Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_randfoldOK (304 loci)

novel_lenNOK_mirtron (289 loci)

block2393 [novel_lenNOK_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	0.300	no	no	0.68/0.68	19/19/0.00	0.0	0.0	1	0	1	0	20	13	3arm	1	1	0.16	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------UGAGGGC-------------------------------	1	novel
		len	cloning frequencies
			T3S2
	----------------------------------------------------------------------------GTGAGGGCTGGGGTCCTGA--------------------	19	1
rat	agccccttcgcgccatccacagctgacctgcccggcatgcctgaacctgctctgacctcccgtgtaaatgagacagGTGAGGGCTGGGGTCCTGAaagaggcgttggaaacgggc
	*******************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003572 ENSRNOG00000002659 C2ta
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000030118 ENSRNOG00000002659 C2ta
rat	.((((.((((((((.((..(((..(((...((((((...(((..((((((((..((.......))....))).))))).)))))))))))))))...)))))))..)))..))))	0.740 -42.40

rat

chromosome:10:5105454:5105568:-1

Same_strand|Boundary_coding|ENSRNOT00000003572|ENSRNOG00000002659 ## ENSRNOG00000002659|protein_coding|C2ta|class II, major histocompatibility complex, transactivator [Source:RefSeq_peptide;Acc:NP_445981]

block7324 [novel_lenNOK_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	0.118	no	no	0.72/0.72	18/18/0.00	0.0	0.0	1	0	1	0	19	10	5arm	1	4	0.22	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------GUAGCGG------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	-------------------AGTAGCGGGGCAGGTGGG--------------------------------------------------------------------------------	18	1
rat	ctggctctggtgtgcagtgAGTAGCGGGGCAGGTGGGgcgctgggaggccctctccctgcagacagggcccctcccacctgttgctccctctgcagtgagctccgaagtgggccggg
	*********************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000026971 ENSRNOG00000019921 Rhbdl1
rat	((((((((((.((((((.((((((((((...((.(((((.(((((((.....))))).......)).))))).))..))))))))))...)))).....)).)))....))))))).	0.790 -58.61

rat

chromosome:10:15100485:15100601:-1

Same_strand|Intronic_coding|ENSRNOT00000026971|ENSRNOG00000019921 ## ENSRNOG00000019921|protein_coding|Rhbdl1|Rhomboid-related protein 1 (EC 3.4.21.105) (RRP) (Rhomboid-like protein 1) (Fragment). [Source:UniProtKB/Swiss-Prot;Acc:O88779]

block20675 [novel_lenNOK_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	0.517	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	11	11	5arm	1	3	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	------------GGUUUGU------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-----------TGGTTTGTATTGCAGAGT--------------------------------------------------------	18	1
rat	ggccctcaattTGGTTTGTATTGCAGAGTttgataagttcctggaagaaagagccaaagctgcagaaacagttccagacctgccc
	*************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004753 ENSRNOG00000003463 Srebf1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000004488 ENSRNOG00000003463 Srebf1
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000058129 ENSRNOG00000003590 NP_001101747.1
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004796 ENSRNOG00000003590 NP_001101747.1
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004910 ENSRNOG00000003590 NP_001101747.1
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000004928 ENSRNOG00000003590 NP_001101747.1
	+++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000058128 ENSRNOG00000003590 NP_001101747.1
rat	(((......(((((.((((.((((((..((((.....(((......))).....)))).))))))..))))..)))))...))).	0.890 -18.60

rat

chromosome:10:46493238:46493322:-1

Same_strand|Boundary_coding|ENSRNOT00000058128|ENSRNOG00000003590 ## Same_strand|Intronic_coding|ENSRNOT00000004753|ENSRNOG00000003463 ## Same_strand|Boundary_non-coding|ENSRNOT00000058155|ENSRNOG00000003463 ## ENSRNOG00000003590|protein_coding|NP_001101747.1|target of myb1-like 2 [Source:RefSeq_peptide;Acc:NP_001101747] ## ENSRNOG00000003463|protein_coding|Srebf1|Sterol regulatory element-binding protein 1 (SREBP-1) (Sterol regulatory element-binding transcription factor 1) (Adipocyte determination- and differentiation-dependent factor 1) (ADD1) [Contains: Processed sterol regulatory element-binding protein 1] (Fr [Source:UniProtKB/Swiss-Prot;Acc:P56720]

block20863 [novel_lenNOK_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	0.028	no	no	0.59/0.67	18/22/0.60	0.2	1.4	5	0	3	0	22	4	3arm	2	1	0.26	1	5	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------GGCUGAC------------------------------------	4	novel
seed	------------------------------------------------------------------GCUGACC-----------------------------------	1	miR-345
		len	cloning frequencies
			T1S1	T1S2	T3S1
	----------------------------------------------------------------TGGCTGACCAGCCCTTCTCAC-----------------------	21	1	1	-
	----------------------------------------------------------------TGGCTGACCAGCCCTTCTCACA----------------------	22	-	1	-
	-----------------------------------------------------------------GGCTGACCAGCCCTTCTC-------------------------	18	-	1	-
	----------------------------------------------------------------TGGCTGACCAGCCCTTCTC-------------------------	19	-	-	1
rat	cctcctacagcaaacaggtgaccgaggggcgggcaggcgggcaggcgagaacagaggagggcccTGGCTGACCAGCCCTTCTCACAggtcatcaacgagggtgaggag
	************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000006753 ENSRNOG00000004159 Fliih
rat	.(((((...((.....(((((((..((((.((((.(((((.(((((..............))).)).))).)).)))).))))...))))))).......)).)))))	0.950 -43.14

rat

chromosome:10:46861321:46861428:-1

Same_strand|Intronic_coding|ENSRNOT00000006753|ENSRNOG00000004159 ## ENSRNOG00000004159|protein_coding|Fliih|flightless I homolog [Source:RefSeq_peptide;Acc:NP_001008280]

block20874 [novel_lenNOK_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	0.543	no	no	0.43/0.50	18/21/0.33	0.0	1.3	3	0	3	0	35	8	3arm	1	1	0.22	2	3	3	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------GACCUUU------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1	T1S2	T4S2
	----------------------------------------------------------------TGACCTTTTCCCTACTCCT-------------------------------------	19	1	-	-
	----------------------------------------------------------------TGACCTTTTCCCTACTCC--------------------------------------	18	-	1	-
	----------------------------------------------------------------TGACCTTTTCCCTACTCCTTA-----------------------------------	21	-	-	1
rat	gtgtccagtgtcctgccagatctttgggtgcggaagaggtatgggggagaggggatccctggccTGACCTTTTCCCTACTCCTTAggacttgagccataaccagttgacagaatgcccac
	************************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000006753 ENSRNOG00000004159 Fliih
rat	(((..((.((((..((((..((((.(((((.(((((((((....(((..((((...))))..))).))))))))).)))))...))))..)).))...........))))...))..)))	0.790 -37.12

rat

chromosome:10:46869479:46869598:-1

Same_strand|Intronic_coding|ENSRNOT00000006753|ENSRNOG00000004159 ## ENSRNOG00000004159|protein_coding|Fliih|flightless I homolog [Source:RefSeq_peptide;Acc:NP_001008280]

block25698 [novel_lenNOK_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	0.022	no	no	0.56/0.59	18/22/0.25	0.0	1.5	4	0	4	0	28	1	3arm	1	0	0.14	3	4	4	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------UUCCCUG------------------------------------------	4	novel
		len	cloning frequencies
			T3S1	T3S2	T4S1	T4S2
	--------------------------------------------------------------TTTCCCTGACCTTCGGTGG-------------------------------	19	-	1	-	1
	--------------------------------------------------------------TTTCCCTGACCTTCGGTGGCAG----------------------------	22	1	-	-	-
	--------------------------------------------------------------TTTCCCTGACCTTCGGTG--------------------------------	18	-	-	1	-
rat	tggcttggctgggtgtggacactatgacctggccatctgatcagggaacacaggacttcagcTTTCCCTGACCTTCGGTGGCAGgtacgtggtgggaatgttcaatctccac
	****************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000026038 ENSRNOG00000019183 Alox15
rat	(((...((.((..(((...(((((((((((.((((.((((((((((((...((........))))))))))...)))))))))))).)))))))...)))..)).)).))).	0.990 -42.80

rat

chromosome:10:57187409:57187520:-1

Same_strand|Intronic_coding|ENSRNOT00000026038|ENSRNOG00000019183 ## ENSRNOG00000019183|protein_coding|Alox15|Arachidonate 12-lipoxygenase, leukocyte-type (EC 1.13.11.31) (12-LOX). [Source:UniProtKB/Swiss-Prot;Acc:Q02759]

block39615 [novel_lenNOK_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	0.078	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	26	6	3arm	2	4	0.22	1	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------UACUCUG------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------------------------------------------------TTACTCTGTCCTGCTCTC--------------------------	18	1
rat	agctttacagctaccacaggttccttagaccagcctggaagagttgggaacaaacaccaggcgatcctctTTACTCTGTCCTGCTCTCtcaggaggcccagtgtgggctgaagc
	******************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000012462 ENSRNOG00000009370 Tbkbp1
rat	.((((..(((((..(((.(((((((.(((..(((..((((((((.((((...............))))....))))).))).))).))).))))).))..)))..)))))))))	0.560 -36.46

rat

chromosome:10:85869181:85869294:-1

Same_strand|Intronic_non-coding|ENSRNOT00000012462|ENSRNOG00000009370 ## Same_strand|Boundary_non-coding|ENSRNOT00000051388|ENSRNOG00000009370 ## ENSRNOG00000009370|protein_coding|Tbkbp1|TBK1 binding protein 1 [Source:RefSeq_peptide;Acc:NP_742018]

block46046 [novel_lenNOK_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	0.224	no	no	0.16/0.16	19/19/0.00	0.0	0.0	1	0	1	0	13	10	3arm	3	3	0.05	1	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------UUUAUGU------------------------	1	novel
		len	cloning frequencies
			T1S2
	---------------------------------------------------------------TTTTATGTTTTGTGTTTTT-------------	19	1
rat	tgttgagttcatgagagctgcgggacatgatcacattgggaaaaccttaaaacttcaaaaataTTTTATGTTTTGTGTTTTTaagaccttgccac
	***********************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>	ENSRNOT00000055100 ENSRNOG00000015626 LOC688885
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>	ENSRNOT00000020904 ENSRNOG00000015626 LOC688885
rat	((..(((.((.(((((((.(((((((((((.........(((...........))).........)))))))))))))))))).)).)))..)).	0.940 -19.27

rat

chromosome:10:96396043:96396137:-1

Same_strand|Boundary_non-coding|ENSRNOT00000020980|ENSRNOG00000015626 ## Same_strand|Intronic_coding|ENSRNOT00000020904|ENSRNOG00000015626 ## ENSRNOG00000015626|protein_coding|LOC688885|

block47465 [novel_lenNOK_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	0.533	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	14	25	3arm	1	3	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------AAGGUUU------------------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------------------------------------------------------AAAGGTTTGGGCAGGGCC--------------	18	1
rat	gtctctcttcaggttggcagatgcactcaagctgcaggaccagctgaagtctccggtgaagacgctgtcagagggagtgaagagAAAGGTTTGGGCAGGGCCccgggagaagggct
	********************************************************************************************************************
	+++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++	ENSRNOT00000005665 ENSRNOG00000004147
rat	(((..(((((.((..(((...(((...((((((.((...((..((((.((((.......))))....))))..))..))........)))))).)))..))))).)))))..))).	0.640 -36.40

rat

chromosome:10:99483541:99483656:-1

Same_strand|Boundary_coding|ENSRNOT00000005665|ENSRNOG00000004147 ## ENSRNOG00000004147|protein_coding||

block53119 [novel_lenNOK_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	0.037	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	26	3	3arm	1	2	0.16	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------UCUGCCU-------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	--------------------------------------------------------ATCTGCCTTCCTTGTCCCC--------------------------	19	1
rat	ggttcaagtgtgtcccagtctgccagggacaagcaaagggtagggagttggccctcATCTGCCTTCCTTGTCCCCagtggaccccgaaggatgactgggct
	*****************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000054970 ENSRNOG00000036697 Mafg
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000054951 ENSRNOG00000036683 NP_001100543.1
rat	((..((.((.(((((..((((((..((((((((...(((((((((((......))).)))))))).))))))))..))))))......)))))))))..))	0.830 -40.90

rat

chromosome:10:110011541:110011641:-1

Same_strand|Intronic_non-coding|ENSRNOT00000054970|ENSRNOG00000036697 ## Same_strand|Intronic_coding|ENSRNOT00000054951|ENSRNOG00000036683 ## Same_strand|Boundary_non-coding|ENSRNOT00000051462|ENSRNOG00000036697 ## ENSRNOG00000036697|protein_coding|Mafg|v-maf musculoaponeurotic fibrosarcoma oncogene family, protein G [Source:RefSeq_peptide;Acc:NP_071781] ## ENSRNOG00000036683|protein_coding|NP_001100543.1|sirtuin 7 [Source:RefSeq_peptide;Acc:NP_001100543]

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