Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_loopOverlap_nonpairedHIGH_bulgeHIGH (676 loci)

block3141029 [novel_lenNOK_shortStem_loopOverlap_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	0.120	no	no	0.22/0.22	18/18/0.00	0.0	0.0	1	0	1	0	4	-3	5arm_loop	1	nd	0.39	4	1	1	na	na

		reads	miRBase family seed
seed	-----UGGAAUA--------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----TTGGAATATATTGCAAAA----------------------------	18	1
rat	aagcTTGGAATATATTGCAAAAtgttgatgcctcagttgtctttcaagct
	**************************************************
rat	.(((((((((.(((..(((.........)))......))).)))))))))	0.740 -9.90

rat

chromosome:X:148126590:148126639:1

intergenic

block233778 [novel_lenNOK_shortStem_loopOverlap_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	0.461	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	4	-4	5arm_loop	1	nd	0.47	5	1	1	na	na

		reads	miRBase family seed
seed	-----ACAGUGG-----------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----GACAGTGGAAAAGAGCCCA------------------------------	19	1
rat	gctgGACAGTGGAAAAGAGCCCAttatcctatccctctttctatagcctgagc
	*****************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000056932 ENSRNOG00000037566 RGD1560398_predicted
rat	(((((...((((.((((((...............))))))))))..))..)))	0.830 -8.86

rat

chromosome:12:43061564:43061616:1

Same_strand|Intronic_non-coding|ENSRNOT00000056932|ENSRNOG00000037566 ## ENSRNOG00000037566|protein_coding|RGD1560398_predicted|

block349823 [novel_lenNOK_shortStem_loopOverlap_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	0.47/0.58	18/21/0.56	0.6	1.1	9	0	3	0	1	-1	3arm	2	nd	0.33	4	9	3	na	na

		reads	miRBase family seed
seed	-----------------------------CCUCAUC-------------	6	novel
seed	----------------------------GCCUCAU--------------	2	miR-421
seed	--------------------------CUGCCUC----------------	1	novel
		len	cloning frequencies
			T1S1	T4S2	T5S1
	----------------------------GCCTCATCCAATGAACGGGT-	20	1	1	2
	----------------------------GCCTCATCCAATGAACGGG--	19	-	-	2
	-------------------------ACTGCCTCATCCAATGAAC-----	19	1	-	-
	---------------------------TGCCTCATCCAATGAACGGGT-	21	1	-	-
	---------------------------TGCCTCATCCAATGAACG----	18	1	-	-
rat	tgccagtttacaggttctggtagggACTGCCTCATCCAATGAACGGGTa
	*************************************************
rat	((((.(((((..((....(((((...)))))....))..))))).))))	1.000 -15.10

rat

chromosome:14:42006923:42006971:-1

intergenic

block881274 [novel_lenNOK_shortStem_loopOverlap_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	0.383	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	1	-4	5arm_loop	1	nd	0.32	5	1	1	na	na

		reads	miRBase family seed
seed	--GCACAGC----------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-TGCACAGCATCCTGGATGA-----------------------------------------	19	1
rat	cTGCACAGCATCCTGGATGAaagatggtgttgactcccaggcaacctgctgtatcctgcag
	*************************************************************
rat	((((((((((.(((((....................))))).....)))))).....))))	0.920 -15.35

rat

chromosome:1:129010512:129010572:-1

intergenic

block213263 [novel_lenNOK_shortStem_loopOverlap_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	0.093	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	1	-4	5arm_loop	2	nd	0.32	5	1	1	na	na

		reads	miRBase family seed
seed	--CGCUUUU--------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-GCGCTTTTGACTCAGGATT---------------------------	19	1
rat	gGCGCTTTTGACTCAGGATTtaaaaactggaacggtgaaggcgaccg
	***********************************************
rat	(((((((((.((((((..........)))....)))))))))).)).	1.000 -12.80

rat

chromosome:12:12050150:12050196:1

intergenic

novel_shortStem_bulgeHIGH (639 loci)

block1343 [novel_shortStem_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	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	0	13	5arm	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	-UGUCAGC-----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S2
	CTGTCAGCTCTATTCAAGCT-----------------------------------------------------	20	1
rat	CTGTCAGCTCTATTCAAGCTcatgtgtgcacatatggatgtgtctttgcatgtgcatatgtatgagcatgtca
	*************************************************************************
rat	.((.(((((((((....((.((((((.((((((....))))))...)))))).))....))).)))).)).))	0.950 -22.20

rat

chromosome:10:2658966:2659038:-1

intergenic

block2480 [novel_shortStem_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	0.045	no	no	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	2	2	5arm	1	nd	0.30	4	1	1	na	na

		reads	miRBase family seed
seed	---CUCCAUC-------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	--TCTCCATCATCAATGATCAG-------------------------	20	1
rat	agTCTCCATCATCAATGATCAGggatgccctgctcacctggggagct
	***********************************************
	---------------------------------------------------------	ENSRNOT00000003465 ENSRNOG00000002571 RGD1307081
rat	((.((((.(((....(((.(((((...))))).)))..)))))))))	0.970 -15.00

rat

chromosome:10:5247460:5247506:-1

Opposite_strand|Intronic_coding|ENSRNOT00000003465|ENSRNOG00000002571 ## ENSRNOG00000002571|protein_coding|RGD1307081|Putative uncharacterized protein RGD1307081 (Tektin5). [Source:UniProtKB/TrEMBL;Acc:Q6AYH7]

block6736 [novel_shortStem_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	0.152	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	0	16	3arm	1	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------CAAGACU------------	1	novel
		len	cloning frequencies
			T2S2
	------------------------------------------------------------------TCAAGACTTAAAAGCTGCAA	20	1
rat	ttgtagttttcttctctaaaactgaactgaataagacttttcaataaatcattctgaaggcttagcTCAAGACTTAAAAGCTGCAA
	**************************************************************************************
rat	.(((((((((....(((..........(((.((((.((((..(((.....)))..)))).))))..))))))....))))))))).	0.410 -13.40

rat

chromosome:10:14101854:14101939:-1

intergenic

block8053 [novel_shortStem_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	0.338	no	no	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	2	33	3arm	1	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------AGCCUUU------------------	1	novel
		len	cloning frequencies
			T2S1
	--------------------------------------------------------------------------------------AAGCCTTTGTAGTGTAGCAGGAAG--	24	1
rat	actttctttacaagttactcagtttcccagtaagggtgagagggtctctgaaaggagcatagcctcgcgcctcatattcagtggtcAAGCCTTTGTAGTGTAGCAGGAAGtg
	****************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043415 ENSRNOG00000033169 LOC685957
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000050024 ENSRNOG00000033169 LOC685957
rat	((((((((((((...(((...((((.((((((.(((((.((((((((((....)))).))..)))).)))))..)))....)))..))))....))).))))).))))))).	0.780 -31.40

rat

chromosome:10:15997874:15997985:-1

Same_strand|Intronic_coding|ENSRNOT00000050024|ENSRNOG00000033169 ## ENSRNOG00000033169|protein_coding|LOC685957|cytoplasmic polyadenylation element binding protein 4 [Source:RefSeq_peptide;Acc:NP_001100462]

block13376 [novel_shortStem_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	0.316	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	0	11	5arm	1	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	-UUCAGGA------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	TTTCAGGATCCTTTTTCCCC------------------------------------------------------------	20	1
rat	TTTCAGGATCCTTTTTCCCCaccatgctgctcactccaagctataaacagcagtcttattgagatggggttctttggagg
	********************************************************************************
	------------------------------------------------------------------------------------------	ENSRNOT00000047970 ENSRNOG00000028845 Ebf1
rat	((((((((((((.((((........((((((.................))))))......)))).))))))))..)))).	0.890 -16.87

rat

chromosome:10:30143517:30143596:-1

Opposite_strand|Intronic_coding|ENSRNOT00000047970|ENSRNOG00000028845 ## ENSRNOG00000028845|protein_coding|Ebf1|Transcription factor COE1 (OE-1) (O/E-1) (Early B-cell factor) (Olfactory neuronal transcription factor) (Olf-1). [Source:UniProtKB/Swiss-Prot;Acc:Q63398]

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