Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_cloningOK_shortStem_loopOverlap_nonpairedHIGH (13 loci)

block951060 [novel_lenNOK_cloningOK_shortStem_loopOverlap_nonpairedHIGH]

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	0.42/0.44	18/19/0.00	0.0	0.0	8	0	5	0	1	-2	5arm_loop	1	nd	0.39	3	11	5	na	na

		reads	miRBase family seed
seed	--GGAAACA--------------------------------------	11	novel
		len	cloning frequencies
			T1S2	T2S1	T2S2	T4S2	T5S1
	-TGGAAACACTTCGTGTCT----------------------------	18	-	4	4	1	1
	-TGGAAACACTTCGTGTCTA---------------------------	19	1	-	-	-	-
rat	cTGGAAACACTTCGTGTCTaaactcaacacgttcagtctgcctccag
	***********************************************
	---------------------------------------------------------	ENSRNOT00000060971 ENSRNOG00000039743 NP_001034431.2
rat	(((((...(((.(((((.........)))))...))).....)))))	0.990 -9.50

rat

chromosome:1:30114000:30114046:1

Opposite_strand|Intronic_coding|ENSRNOT00000060971|ENSRNOG00000039743 ## ENSRNOG00000039743|protein_coding|NP_001034431.2|similar to DHHC-containing protein 10 (LOC499000), mRNA [Source:RefSeq_dna;Acc:NM_001039342]

block1142631 [novel_lenNOK_cloningOK_shortStem_loopOverlap_nonpairedHIGH]

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	0.034	no	no	0.60/0.63	18/20/0.09	0.0	0.2	10	0	2	0	1	-1	5arm_loop	1	nd	0.33	2	11	2	na	na

		reads	miRBase family seed
seed	--AAGACAC-------------------------------------	11	novel
		len	cloning frequencies
			T2S1	T2S2
	-CAAGACACAGTGGCACGC---------------------------	18	5	3
	-CAAGACACAGTGGCACGCG--------------------------	19	-	2
	-CAAGACACAGTGGCACGCGA-------------------------	20	-	1
rat	cCAAGACACAGTGGCACGCGataacagcttgagaattgaatcttgg
	**********************************************
rat	((((((..((((..((.((.......)).))...))))..))))))	1.000 -12.90

rat

chromosome:2:45086357:45086402:-1

intergenic

block1440875 [novel_lenNOK_cloningOK_shortStem_loopOverlap_nonpairedHIGH]

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	0.173	no	no	0.40/0.44	18/20/0.02	0.0	0.0	48	0	2	0	4	-1	5arm_loop	1	nd	0.33	2	49	2	na	na

		reads	miRBase family seed
seed	-----CCUCACA--------------------------------------	49	novel
		len	cloning frequencies
			T2S1	T2S2
	----TCCTCACACTGTTAGGTT----------------------------	18	20	28
	----TCCTCACACTGTTAGGTTAA--------------------------	20	1	-
rat	gcctTCCTCACACTGTTAGGTTaatatgctgagccatgtgtatggactgc
	**************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000007906 ENSRNOG00000022015 NP_001101306.1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000007776 ENSRNOG00000022015 NP_001101306.1
rat	((..(((..((((.(((.(((......))).)))...))))..)))..))	1.000 -12.00

rat

chromosome:3:14214549:14214598:1

Same_strand|Intronic_coding|ENSRNOT00000007776|ENSRNOG00000022015 ## ENSRNOG00000022015|protein_coding|NP_001101306.1|centrosomal protein 1 [Source:RefSeq_peptide;Acc:NP_001101306]

block1605492 [novel_lenNOK_cloningOK_shortStem_loopOverlap_nonpairedHIGH]

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	0.274	no	no	0.44/0.44	18/18/0.00	0.0	0.0	10	0	2	0	4	-4	3arm_loop	1	nd	0.44	3	10	2	na	na

		reads	miRBase family seed
seed	-------------------------GGAGUGU--------------	10	miR-122
		len	cloning frequencies
			T2S1	T2S2
	------------------------TGGAGTGTGACAAGTGTT----	18	4	6
rat	atgatgcacatgaaacacgttggcTGGAGTGTGACAAGTGTTtagt
	**********************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055712 ENSRNOG00000008667 NP_001099226.1
rat	.....((((.((..((((..........))))..)).)))).....	1.000 -8.70

rat

chromosome:4:172295731:172295776:-1

Same_strand|Boundary_non-coding|ENSRNOT00000011461|ENSRNOG00000008667 ## Same_strand|Intronic_non-coding|ENSRNOT00000055712|ENSRNOG00000008667 ## ENSRNOG00000008667|protein_coding|NP_001099226.1|phosphatidylethanlomine binding protein 2 [Source:RefSeq_peptide;Acc:NP_001099226]

block1876647 [novel_lenNOK_cloningOK_shortStem_loopOverlap_nonpairedHIGH]

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	0.064	no	no	0.50/0.50	18/18/0.00	0.0	0.0	10	0	2	0	4	-3	3arm_loop	2	nd	0.33	2	10	2	na	na

		reads	miRBase family seed
seed	----------------------AAGGCAG--------------	10	novel
		len	cloning frequencies
			T4S1	T4S2
	---------------------TAAGGCAGCCCTTTTGCT----	18	4	6
rat	tcttagggaaagtggccccaaTAAGGCAGCCCTTTTGCTctga
	*******************************************
	-----------------------------------------------------	ENSRNOT00000056882 ENSRNOG00000019236 LOC500532
rat	((..((.(((((.(((.((.....))..)))))))).))..))	1.000 -12.50

rat

chromosome:5:137645366:137645408:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000026201|ENSRNOG00000019236 ## Opposite_strand|Intronic_coding|ENSRNOT00000056882|ENSRNOG00000019236 ## ENSRNOG00000019236|protein_coding|LOC500532|

block2040750 [novel_lenNOK_cloningOK_shortStem_loopOverlap_nonpairedHIGH]

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	0.67/0.70	18/20/0.09	0.0	0.1	17	0	7	0	4	-1	3arm_loop	1	nd	0.32	2	22	7	na	na

		reads	miRBase family seed
seed	------------------------CCCUGUC----------------	22	miR-339
		len	cloning frequencies
			T1S1	T2S1	T2S2	T3S2	T4S2	T5S1	T5S2
	-----------------------TCCCTGTCCTCCAGGGGTC-----	19	3	1	-	4	4	4	-
	-----------------------TCCCTGTCCTCCAGGGGT------	18	-	1	1	-	-	1	1
	-----------------------TCCCTGTCCTCCAGGGGTCC----	20	-	-	2	-	-	-	-
rat	gtctgctctgagtacctgggaccTCCCTGTCCTCCAGGGGTCCtgac
	***********************************************
rat	(((.((((((((.((..(((....))).)).)))..)))))...)))	0.420 -14.20

rat

chromosome:6:93458348:93458394:1

intergenic

block2581369 [novel_lenNOK_cloningOK_shortStem_loopOverlap_nonpairedHIGH]

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	0.208	no	no	0.44/0.56	18/20/0.36	1.0	0.3	45	0	10	0	0	-5	3arm	1	nd	0.44	3	45	10	na	na

		reads	miRBase family seed
seed	------------------------------GUGUUCA-------------	17	miR-124*
seed	-------------------------------UGUUCAA------------	14	novel
seed	--------------------------------GUUCAAA-----------	11	novel
seed	---------------------------------UUCAAAG----------	2	novel
seed	----------------------------AAGUGUU---------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	-----------------------------AGTGTTCAAAGCAGGCACGA-	20	2	1	3	2	-	3	2	-	2	-
	------------------------------GTGTTCAAAGCAGGCACGA-	19	-	1	2	3	2	2	1	1	-	1
	-------------------------------TGTTCAAAGCAGGCACGA-	18	1	1	1	-	1	1	1	-	1	3
	--------------------------------GTTCAAAGCAGGCACGAC	18	-	-	-	1	-	-	-	1	-	-
	-----------------------------AGTGTTCAAAGCAGGCAC---	18	-	-	-	1	1	-	-	-	-	-
	------------------------------GTGTTCAAAGCAGGCACGAC	20	1	-	-	-	-	-	-	-	-	-
	-------------------------------TGTTCAAAGCAGGCACGAC	19	-	-	-	-	-	-	-	1	-	-
	---------------------------TAAGTGTTCAAAGCAGGC-----	18	-	-	1	-	-	-	-	-	-	-
rat	gtcatacagtgaatgacaagtgaatgaTAAGTGTTCAAAGCAGGCACGAC
	**************************************************
rat	........(((..((.....(((((.......)))))...))..)))...	0.700 -8.60

rat

chromosome:9:29119490:29119539:1

intergenic

block2640586 [novel_lenNOK_cloningOK_shortStem_loopOverlap_nonpairedHIGH]

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	0.209	no	no	0.61/0.61	18/18/0.00	0.0	0.0	36	0	10	0	4	-2	3arm_loop	1	nd	0.33	3	39	10	na	na

		reads	miRBase family seed
seed	---------------------------GGGAAUG--------------	39	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	--------------------------GGGGAATGCTTGGCTTGG----	18	4	1	3	6	5	8	2	3	3	4
rat	aggatcaagtggtcaggttgaaacccGGGGAATGCTTGGCTTGGgttc
	************************************************
	----------------------------------------------------------	ENSRNOT00000045096 ENSRNOG00000034177 Efna5
	----------------------------------------------------------	ENSRNOT00000043566 ENSRNOG00000034177 Efna5
rat	.(((((....((((((((.....((...))...))))))))..)))))	0.520 -11.70

rat

chromosome:9:101417806:101417853:1

Opposite_strand|Intronic_coding|ENSRNOT00000045096|ENSRNOG00000034177 ## ENSRNOG00000034177|protein_coding|Efna5|Ephrin-A5 precursor (EPH-related receptor tyrosine kinase ligand 7) (LERK-7) (AL-1). [Source:UniProtKB/Swiss-Prot;Acc:P97605]

novel_lenNOK_multiarm_DicerNOK_Multihit_shortStem_nonpairedHIGH (13 loci)

sblock11216 [novel_lenNOK_multiarm_DicerNOK_Multihit_shortStem_nonpairedHIGH]

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	0.317	no	no	0.37/0.63	19/19/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	0 4	38 26	5arm 3arm	13 13	nd nd	0.42 0.53	2 4	2	2	-4	-4

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------------CUCCAGC---------------	1	novel
seed	-UCUUGAC----------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1	T5S1
	TTCTTGACCTTCTTCACTA-----------------------------------------------------------------------------------------------	19	1	-
	-------------------------------------------------------------------------------------------GCTCCAGCAGGGGACTTCT----	19	-	1
rat	TTCTTGACCTTCTTCACTAtaccatgctacagtcattagcctcttctaggacctactaaaatcaaagggggtcaatctagatactgagtgtGCTCCAGCAGGGGACTTCTtgaa
	******************************************************************************************************************
rat	.((..((..(((((..((....((((((.((((...........(((((((((..((........))..))))...))))).))))))))))....))..)))))..))..)).	0.650 -24.20

rat

chromosome:7:18782199:18782312:1

intergenic

sblock1588 [novel_lenNOK_multiarm_DicerNOK_Multihit_shortStem_nonpairedHIGH]

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	0.067	no	no	0.37/0.50	19/20/0.67	0.0 0.0	0.0 0.0	2 1	0 0	1 1	0 0	0 4	4 0	5arm 3arm	20 20	nd nd	0.35 0.32	4 3	3	1	-3	-4

		reads	miRBase family seed
seed	-GCCAGCU-----------------------------------------------	2	novel
seed	---------------------------------UCACAAC---------------	1	novel
		len	cloning frequencies
			T5S1
	TGCCAGCTCTCCAATGTTGT-----------------------------------	20	2
	--------------------------------TTCACAACAGCTAGAATCT----	19	1
rat	TGCCAGCTCTCCAATGTTGTaggatatccactTTCACAACAGCTAGAATCTtgca
	*******************************************************
	-----------------------------------------------------------------	ENSRNOT00000048246 ENSRNOG00000039174 RGD1563865_predicted
rat	.((.((.(((....((((((.(((........)))))))))...)))..)).)).	1.000 -10.70

rat

chromosome:1:52046179:52046233:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000059936|ENSRNOG00000039174 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000048246|ENSRNOG00000039174 ## ENSRNOG00000039174|protein_coding|RGD1563865_predicted|

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