Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_cloningHIGH_shortStem_nonpairedHIGH (48 loci)

novel_lenNOK_loopOverlap_mirtron_nonpairedHIGH_bulgeHIGH (48 loci)

block5200 [novel_lenNOK_loopOverlap_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	0.188	no	no	0.50/0.56	18/22/0.50	0.5	2.5	2	0	2	0	32	-8	5arm_loop_3arm	1	1	0.50	4	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------UGACCAC----------------------------------------------------------	1	novel
seed	----------------------------------GACCACU---------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1	T5S2
	--------------------------------CTGACCACTCACTCCATC------------------------------------------------	18	-	1
	---------------------------------TGACCACTCACTCCATCTCACA-------------------------------------------	22	1	-
rat	gctgaggaaggtaggttcactgcttctttgtcCTGACCACTCACTCCATCTCACAggatgaggtacacagggctgatgggaatactgctcaccctggt
	**************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000009283 ENSRNOG00000006873 Dnase1
rat	(((..((..(((((((((.((...((...((((((....((((.(((........))))))).....)))))).)).)))))).)))))..))..)))	0.810 -29.90

rat

chromosome:10:11765073:11765170:-1

Same_strand|Intronic_non-coding|ENSRNOT00000009283|ENSRNOG00000006873 ## ENSRNOG00000006873|protein_coding|Dnase1|Deoxyribonuclease-1 precursor (EC 3.1.21.1) (Deoxyribonuclease I) (DNase I). [Source:UniProtKB/Swiss-Prot;Acc:P21704]

block32667 [novel_lenNOK_loopOverlap_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	0.175	no	no	0.42/0.42	19/19/0.00	0.0	0.0	1	0	1	0	34	-4	5arm_loop	1	1	0.53	5	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------UCACCUG--------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------------------TTCACCTGTTTCCCTGTAA---------------------------------------------	19	1
rat	gctagctgaagacacagtgcctcctgccactcatTTCACCTGTTTCCCTGTAAgaggccaaaattcggaaatgaggaaaagctggtgcctttgctgca
	**************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000055932 ENSRNOG00000037100 RGD1559875_predicted
rat	((.(((.((((.....(((((..((....((((((((....((((.(((.....)))...))))...))))))))....))..)))))))))))))).	0.910 -26.40

rat

chromosome:10:71595967:71596064:-1

Same_strand|Intronic_coding|ENSRNOT00000055932|ENSRNOG00000037100 ## ENSRNOG00000037100|protein_coding|RGD1559875_predicted|

block39368 [novel_lenNOK_loopOverlap_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	0.018	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	17	-3	3arm_loop	1	0	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------AUGGUCU----------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------------------------------------GATGGTCTCGTTTTCCCAG-----------------	19	1
rat	gcgaatgggcatgggaggaggagagggagagcttagaGATGGTCTCGTTTTCCCAGgagccagccgggatcgt
	*************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000011474 ENSRNOG00000008642 Snx11
rat	((((...(((.(((.....((((((.((((.((.......)))))).))))))......))))))....))))	0.970 -22.20

rat

chromosome:10:85524839:85524911:-1

Same_strand|Intronic_non-coding|ENSRNOT00000011474|ENSRNOG00000008642 ## ENSRNOG00000008642|protein_coding|Snx11|sorting nexin 11 (Snx11), mRNA [Source:RefSeq_dna;Acc:NM_001012012]

block60073 [novel_lenNOK_loopOverlap_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	0.335	no	no	0.50/0.55	18/22/0.25	0.0	1.0	4	0	1	0	27	-8	5arm_loop_3arm	2	0	0.50	6	4	1	na	na

		reads	miRBase family seed
seed	----------------------------CUGAUGA------------------------------------------------	4	novel
		len	cloning frequencies
			T1S1
	---------------------------CCTGATGACTCTCTCTTC--------------------------------------	18	3
	---------------------------CCTGATGACTCTCTCTTCCCAG----------------------------------	22	1
rat	gaggagcatgagctgaagcaacctgtaCCTGATGACTCTCTCTTCCCAGgaaccatctgtaagcattaactacattgtcctcc
	***********************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000015092 ENSRNOG00000010771 Q9ERV0_RAT
rat	(((((..(((((.(((.((......(((..((((..((.((......))))..)))).))).)).))).)).)))..))))).	0.650 -16.20

rat

chromosome:10:13834964:13835046:1

Same_strand|Intronic_coding|ENSRNOT00000015092|ENSRNOG00000010771 ## ENSRNOG00000010771|protein_coding|Q9ERV0_RAT|Pkd1 (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q9ERV0]

block68783 [novel_lenNOK_loopOverlap_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	0.059	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	16	-3	5arm_loop	2	4	0.56	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------CCUUGGG----------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------TCCTTGGGTTGAAGGGTT------------------------------------	18	1
rat	ctactggggttatttgTCCTTGGGTTGAAGGGTTggaaatcgtgccaaatgggataacattgccggtgga
	**********************************************************************
	+++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004688 ENSRNOG00000003399 Hnrph1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004572 ENSRNOG00000003399 Hnrph1
	+++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000059190 ENSRNOG00000003399 Hnrph1
rat	(((((((......(((((((..(((....((........))..)))....))))))).....))))))).	0.510 -19.30

rat

chromosome:10:35924718:35924787:1

Same_strand|Boundary_coding|ENSRNOT00000059190|ENSRNOG00000003399 ## Same_strand|Intronic_coding|ENSRNOT00000004572|ENSRNOG00000003399 ## ENSRNOG00000003399|protein_coding|Hnrph1|Heterogeneous nuclear ribonucleoprotein H (hnRNP H) (Ratsg1). [Source:UniProtKB/Swiss-Prot;Acc:Q8VHV7]

block73711 [novel_lenNOK_loopOverlap_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	0.158	no	no	0.68/0.68	19/19/0.00	0.0	0.0	1	0	1	0	38	-3	5arm_loop	1	3	0.58	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------ACGGUGA------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--------------------------------------GACGGTGAGCCCAGGCCAT-------------------------------------------------	19	1
rat	gccaagtcattggacaggaggtccacagaatcctccatGACGGTGAGCCCAGGCCATgtgccaagttctctggagatctgtgccactaccactgctacttttggcc
	**********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000039444 ENSRNOG00000003226 MRIP_RAT
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004357 ENSRNOG00000003226 MRIP_RAT
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040865 ENSRNOG00000003226 MRIP_RAT
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004374 ENSRNOG00000003226 MRIP_RAT
rat	((((((....(((.(((..(((.((((((...(((((.((....((((...(((.....)))..))))))))))).)))))).....))).))))))..)))))).	0.670 -33.40

rat

chromosome:10:46056020:46056125:1

Same_strand|Boundary_coding|ENSRNOT00000004374|ENSRNOG00000003226 ## Same_strand|Intronic_coding|ENSRNOT00000039444|ENSRNOG00000003226 ## ENSRNOG00000003226|protein_coding|MRIP_RAT|Myosin phosphatase Rho-interacting protein (Rho-interacting protein 3) (p116Rip) (RIP3). [Source:UniProtKB/Swiss-Prot;Acc:Q9ERE6]

block77493 [novel_lenNOK_loopOverlap_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	0.019	no	no	0.50/0.50	18/18/0.00	0.0	0.0	2	0	2	0	24	-4	3arm_loop	1	1	0.50	5	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------UAUCCUC----------------------------------	2	novel
		len	cloning frequencies
			T3S2	T4S2
	--------------------------------TTATCCTCTGTGTCCCCA------------------------	18	1	1
rat	ccgggggcacagagggcacagcggcacaaggtTTATCCTCTGTGTCCCCAgcactgtgctgttgctgaacccgg
	**************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000032785 ENSRNOG00000023428 RGD1563261_predicted
rat	(((((..((..((.(((((((.(((((((((.....))).)))))).......))))))).))..))..)))))	0.760 -33.10

rat

chromosome:10:55241655:55241728:1

Same_strand|Intronic_coding|ENSRNOT00000032785|ENSRNOG00000023428 ## ENSRNOG00000023428|protein_coding|RGD1563261_predicted|

block119724 [novel_lenNOK_loopOverlap_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	0.113	no	no	0.32/0.33	18/19/0.00	0.7	0.3	3	0	3	0	18	-5	5arm_loop_3arm	2	2	0.42	5	3	3	na	na

		reads	miRBase family seed
seed	--------------------UAACUGA-------------------------------------------	2	novel
seed	-------------------GUAACUG--------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1
	-------------------GTAACTGATAATTTTCCC---------------------------------	18	1	-	-
	------------------AGTAACTGATAATTTTCCC---------------------------------	19	-	-	1
	-------------------GTAACTGATAATTTTCCCT--------------------------------	19	-	1	-
rat	ttgaaatgttattaaactAGTAACTGATAATTTTCCCTaggttttagaagactgagtttagacattcagt
	**********************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000002231 ENSRNOG00000001632 NP_001100576.1
rat	(((.((((((..(((((((((..((((.(((((.....)))))))))...))).))))))))))))))).	1.000 -12.60

rat

chromosome:11:36343719:36343788:-1

Same_strand|Intronic_coding|ENSRNOT00000002231|ENSRNOG00000001632 ## ENSRNOG00000001632|protein_coding|NP_001100576.1|bromodomain and WD repeat domain containing 1 [Source:RefSeq_peptide;Acc:NP_001100576]

block138777 [novel_lenNOK_loopOverlap_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	0.740	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	36	-3	3arm_loop	1	2	0.50	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------AAGUGUG----------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	----------------------------------------------AAAGTGTGTCTGAGGCTC------------------------------------	18	1
rat	tccctgctggcatcttgcaggcccccttctatgctcacaaccacccAAAGTGTGTCTGAGGCTCtggggccgtgtgggtgaactgagagacaagctggag
	****************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043701 ENSRNOG00000001715 Ece2
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000049511 ENSRNOG00000001715 Ece2
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000044482 ENSRNOG00000001715 Ece2
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042833 ENSRNOG00000001715 Ece2
rat	(((..(((..((.((..((((((((((((...((.(((...........))).))..))))....)))))).))..))))............))).))).	0.460 -30.54

rat

chromosome:11:82495145:82495244:-1

Same_strand|Boundary_non-coding|ENSRNOT00000002334|ENSRNOG00000001715 ## Same_strand|Boundary_coding|ENSRNOT00000049511|ENSRNOG00000001715 ## ENSRNOG00000001715|protein_coding|Ece2|endothelin-converting enzyme 2 [Source:RefSeq_peptide;Acc:NP_001002815]

block158459 [novel_lenNOK_loopOverlap_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	0.241	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	18	-4	5arm_loop	1	4	0.44	5	1	1	na	na

		reads	miRBase family seed
seed	-------------------GGUUACA-------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	------------------TGGTTACATTTCTTGACT---------------------------	18	1
rat	atgttttataaccatctcTGGTTACATTTCTTGACTtaaggagaagccagctgttttgcacat
	***************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000002232 ENSRNOG00000001634 LOC680866
rat	((((.....(((.....((((((...((((((......))))))))))))..)))....))))	0.530 -10.10

rat

chromosome:11:44755064:44755126:1

Same_strand|Boundary_non-coding|ENSRNOT00000035074|ENSRNOG00000001634 ## Same_strand|Intronic_non-coding|ENSRNOT00000002232|ENSRNOG00000001634 ## ENSRNOG00000001634|protein_coding|LOC680866|G protein-coupled receptor 128 [Source:RefSeq_peptide;Acc:NP_001100568]

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