14:49144056:49144175:-1

Opposite_strand|Intronic_coding|ENSRNOT00000049147|ENSRNOG00000032644 ## ENSRNOG00000032644|protein_coding||

block354474 [novel_Multihit_shortStem_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	0.416	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	1	22	5arm	19	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	--UCUUACA-----------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	-TTCTTACACTGTCAGACCCA-----------------------------------------------------------------------------------	20	1
rat	gTTCTTACACTGTCAGACCCAtttgaagctcatcatttctcctaacccattgaggctgaaattaactgagagaaaatgatgttgattgacagcacttgcagaat
	********************************************************************************************************
	------------------------------------------------------------------------------------------------------------------	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
rat	(((((....(((((((((.(((((....((((..(((((.(((.........)))..)))))....))))...)))))..)))...)))))).......)))))	0.750 -18.90

rat

chromosome:14:49747690:49747793:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000050021|ENSRNOG00000032207 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000043791|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7]

block372815 [novel_Multihit_shortStem_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	0.057	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	0	7	5arm	35	nd	0.27	4	1	1	na	na

		reads	miRBase family seed
seed	-GAUUGAG----------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	GGATTGAGCACATCAAGCACTC--------------------------------------------	22	1
rat	GGATTGAGCACATCAAGCACTCgaagagcagagacggcttcctgaagtgggtgatggagaacgatc
	******************************************************************
rat	.(((((....(((((..((((((..((((.......))))..))).)))..))))).....)))))	1.000 -18.10

rat

chromosome:14:99058246:99058311:-1

intergenic

block673655 [novel_Multihit_shortStem_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	0.076	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	4	1	5arm	22	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-----CACUUUU----------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	----GCACTTTTGATGTGTCAATCCTC-------------------------------------------	23	1
rat	ggtgGCACTTTTGATGTGTCAATCCTCactcactattgaggatgaaatttttgaagtcaaatcaactgct
	**********************************************************************
rat	(((((....((((((...((((((((((........)))))))........))).))))))....)))))	0.800 -16.20

rat

chromosome:17:75127966:75128035:1

intergenic

block769491 [novel_Multihit_shortStem_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	0.215	no	no	0.30/0.30	20/20/1.00	0.0	0.0	1	0	1	0	2	39	5arm	14	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	---AAAACUU------------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	--TAAAACTTCCTGAGATTTCA------------------------------------------------------------------------------------------------	20	1
rat	gtTAAAACTTCCTGAGATTTCAcaccagcttgaatatgcagtcaaaagttctcctgtctcattatgtacaggtgctttaaatcacatcaagaagtagtctgcatggtaggttacaaca
	**********************************************************************************************************************
rat	(((..((((((((((((((....((...(((((...((..((..(((((...(((((..((...)).))))).)))))..))..)))))))..))))))).)).)).)))))..))).	0.710 -22.60

rat

chromosome:19:14757870:14757987:-1

intergenic

block842790 [novel_Multihit_shortStem_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	0.076	no	no	0.62/0.62	24/24/1.00	0.0	0.0	2	0	1	0	0	4	3arm	17	nd	0.30	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------CAUCUAU----------------	2	novel
		len	cloning frequencies
			T1S1
	-------------------------------------------CCATCTATCCTGAGCCCAGGGAGC	24	2
rat	ctcccctactcctgcagacccatgaatggtgccttctcagggcCCATCTATCCTGAGCCCAGGGAGC
	*******************************************************************
	-----------------------------------------------------------------------------	ENSRNOT00000060054 ENSRNOG00000039226 RGD1561706_predicted
rat	(((((......((.(((....(((.((((.((((.....)))))))).))).)))))....))))).	0.640 -19.10

rat

chromosome:1:48967685:48967751:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000039923|ENSRNOG00000039226 ## Opposite_strand|Intronic_coding|ENSRNOT00000060054|ENSRNOG00000039226 ## ENSRNOG00000039226|protein_coding|RGD1561706_predicted|

block844967 [novel_Multihit_shortStem_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	0.076	no	no	0.62/0.62	24/24/1.00	0.0	0.0	2	0	1	0	0	4	3arm	17	nd	0.30	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------CAUCUAU----------------	2	novel
		len	cloning frequencies
			T1S1
	-------------------------------------------CCATCTATCCTGAGCCCAGGGAGC	24	2
rat	ctcccctactcctgcagacccatgaatggtgccttctcagggcCCATCTATCCTGAGCCCAGGGAGC
	*******************************************************************
rat	(((((......((.(((....(((.((((.((((.....)))))))).))).)))))....))))).	0.640 -19.10

rat

chromosome:1:50381919:50381985:-1

intergenic

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