Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_loopOverlap_mirtron (39 loci)

block2757149 [novel_lenNOK_loopOverlap_mirtron]

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	0.316	no	no	0.67/0.67	18/18/0.00	0.0	0.0	1	0	1	0	26	-4	3arm_loop	1	0	0.22	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------UUUCCUC------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	--------------------------------------------------------------------------TTTTCCTCCGGCCCCCAG--------------------------	18	1
rat	tccaggactagactccaggctgggtgctgctgatggggaccagaggcttttccttcacacaccccccccctttcTTTTCCTCCGGCCCCCAGctgattccgcgccgcttagactggga
	**********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000003127 ENSRNOG00000002291 Brwd3_predicted
rat	(((((..((((......(((((((....((((..((((.((.((((................................)))).))))))))))....)))).)))..)))).))))).	0.790 -35.75

rat

chromosome:X:97130212:97130329:-1

Same_strand|Boundary_non-coding|ENSRNOT00000057431|ENSRNOG00000002291 ## Same_strand|Intronic_coding|ENSRNOT00000003127|ENSRNOG00000002291 ## ENSRNOG00000002291|protein_coding|Brwd3_predicted|

block2974304 [novel_lenNOK_loopOverlap_mirtron]

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	0.652	no	no	0.37/0.43	19/23/0.33	0.0	1.3	3	0	1	0	17	-1	5arm_loop	2	2	0.26	2	3	1	na	na

		reads	miRBase family seed
seed	------------------CUUCUUU------------------------------------------------------	3	novel
		len	cloning frequencies
			T3S1
	-----------------CCTTCTTTATTTTCCACCT-------------------------------------------	19	2
	-----------------CCTTCTTTATTTTCCACCTAGCC---------------------------------------	23	1
rat	tctgagtactacaaatgCCTTCTTTATTTTCCACCTAGCCcagcagaggaattatattttggaagcattgaatctgggg
	*******************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004494 ENSRNOG00000003350 RGD1563952_predicted
	+++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000047646 ENSRNOG00000003350 RGD1563952_predicted
	+++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004533 ENSRNOG00000003350 RGD1563952_predicted
rat	.((.((.......((((.(((((.(((.((((..((.((...)))).))))..)))....)))))))))....)).)).	1.000 -13.10

rat

chromosome:X:50194548:50194626:1

Same_strand|Boundary_coding|ENSRNOT00000047646|ENSRNOG00000003350 ## ENSRNOG00000003350|protein_coding|RGD1563952_predicted|

block1592457 [novel_lenNOK_loopOverlap_mirtron]

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	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	28	-1	5arm_loop	1	0	0.16	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------GUGCUCG----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------GGTGCTCGTTTGTTTGCAG-----------------------------------------------------------------	19	1
rat	gggtgctgtagcctacattggttctaaaGGTGCTCGTTTGTTTGCAGgtcaatgtgcggaatgggatgagcttgcacgactgccttatgaaagctctgaaggttagaggcct
	****************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000013831 ENSRNOG00000010153 Raf1
rat	((((.((.((((((.((....(((..(((((((((((((.((((((........))))))...))))))))..........)))))..))).....)).)))))).))))))	0.910 -32.50

rat

chromosome:4:151770175:151770286:-1

Same_strand|Intronic_coding|ENSRNOT00000013831|ENSRNOG00000010153 ## ENSRNOG00000010153|protein_coding|Raf1|RAF proto-oncogene serine/threonine-protein kinase (EC 2.7.11.1) (Raf- 1) (C-RAF) (cRaf). [Source:UniProtKB/Swiss-Prot;Acc:P11345]

novel_shortStem_loopOverlap_randfoldOK (39 loci)

block216970 [novel_shortStem_loopOverlap_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	0.004	no	no	0.48/0.48	21/21/1.00	0.0	0.0	2	0	2	0	0	-1	5arm_loop	2	nd	0.24	2	2	2	na	na

		reads	miRBase family seed
seed	-ACAUGUG------------------------------------------------------	2	novel
		len	cloning frequencies
			T2S1	T2S2
	TACATGTGTGTGCACACACAG-----------------------------------------	21	1	1
rat	TACATGTGTGTGCACACACAGaactataatgcccacacatgtttgtacgcacacactaggta
	**************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000001784 ENSRNOG00000001317 NM_001107128.1
rat	(((..(((((((((((.(((...................))).)))..))))))))...)))	0.970 -16.31

rat

chromosome:12:16543629:16543690:1

Same_strand|Intronic_coding|ENSRNOT00000001784|ENSRNOG00000001317 ## ENSRNOG00000001317|protein_coding|NM_001107128.1|zinc finger protein 68 (predicted) (Zfp68_predicted), mRNA [Source:RefSeq_dna;Acc:NM_001107128]

block462974 [novel_shortStem_loopOverlap_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	0.55/0.55	22/22/1.00	0.0	0.0	1	0	1	0	1	-2	3arm_loop	1	nd	0.14	1	1	1	na	na

		reads	miRBase family seed
seed	------------------------UGCAUCG---------------	1	novel
		len	cloning frequencies
			T2S1
	-----------------------ATGCATCGTCACTGCAGAGACC-	22	1
rat	aggtttcactgtggggcgagcaaATGCATCGTCACTGCAGAGACCt
	**********************************************
rat	(((((((..((((((((((((....)).))))).))))))))))))	1.000 -20.70

rat

chromosome:15:89316284:89316329:-1

intergenic

block509563 [novel_shortStem_loopOverlap_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	0.003	no	no	0.25/0.25	20/20/1.00	0.0	0.0	1	0	1	0	4	-1	3arm	1	nd	0.15	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------UUUAGAU----------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------------------TTTTAGATTTTGTGCCTTTA----	20	1
rat	acttaaaaatttaggcactcactccaatatctgagttcatTTTTAGATTTTGTGCCTTTAagta
	****************************************************************
rat	((((((......((((((..........(((((((......)))))))...)))))))))))).	0.990 -14.42

rat

chromosome:15:93973171:93973234:1

intergenic

block528936 [novel_shortStem_loopOverlap_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	0.006	no	no	0.50/0.50	24/24/1.00	0.0	0.0	2	0	1	0	4	-1	3arm	10	nd	0.29	3	2	1	na	na

		reads	miRBase family seed
seed	---------------------------------UGGACAG--------------------	2	novel
		len	cloning frequencies
			T3S1
	--------------------------------ATGGACAGTTCCACTTCCTCTGAG----	24	2
rat	gaccccagaagggaactgacagagaggaagaaATGGACAGTTCCACTTCCTCTGAGggtt
	************************************************************
rat	((((((((((((((((((.((............))..))))))).))...)))).)))))	0.420 -21.60

rat

chromosome:16:27499271:27499330:-1

intergenic

block528951 [novel_shortStem_loopOverlap_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	0.006	no	no	0.50/0.50	24/24/1.00	0.0	0.0	2	0	1	0	4	-1	3arm	10	nd	0.29	3	2	1	na	na

		reads	miRBase family seed
seed	---------------------------------UGGACAG--------------------	2	novel
		len	cloning frequencies
			T3S1
	--------------------------------ATGGACAGTTCCACTTCCTCTGAG----	24	2
rat	gaccccagaagggaactgacagagaggaagaaATGGACAGTTCCACTTCCTCTGAGggtt
	************************************************************
rat	((((((((((((((((((.((............))..))))))).))...)))).)))))	0.420 -21.60

rat

chromosome:16:27502947:27503006:-1

intergenic

block549737 [novel_shortStem_loopOverlap_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	0.003	no	no	0.38/0.38	21/21/1.00	0.0	0.0	1	0	1	0	2	-1	5arm_loop	1	nd	0.29	2	1	1	na	na

		reads	miRBase family seed
seed	---GGGUUCC------------------------------------------	1	miR-23a*
		len	cloning frequencies
			T5S1
	--TGGGTTCCAGTGATTTAATCA-----------------------------	21	1
rat	gcTGGGTTCCAGTGATTTAATCAaagcagaaggaattccatggagtcctagc
	****************************************************
	--------------------------------------------------------------	ENSRNOT00000057897 ENSRNOG00000030719 Csmd1
	--------------------------------------------------------------	ENSRNOT00000044850 ENSRNOG00000030719 Csmd1
	--------------------------------------------------------------	ENSRNOT00000040648 ENSRNOG00000030719 Csmd1
rat	(((((((((((..(((((..((......))..)))))...))))).))))))	0.810 -17.80

rat

chromosome:16:78352554:78352605:-1

Opposite_strand|Intronic_coding|ENSRNOT00000057897|ENSRNOG00000030719 ## ENSRNOG00000030719|protein_coding|Csmd1|CUB and Sushi multiple domains 1 [Source:RefSeq_peptide;Acc:NP_001032404]

block599456 [novel_shortStem_loopOverlap_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	0.54/0.54	24/24/1.00	0.0	0.0	2	0	1	0	0	-1	3arm	1	nd	0.26	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------------------CCUCCCU----------------	2	novel
		len	cloning frequencies
			T3S1
	----------------------------------------------------------------------------------------------ACCTCCCTCAGCTTGTATACCCAG	24	2
rat	ctggggacagttgctgctgggggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtaacctcccctcccccttccACCTCCCTCAGCTTGTATACCCAG
	**********************************************************************************************************************
rat	(((((.(((...((((..(((((........................................................................)))))..)))).)))...)))))	1.000 -19.17

rat

chromosome:17:14841295:14841412:-1

intergenic

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