Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_5varHIGH_randfoldOK (7 loci)

block1413617 [novel_lenNOK_shortStem_5varHIGH_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	0.53/0.58	19/24/0.33	1.7	0.0	3	0	1	0	2	24	5arm	2	nd	0.21	2	3	1	na	na

		reads	miRBase family seed
seed	--------GACCACU----------------------------------------------------------------------------------------------	2	novel
seed	---CUCCUGA---------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------TGACCACTGTGTAGCACAG-----------------------------------------------------------------------------------	19	2
	--GCTCCTGACCACTGTGTAGCACAG-----------------------------------------------------------------------------------	24	1
rat	gtGCTCCTGACCACTGTGTAGCACAGccttcctccttatccccacacttccaccagagctgctgtctctgaggattctaggcttgtgctcttactctggacatcttcac
	*************************************************************************************************************
rat	(((....((.(((..(((.((((((((((...((((((....((((.(((.....))).)).))....))))))....))))).)))))..)))..))).))....)))	1.000 -29.50

rat

chromosome:3:141083130:141083238:-1

intergenic

novel_multiarm_DicerNOK_shortStem_nonpairedHIGH (7 loci)

sblock10606 [novel_multiarm_DicerNOK_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	0.285	no	no	0.43/0.50	20/25/0.86	0.0 0.0	2.0 0.8	2 5	0 0	1 1	0 0	0 2	14 27	5arm 3arm	10 10	nd nd	0.32 0.40	2 4	7	1	2	-3

		reads	miRBase family seed
seed	-------------------------------------------------------------------------UUGCUUU----------------	5	novel
seed	-AGUACUC----------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	------------------------------------------------------------------------CTTGCTTTTCATATGACGGGGG--	22	3
	------------------------------------------------------------------------CTTGCTTTTCATATGACGGG----	20	2
	TAGTACTCATCAGGTGACACATGAG-----------------------------------------------------------------------	25	1
	TAGTACTCATCAGGTGACACA---------------------------------------------------------------------------	21	1
rat	TAGTACTCATCAGGTGACACATGAGccgatgcccagggacatccatccctgaactacagaggctgtccttctCTTGCTTTTCATATGACGGGGGct
	************************************************************************************************
rat	.((..(((.(((.((((..((.(((..((((((((((((......)))))).........))).)))...))).))....)))).))).)))..))	0.480 -25.60

rat

chromosome:7:17113283:17113378:-1

intergenic

sblock10637 [novel_multiarm_DicerNOK_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	0.285	no	no	0.43/0.50	20/25/0.86	0.0 0.0	2.0 0.8	2 5	0 0	1 1	0 0	0 2	14 27	5arm 3arm	10 10	nd nd	0.32 0.40	2 4	7	1	2	-3

		reads	miRBase family seed
seed	-------------------------------------------------------------------------UUGCUUU----------------	5	novel
seed	-AGUACUC----------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	------------------------------------------------------------------------CTTGCTTTTCATATGACGGGGG--	22	3
	------------------------------------------------------------------------CTTGCTTTTCATATGACGGG----	20	2
	TAGTACTCATCAGGTGACACATGAG-----------------------------------------------------------------------	25	1
	TAGTACTCATCAGGTGACACA---------------------------------------------------------------------------	21	1
rat	TAGTACTCATCAGGTGACACATGAGccgatgcccagggacatccatccctgaactacagaggctgtccttctCTTGCTTTTCATATGACGGGGGct
	************************************************************************************************
rat	.((..(((.(((.((((..((.(((..((((((((((((......)))))).........))).)))...))).))....)))).))).)))..))	0.480 -25.60

rat

chromosome:7:17374643:17374738:-1

intergenic

sblock11159 [novel_multiarm_DicerNOK_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	0.285	no	no	0.43/0.50	20/25/0.86	0.0 0.0	2.0 0.8	2 5	0 0	1 1	0 0	0 2	14 27	5arm 3arm	10 10	nd nd	0.32 0.40	2 4	7	1	2	-3

		reads	miRBase family seed
seed	-------------------------------------------------------------------------UUGCUUU----------------	5	novel
seed	-AGUACUC----------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	------------------------------------------------------------------------CTTGCTTTTCATATGACGGGGG--	22	3
	------------------------------------------------------------------------CTTGCTTTTCATATGACGGG----	20	2
	TAGTACTCATCAGGTGACACATGAG-----------------------------------------------------------------------	25	1
	TAGTACTCATCAGGTGACACA---------------------------------------------------------------------------	21	1
rat	TAGTACTCATCAGGTGACACATGAGccgatgcccagggacatccatccctgaactacagaggctgtccttctCTTGCTTTTCATATGACGGGGGct
	************************************************************************************************
rat	.((..(((.(((.((((..((.(((..((((((((((((......)))))).........))).)))...))).))....)))).))).)))..))	0.480 -25.60

rat

chromosome:7:17175400:17175495:1

intergenic

sblock11178 [novel_multiarm_DicerNOK_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	0.285	no	no	0.43/0.50	20/25/0.86	0.0 0.0	2.0 0.8	2 5	0 0	1 1	0 0	0 2	14 27	5arm 3arm	10 10	nd nd	0.32 0.40	2 4	7	1	2	-3

		reads	miRBase family seed
seed	-------------------------------------------------------------------------UUGCUUU----------------	5	novel
seed	-AGUACUC----------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S1
	------------------------------------------------------------------------CTTGCTTTTCATATGACGGGGG--	22	3
	------------------------------------------------------------------------CTTGCTTTTCATATGACGGG----	20	2
	TAGTACTCATCAGGTGACACATGAG-----------------------------------------------------------------------	25	1
	TAGTACTCATCAGGTGACACA---------------------------------------------------------------------------	21	1
rat	TAGTACTCATCAGGTGACACATGAGccgatgcccagggacatccatccctgaactacagaggctgtccttctCTTGCTTTTCATATGACGGGGGct
	************************************************************************************************
rat	.((..(((.(((.((((..((.(((..((((((((((((......)))))).........))).)))...))).))....)))).))).)))..))	0.480 -25.60

rat

chromosome:7:17422106:17422201:1

intergenic

sblock480 [novel_multiarm_DicerNOK_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	0.461	no	no	0.62/0.70	20/21/1.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	0 1	14 14	5arm 3arm	1 1	nd nd	0.33 0.50	3 5	2	2	4	0

		reads	miRBase family seed
seed	------------------------------------------------------GAGCGGA-------------	1	novel
seed	-GAGCAUC------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T4S2
	-----------------------------------------------------GGAGCGGACACGGAGCTGTC-	20	1	-
	GGAGCATCAAGCCTGCTGCTG-----------------------------------------------------	21	-	1
rat	GGAGCATCAAGCCTGCTGCTGgggaacagttggaggagactgaggctccctgcGGAGCGGACACGGAGCTGTCg
	**************************************************************************
rat	(((((.((...((..((((.(((((...(((..((....))..))))))))))))...)).....))))).)).	0.820 -23.60

rat

chromosome:1:53586123:53586196:-1

intergenic

sblock5621 [novel_multiarm_DicerNOK_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	0.332	no	no	0.45/0.50	20/22/1.00	0.0 0.0	0.8 0.0	5 1	0 0	3 1	0 0	4 14	11 0	5arm 3arm	2 3	nd nd	0.32 0.45	3 3	6	4	-10	-10

		reads	miRBase family seed
seed	-----CCCAACA------------------------------------------------------------------	5	novel
seed	-------------------------------------------UACCUGA----------------------------	1	novel
		len	cloning frequencies
			T2S2	T3S1	T3S2	T5S1
	----TCCCAACATTCTCACCGACATC----------------------------------------------------	22	1	2	-	-
	----TCCCAACATTCTCACCGACA------------------------------------------------------	20	-	1	-	1
	------------------------------------------GTACCTGAATGAGATCAAGGAC--------------	22	-	-	1	-
rat	ccggTCCCAACATTCTCACCGACATCaccccaagggcgtccaGTACCTGAATGAGATCAAGGACagtgtggtggctgg
	******************************************************************************
rat	((((((((.(((((.((...((..(((.....(((((.....)).)))...)))..))...)).))))))).))))))	0.720 -22.20

rat

chromosome:18:12708036:12708113:1

intergenic

sblock9629 [novel_multiarm_DicerNOK_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	0.986	no	no	0.58/0.62	19/22/0.83	0.0 0.6	0.0 0.0	1 5	0 0	1 2	0 0	8 3	4 8	5arm 3arm	1 1	nd nd	0.42 0.48	3 4	6	3	6	11

		reads	miRBase family seed
seed	---------------------------------------------GCCCGCU----------------	3	novel
seed	--------------------------------------------AGCCCGC-----------------	2	novel
seed	---------CAGCCCA----------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T2S1	T4S1
	--------------------------------------------AGCCCGCTGCTCAGGAATCTC---	21	1	2	-
	-------------------------------------------TAGCCCGCTGCTCAGGAATCTC---	22	-	2	-
	--------ACAGCCCAGTGAACCTCAG-----------------------------------------	19	-	-	1
rat	gtgtgtccACAGCCCAGTGAACCTCAGgaactaacgtgtgaagTAGCCCGCTGCTCAGGAATCTCgcc
	********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000055509 ENSRNOG00000018289 LOC365828
rat	(((..(((.((((...((..((.(((...((....)).))).)).))..))))....)))....))).	0.640 -13.10

rat

chromosome:5:168050212:168050279:-1

Same_strand|Intronic_coding|ENSRNOT00000055509|ENSRNOG00000018289 ## Same_strand|Boundary_non-coding|ENSRNOT00000024711|ENSRNOG00000018289 ## ENSRNOG00000018289|protein_coding|LOC365828|Protein DJ-1 (Parkinson disease protein 7 homolog) (Contraception- associated protein 1) (Protein CAP1) (Fertility protein SP22). [Source:UniProtKB/Swiss-Prot;Acc:O88767]

novel_shortStem_5varHIGH_randfoldOK (7 loci)

block1065156 [novel_shortStem_5varHIGH_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	0.67/0.71	20/21/1.00	1.2	1.0	4	0	3	0	0	41	3arm	1	nd	0.25	3	4	3	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------------------------------------------GUGCCUG-------------	2	novel
seed	--------------------------------------------------------------------------------------------------ACGUGCC---------------	1	novel
seed	---------------------------------------------------------------------------------------------------CGUGCCU--------------	1	novel
		len	cloning frequencies
			T1S1	T2S2	T3S2
	--------------------------------------------------------------------------------------------------ACGTGCCTGTGCTCCGAGACC-	21	-	-	1
	---------------------------------------------------------------------------------------------------CGTGCCTGTGCTCCGAGACCC	21	-	1	-
	---------------------------------------------------------------------------------------------------CGTGCCTGTGCTCCGAGACC-	20	-	-	1
	-------------------------------------------------------------------------------------------------CACGTGCCTGTGCTCCGAGAC--	21	1	-	-
rat	ggggcggggcggggcggggcggggccgctgtagctgtaaggagctggaggtaccactgcctcggttctcaggcagctgcaggagacagagggcagcgCACGTGCCTGTGCTCCGAGACCC
	************************************************************************************************************************
rat	(((.((((((((((((..(((..(((.((((((((((..((((((.((((((....))))))))))))...)))))))))).........)))..)))...))))).)))))))...)))	1.000 -62.70

rat

chromosome:20:10774734:10774853:-1

intergenic

block1384286 [novel_shortStem_5varHIGH_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	0.50/0.55	19/22/0.80	1.2	2.6	5	0	4	0	4	1	5arm	1	41	0.14	2	5	4	na	na

		reads	miRBase family seed
seed	-----GCAGGAG----------------------------------------------------------	3	novel
seed	-------AGGAGAC--------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T1S2	T4S2	T5S1
	------CAGGAGACACAGTGCTAAGAGC------------------------------------------	22	-	-	-	2
	----TGCAGGAGACACAGTGCTAA----------------------------------------------	20	1	-	1	-
	----TGCAGGAGACACAGTGCTA-----------------------------------------------	19	-	1	-	-
rat	tctgTGCAGGAGACACAGTGCTAAGAGCcaggcaggctctcatctctgtgtactgtgccctcctcttagg
	**********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>	ENSRNOT00000010142 ENSRNOG00000007478 Cry2
rat	.(((...(((((.((((((((..((((((.....)))))).........))))))))..)))))..))).	0.710 -27.50

rat

chromosome:3:76810229:76810298:-1

Same_strand|Intronic_coding|ENSRNOT00000010142|ENSRNOG00000007478 ## ENSRNOG00000007478|protein_coding|Cry2|Cryptochrome-2. [Source:UniProtKB/Swiss-Prot;Acc:Q923I8]

Back to summary page

other hairpins:

Jump 10 pages back

Page 31048

Jump 10 pages forward

©2008 InteRNA Genomics B.V.