Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_mirtron_randfoldOK_bulgeHIGH (9 loci)

block2260962 [novel_mirtron_randfoldOK_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	0.001	no	no	0.64/0.67	21/22/1.00	0.0	0.5	4	0	2	0	28	8	3arm	1	3	0.18	4	4	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------CCAUGUC------------------------------------------	4	novel
		len	cloning frequencies
			T1S1	T1S2
	----------------------------------------------------------------------TCCATGTCCCTCCCTGACCCC-----------------------------	21	-	2
	----------------------------------------------------------------------TCCATGTCCCTCCCTGACCCCA----------------------------	22	2	-
rat	ggggtatctggtctagcttagaatgggtggggctggagggagatcgtggtggctccagtgccctggaactTCCATGTCCCTCCCTGACCCCAcagtcattgtttgagcgacagggcctcc
	************************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000047960 ENSRNOG00000032936 Shank3
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000045913 ENSRNOG00000032936 Shank3
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000055773 ENSRNOG00000032936 Shank3
rat	(((((.((((.....((((((((((.((((((..(((((((...(((((.((.(((((....))))).)).))))))))))))....))))))...)))..)))))))..))))))))).	1.000 -56.30

rat

chromosome:7:127860880:127860999:1

Same_strand|Intronic_coding|ENSRNOT00000045913|ENSRNOG00000032936 ## ENSRNOG00000032936|protein_coding|Shank3|SH3 and multiple ankyrin repeat domains protein 3 (Shank3) (Proline- rich synapse-associated protein 2) (ProSAP2) (SPANK-2). [Source:UniProtKB/Swiss-Prot;Acc:Q9JLU4]

block2417733 [novel_mirtron_randfoldOK_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	0.008	no	no	0.62/0.62	21/24/1.00	0.0	1.0	3	0	2	0	26	2	3arm	1	1	0.21	4	3	2	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------GACCUCC------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2
	-------------------------------------------------------------------TGACCTCCATGGCCTTCCCCA-----------------------------	21	1	1
	-------------------------------------------------------------------TGACCTCCATGGCCTTCCCCAGTC--------------------------	24	-	1
rat	agctgacccagttaggtgagtaggcctgggcttgggagggtcatgggcaagctaaaaacagggagagTGACCTCCATGGCCTTCCCCAGTCcctggcaggctgtacgaggtgaagct
	*********************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000044706 ENSRNOG00000033496 NP_001102237.1
	>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000040854 ENSRNOG00000033496 NP_001102237.1
rat	((((.(((..((......(((..(((.(((((.((((((((((((((...(((............)))....)))))))))))))).)))))..)))..)))..))..)))..))))	0.750 -50.20

rat

chromosome:8:69374487:69374603:1

Same_strand|Boundary_coding|ENSRNOT00000040854|ENSRNOG00000033496 ## ENSRNOG00000033496|protein_coding|NP_001102237.1|neighbor of Punc E11 [Source:RefSeq_peptide;Acc:NP_001102237]

novel_mirtron_randfoldOK_nonpairedHIGH_bulgeHIGH (9 loci)

block70669 [novel_mirtron_randfoldOK_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	0.007	no	no	0.55/0.55	20/20/1.00	0.0	0.0	7	0	4	0	25	10	3arm	1	1	0.40	4	7	4	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------CUUCUGU-------------------------------------	7	novel
		len	cloning frequencies
			T2S1	T2S2	T3S1	T5S2
	----------------------------------------------------------------------CCTTCTGTCTTCTCCCTCCA-------------------------	20	3	2	1	1
rat	gtaattgagtgatcggccttgggtggagcagggcagtgcccaggattgtttaacagactctaaacacaggCCTTCTGTCTTCTCCCTCCAgccaccatgcctatcactcggatgc
	*******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000058927 ENSRNOG00000008144 Irf1
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000010968 ENSRNOG00000008144 Irf1
rat	(((.(((((((((.(((..(((.(((((.(((((((.(((......((((((........))))))..)))...)))))))....))))).)))....))).))))))))).)))	0.880 -43.10

rat

chromosome:10:39221689:39221803:1

Same_strand|Intronic_non-coding|ENSRNOT00000058927|ENSRNOG00000008144 ## ENSRNOG00000008144|protein_coding|Irf1|Interferon regulatory factor 1 (IRF-1). [Source:UniProtKB/Swiss-Prot;Acc:P23570]

block86887 [novel_mirtron_randfoldOK_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	0.010	no	no	0.53/0.59	19/22/0.80	0.2	2.6	5	0	3	0	13	11	3arm	1	0	0.36	4	5	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------UGGCUCU----------------------------	4	novel
seed	------------------------------------------------------------------GGCUCUC---------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T4S2
	----------------------------------------------------------------ATGGCTCTCTCCTCTCTTCCCA--------------	22	1	1	1
	----------------------------------------------------------------ATGGCTCTCTCCTCTCTTC-----------------	19	-	-	1
	-----------------------------------------------------------------TGGCTCTCTCCTCTCTTCCCAG-------------	22	1	-	-
rat	catcacccaacctcatcccaagactgaggcctcagcaaggggccagccaccatgtggtagccccATGGCTCTCTCCTCTCTTCCCAGgtctgctagatgt
	****************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>	ENSRNOT00000003886 ENSRNOG00000002852 RGD1559961_predicted
rat	((((...((((((......((((..((((....(((..(((((..(((((...))))).)))))...)))....))))))))...)))).))...)))).	0.850 -31.70

rat

chromosome:10:73175112:73175211:1

Same_strand|Intronic_coding|ENSRNOT00000003886|ENSRNOG00000002852 ## ENSRNOG00000002852|protein_coding|RGD1559961_predicted|

block140705 [novel_mirtron_randfoldOK_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	0.004	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	28	14	5arm	1	0	0.40	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------UUACUGU------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------CTTACTGTGCACTCTTTCAG------------------------------------------------------------------------	20	1
rat	actggtcctcagggagcattccagctgcCTTACTGTGCACTCTTTCAGgaattgcatgccatcttcccatggctggtggagagcatcttaggcagcctggatggtgtccttgttggctgg
	************************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000043545 ENSRNOG00000001875 RGD1310674
	+++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000002563 ENSRNOG00000001875 RGD1310674
rat	.((((((..((((((.((((((((((((((....((((.((((.(((..........(((((......)))))))).)))).))))...))))))).))))..)))))))))..))))))	0.930 -50.10

rat

chromosome:11:85369831:85369950:-1

Same_strand|Intronic_coding|ENSRNOT00000002563|ENSRNOG00000001875 ## ENSRNOG00000001875|protein_coding|RGD1310674|RGD1310674 protein. [Source:UniProtKB/TrEMBL;Acc:Q5U2Q9]

block793787 [novel_mirtron_randfoldOK_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	0.001	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	28	2	5arm	1	2	0.40	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------AAGGAUC---------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------TAAGGATCTCTCTGCCCCAT---------------------------------------------------------	20	1
rat	tccttgcctgcatcgtcattcttctgggTAAGGATCTCTCTGCCCCATggtccaaccgatgcacatgcttcaagagacttacccagtacagagtgactgcaagga
	*********************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000018535 ENSRNOG00000013481 Cdh11
rat	(((((((.......((((((((.(((((((((..(((....((..(((((.....)).))).....))....)))..)))))))))...)))))))).)))))))	0.440 -40.30

rat

chromosome:19:2377917:2378021:1

Same_strand|Boundary_non-coding|ENSRNOT00000061567|ENSRNOG00000013481 ## Same_strand|Intronic_coding|ENSRNOT00000018535|ENSRNOG00000013481 ## ENSRNOG00000013481|protein_coding|Cdh11|Cadherin-11 (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q9JIW2]

block1028920 [novel_mirtron_randfoldOK_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	0.003	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	12	13	3arm	1	1	0.40	5	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------ACCUCCC------------------------	1	novel
		len	cloning frequencies
			T1S2
	----------------------------------------------------------------------------AACCTCCCTCTGTCCTCTCA------------	20	1
rat	gggacatttccgtccaaagatcagaagggggtctctgagtccctcatgggggcttaagaacaagagccctcatggtAACCTCCCTCTGTCCTCTCAgggaagtggact
	************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>	ENSRNOT00000028195 ENSRNOG00000020776 Dhcr7
rat	((..(((((((......((..((((.((((((...........((((((((((((........))))))))))))..)))))).))))..)).....)))))))..))	0.420 -42.42

rat

chromosome:1:204249995:204250102:1

Same_strand|Intronic_coding|ENSRNOT00000028195|ENSRNOG00000020776 ## ENSRNOG00000020776|protein_coding|Dhcr7|7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol Delta(7)-reductase). [Source:UniProtKB/Swiss-Prot;Acc:Q9Z2Z8]

block1434356 [novel_mirtron_randfoldOK_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	0.009	no	no	0.64/0.64	22/22/1.00	0.0	0.0	2	0	2	0	10	15	5arm	1	1	0.41	4	2	2	na	na

		reads	miRBase family seed
seed	-----------CCUGACC---------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2
	----------GCCTGACCCTGCAGTTCCCACA-------------------------------------------------------------------------	22	1	1
rat	ggggtggcggGCCTGACCCTGCAGTTCCCACAgaccatgtggtgtgcgaggaagagtgcaagtacgccatgctggccctgaactgcatctgcccggccacctcca
	*********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000061773 ENSRNOG00000017283 Kcnt1
	++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000023542 ENSRNOG00000017283 Kcnt1
	++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000023817 ENSRNOG00000017283 Kcnt1
rat	((((((((((((..((...((((((((....((.(((((((((((((..............)))))))))).)))..)))))))))))).))))).))))).)).	0.980 -50.24

rat

chromosome:3:4073441:4073545:1

Same_strand|Intronic_coding|ENSRNOT00000061773|ENSRNOG00000017283 ## ENSRNOG00000017283|protein_coding|Kcnt1|Potassium channel subfamily T member 1 (Sequence like a calcium- activated potassium channel subunit). [Source:UniProtKB/Swiss-Prot;Acc:Q9Z258]

block1691696 [novel_mirtron_randfoldOK_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	0.008	no	no	0.36/0.36	22/22/1.00	0.0	0.0	1	0	1	0	8	24	3arm	3	1	0.41	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------------UGAGUGA----------------------	1	novel
		len	cloning frequencies
			T2S2
	----------------------------------------------------------------------------------GTGAGTGAACATTTTGTAAGTG--------	22	1
rat	gtggagaacaatcaagattcttactgccttggtgccaatgggaggcacacctcatcctggttggtaactcccaaatctctagGTGAGTGAACATTTTGTAAGTGgactctac
	****************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++	ENSRNOT00000041957 ENSRNOG00000005599 LOC297568
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000036555 ENSRNOG00000005599 LOC297568
rat	((((((..((..((((((..(((((..(((((......((((((..(((((.......)))..))..)))))).....)))))..)))))..))))))....))..))))))	0.950 -36.00

rat

chromosome:4:158230886:158230997:1

Same_strand|Intronic_non-coding|ENSRNOT00000036555|ENSRNOG00000005599 ## Same_strand|Boundary_non-coding|ENSRNOT00000044408|ENSRNOG00000005599 ## Same_strand|Boundary_coding|ENSRNOT00000041957|ENSRNOG00000005599 ## ENSRNOG00000005599|protein_coding|LOC297568|Alpha-1-inhibitor 3 precursor (Alpha-1-inhibitor III) (Alpha-1- inhibitor 3 variant II). [Source:UniProtKB/Swiss-Prot;Acc:P14046]

block1791407 [novel_mirtron_randfoldOK_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	0.001	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	30	8	3arm	1	2	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------CCUCCUC---------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	-----------------------------------------------------------------TCCTCCTCCTCCTGCCATGACAC------------------------------	23	1
rat	gtctctcttccaagcaggaggtagggactgaatggcaggttgtggggtggggctcaagctaatccTCCTCCTCCTCCTGCCATGACACagcctggtccagctcaagcttggaatgaca
	**********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000031225 ENSRNOG00000022838 Cnksr1
rat	(((....((((((((..((((..(((.(((.((((((((....((((..((((....))....))..))))....))))))))....))))))...))...))..)))))))).))).	0.980 -49.10

rat

chromosome:5:152973800:152973917:-1

Same_strand|Intronic_coding|ENSRNOT00000031225|ENSRNOG00000022838 ## ENSRNOG00000022838|protein_coding|Cnksr1|connector enhancer of kinase suppressor of Ras 1 [Source:RefSeq_peptide;Acc:NP_001034100]

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