Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_multiarm_DicerNOK_Multihit (25 loci)

sblock8663 [novel_multiarm_DicerNOK_Multihit]

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	0.054	no	no	0.50/0.65	20/20/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	31 15	4 9	5arm 3arm	26 29	nd nd	0.45 0.30	4 3	2	1	9	11

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CUGGACG---------------------------	1	novel
seed	--------------------------------CACCCCC--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------------------------------------------------CCTGGACGTACTGAATCTTG---------------	20	1
	-------------------------------ACACCCCCAGGGAGACACTG--------------------------------------------------------	20	1
rat	ggggctctatgttgccagaggtgccttctgtACACCCCCAGGGAGACACTGtcccgagaaaaagggtcgttcCCTGGACGTACTGAATCTTGcctttggacacctcc
	***********************************************************************************************************
rat	((((........(((((((((((..(((.((((....((((((((....((.(((........))).))))))))))..)))).)))...))))))))).)))))).	0.890 -38.80

rat

chromosome:4:150735413:150735519:-1

intergenic

sblock8669 [novel_multiarm_DicerNOK_Multihit]

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	0.054	no	no	0.50/0.65	20/20/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	31 15	4 9	5arm 3arm	26 29	nd nd	0.45 0.30	4 3	2	1	9	11

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CUGGACG---------------------------	1	novel
seed	--------------------------------CACCCCC--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------------------------------------------------CCTGGACGTACTGAATCTTG---------------	20	1
	-------------------------------ACACCCCCAGGGAGACACTG--------------------------------------------------------	20	1
rat	ggggctctatgttgccagaggtgccttctgtACACCCCCAGGGAGACACTGtcccgagaaaaagggtcgttcCCTGGACGTACTGAATCTTGcctttggacacctcc
	***********************************************************************************************************
rat	((((........(((((((((((..(((.((((....((((((((....((.(((........))).))))))))))..)))).)))...))))))))).)))))).	0.890 -38.80

rat

chromosome:4:150739748:150739854:-1

intergenic

sblock8675 [novel_multiarm_DicerNOK_Multihit]

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	0.054	no	no	0.50/0.65	20/20/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	31 15	4 9	5arm 3arm	26 29	nd nd	0.45 0.30	4 3	2	1	9	11

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CUGGACG---------------------------	1	novel
seed	--------------------------------CACCCCC--------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------------------------------------------------CCTGGACGTACTGAATCTTG---------------	20	1
	-------------------------------ACACCCCCAGGGAGACACTG--------------------------------------------------------	20	1
rat	ggggctctatgttgccagaggtgccttctgtACACCCCCAGGGAGACACTGtcccgagaaaaagggtcgttcCCTGGACGTACTGAATCTTGcctttggacacctcc
	***********************************************************************************************************
rat	((((........(((((((((((..(((.((((....((((((((....((.(((........))).))))))))))..)))).)))...))))))))).)))))).	0.890 -38.80

rat

chromosome:4:150752670:150752776:-1

intergenic

sblock8992 [novel_multiarm_DicerNOK_Multihit]

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	0.184	no	no	0.36/0.55	20/23/1.00	0.0 0.0 0.0	0.0 0.0 0.0	2 1 1	0 0 0	1 1 1	0 0 0	4 20 8	24 5 16	5arm 5arm 3arm	48 48 153	nd nd nd	0.30 0.57 0.36	3 6 3	4	2	-4	-1

		reads	miRBase family seed
seed	-----ACCAGGU-----------------------------------------------------------------------------------------	2	novel
seed	---------------------UGACUUC-------------------------------------------------------------------------	1	novel
seed	------------------------------------------------------------------------UGCUCUC----------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1
	----GACCAGGTTGTCTCCTGTGA-----------------------------------------------------------------------------	20	-	2
	-----------------------------------------------------------------------TTGCTCTCAATGACAACTTTGT--------	22	1	-
	--------------------GTGACTTCAACAGCAACTCCCAC----------------------------------------------------------	23	1	-
rat	tgagGACCAGGTTGTCTCCTGTGACTTCAACAGCAACTCCCACtcttccacctttgatgctggggctggcaTTGCTCTCAATGACAACTTTGTaaagctca
	*****************************************************************************************************
	---------------------------------------------------------------------------------------------------------------	ENSRNOT00000023122 ENSRNOG00000017115 NP_001100078.1
rat	.(((.((.((((((((...((.((......((((....((((....((.......))...)))))))).......)).))..)))))))).))....))).	0.570 -23.12

rat

chromosome:4:123558447:123558547:1

Opposite_strand|Intronic_coding|ENSRNOT00000023122|ENSRNOG00000017115 ## ENSRNOG00000017115|protein_coding|NP_001100078.1|coiled-coil-helix-coiled-coil-helix domain containing 6 [Source:RefSeq_peptide;Acc:NP_001100078]

sblock12450 [novel_multiarm_DicerNOK_Multihit]

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	0.125	no	no	0.45/0.70	20/22/1.00	0.0 0.0 0.0	0.0 0.0 0.0	1 1 1	0 0 0	1 1 1	0 0 0	10 19 4	12 3 18	5arm 3arm 3arm	2 52 52	nd nd nd	0.41 0.35 0.20	5 4 2	3	2	0	-13

		reads	miRBase family seed
seed	-----------------------------------------------------CAUCCUA-------------------------------	1	novel
seed	--------------------------------------------------------------------CCUGGCU----------------	1	novel
seed	-----------UCUUACA-------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S2
	----------------------------------------------------TCATCCTAGCTTGATGCCTG-------------------	20	1	-
	-------------------------------------------------------------------GCCTGGCTCGGTGGCCAAAG----	20	-	1
	----------TTCTTACATCAGTCAGGGGCAA-----------------------------------------------------------	22	-	1
rat	tgtggtgttgTTCTTACATCAGTCAGGGGCAAagcagatggccgtcctttgtTCATCCTAGCTTGATGCCTGGCTCGGTGGCCAAAGctat
	*******************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000022676 ENSRNOG00000016486 Nol5
rat	.(((((.(((......(((((((((((....((((.((((..((.....))..))))...))))....))))))).))))..))).)))))	0.930 -27.50

rat

chromosome:9:58259026:58259116:1

Same_strand|Intronic_non-coding|ENSRNOT00000022676|ENSRNOG00000016486 ## ENSRNOG00000016486|protein_coding|Nol5|Nucleolar protein 5 (Nucleolar protein NOP5) (Nopp140-associated protein of 65 kDa). [Source:UniProtKB/Swiss-Prot;Acc:Q9QZ86]

novel_shortStem_mirtron_nonpairedHIGH_bulgeHIGH (25 loci)

block43639 [novel_shortStem_mirtron_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	0.229	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	4	3	3arm	1	0	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------CUUGGCU------------------	1	novel
		len	cloning frequencies
			T1S2
	------------------------------------------------CCTTGGCTTTTGTCTTTCTCAG----	22	1
rat	accagtaaaggcagaagacagattgccttccagcctacacaactagggCCTTGGCTTTTGTCTTTCTCAGgggt
	**************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>	ENSRNOT00000055176 ENSRNOG00000002818 Eftud2
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>	ENSRNOT00000003807 ENSRNOG00000002818 Eftud2
rat	(((.....((...(((((((((..(((.....((((.........))))...))).)))))))))))....)))	0.690 -18.80

rat

chromosome:10:92013229:92013302:-1

Same_strand|Intronic_coding|ENSRNOT00000003807|ENSRNOG00000002818 ## ENSRNOG00000002818|protein_coding|Eftud2|Eftud2 protein (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q5EB83]

block213635 [novel_shortStem_mirtron_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	0.549	no	no	0.52/0.52	23/23/1.00	0.0	0.0	1	0	1	0	2	3	5arm	1	0	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	---GAAACCC--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--TGAAACCCTGCCTCTCATTGCAG-----------------------------------------------	23	1
rat	ccTGAAACCCTGCCTCTCATTGCAGgtttatgaatgaccgagtcccggcacacaagaggtaccggcccacag
	************************************************************************
	++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000060608 ENSRNOG00000001113 Mmd2_predicted
	++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000001474 ENSRNOG00000001113 Mmd2_predicted
	++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000060606 ENSRNOG00000001113 Mmd2_predicted
	......................>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000060604 ENSRNOG00000001113 Mmd2_predicted
rat	.(((....(((((((((...(((.((((.......))))........)))....)))))))..))....)))	0.440 -15.50

rat

chromosome:12:12389611:12389682:1

Same_strand|Intronic_coding|ENSRNOT00000060606|ENSRNOG00000001113 ## Same_strand|Boundary_non-coding|ENSRNOT00000060604|ENSRNOG00000001113 ## ENSRNOG00000001113|protein_coding|Mmd2_predicted|monocyte to macrophage differentiation-associated 2 [Source:RefSeq_peptide;Acc:NP_001032294]

block215903 [novel_shortStem_mirtron_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	0.204	no	no	0.57/0.57	23/23/1.00	0.0	0.0	1	0	1	0	2	8	5arm	1	1	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	---GGUUUGC----------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--GGGTTTGCTGGGTGATGCACTGT-------------------------------------------	23	1
rat	gcGGGTTTGCTGGGTGATGCACTGTaggtgaggggcccttgcacccaggtgaattctgtgaattctgc
	********************************************************************
	>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000001727 ENSRNOG00000022599 Ints1
rat	((((((((((.((((....((((...(((((((....))).))))..)))).)))).)))))).))))	0.890 -22.30

rat

chromosome:12:15339152:15339219:1

Same_strand|Boundary_non-coding|ENSRNOT00000001727|ENSRNOG00000022599 ## ENSRNOG00000022599|protein_coding|Ints1|integrator complex subunit 1 Gene [Source:MGI Symbol;Acc:MGI:1915760]

block256406 [novel_shortStem_mirtron_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	0.228	no	no	0.52/0.52	21/21/1.00	0.0	0.0	2	0	1	0	3	29	3arm	1	0	0.38	4	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------CCAGUGU----------------	2	miR-199a
		len	cloning frequencies
			T2S2
	-------------------------------------------------------------------------------------TCCAGTGTGTCTCTCCCTTAG---	21	2
rat	ctgctgtgaagatggcagactctagtgtacacagagcgtagggagcactgcccactggttgtacctaagctctcacaaatctcacTCCAGTGTGTCTCTCCCTTAGgag
	*************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>	ENSRNOT00000005505 ENSRNOG00000004125 C4bpb
rat	((.(((...(((.((((.(((..((((.....(((((.((((..(((..(((....)))))).)))).))))).........))))..))).)))))))....))).))	0.750 -31.04

rat

chromosome:13:43605785:43605893:-1

Same_strand|Intronic_coding|ENSRNOT00000005505|ENSRNOG00000004125 ## ENSRNOG00000004125|protein_coding|C4bpb|C4b-binding protein beta chain precursor. [Source:UniProtKB/Swiss-Prot;Acc:Q63515]

block374667 [novel_shortStem_mirtron_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	0.348	no	no	0.73/0.73	22/22/1.00	0.0	0.0	1	0	1	0	0	5	3arm	1	2	0.38	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------AACCGGC--------------	1	novel
		len	cloning frequencies
			T1S2
	----------------------------------TAACCGGCCTCCCGCTCCCTGC	22	1
rat	gcaggtcgtgagtgctctgagcccctacgggtggTAACCGGCCTCCCGCTCCCTGC
	********************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>	ENSRNOT00000012131 ENSRNOG00000008917 Ehbp1_predicted
rat	(((((.((.(((.(((....(((((....)).)))....)))))).))...)))))	1.000 -23.20

rat

chromosome:14:102732536:102732591:-1

Same_strand|Intronic_coding|ENSRNOT00000012131|ENSRNOG00000008917 ## ENSRNOG00000008917|protein_coding|Ehbp1_predicted|

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