Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_cloningOK_nonpairedHIGH (12 loci)

block1499759 [novel_cloningOK_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	0.713	no	no	0.43/0.48	19/22/0.93	0.0	0.0	8	0	3	0	10	13	3arm	1	nd	0.33	3	14	3	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------UUGAGCC-----------------------	10	novel
seed	---------------------------------------------------------------------GAGCCAG---------------------	1	novel
seed	------------------------------------------------------------------------CCAGUGG------------------	1	novel
seed	--------------------------------------------------------------------UGAGCCA----------------------	1	novel
seed	-----------------------------------------------------------------------GCCAGUG-------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T5S1
	------------------------------------------------------------------TTTGAGCCAGTGGTAATCACA----------	21	-	2	8
	--------------------------------------------------------------------TGAGCCAGTGGTAATCACA----------	19	-	-	1
	-------------------------------------------------------------------TTGAGCCAGTGGTAATCACA----------	20	-	-	1
	-----------------------------------------------------------------------GCCAGTGGTAATCACATTGTG-----	21	1	-	-
	----------------------------------------------------------------------AGCCAGTGGTAATCACATTGTG-----	22	-	-	1
rat	gggatcctcagcctgggactctttgctggaaatggaggaaatctatcctgtgaggtcatgttgtccTTTGAGCCAGTGGTAATCACAttgtggaact
	*************************************************************************************************
rat	.((.(((.(((..(((......(((((((...(((((((.......((.....))........)))))))..)))))))...)))..))).))).))	0.530 -22.16

rat

chromosome:3:141753841:141753937:1

intergenic

block1848540 [novel_cloningOK_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	0.020	no	no	0.58/0.64	19/26/0.71	0.0	0.0	9	0	5	0	18	1	5arm	1	nd	0.35	3	21	5	na	na

		reads	miRBase family seed
seed	-------------------GAGCACC----------------------------------------------------	20	novel
seed	---------------------GCACCGU--------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T4S1	T5S1
	------------------TGAGCACCGTGGAGCATGCA----------------------------------------	20	1	-	2	2	9
	------------------TGAGCACCGTGGAGCATGCAAGCCC-----------------------------------	25	-	-	-	-	2
	------------------TGAGCACCGTGGAGCATGC-----------------------------------------	19	-	-	-	-	2
	------------------TGAGCACCGTGGAGCATGCAAGCCCT----------------------------------	26	-	-	-	-	1
	------------------TGAGCACCGTGGAGCATGCAAGC-------------------------------------	23	-	1	-	-	-
	--------------------AGCACCGTGGAGCATGCAA---------------------------------------	19	-	-	-	-	1
rat	gggactcgggagagtcccTGAGCACCGTGGAGCATGCAagcccttgcatggccgattgtccccttgactctctgtccc
	******************************************************************************
rat	(((((...((((((((.....(((...(((..(((((((....))))))).)))..)))......)))))))))))))	0.980 -32.60

rat

chromosome:5:79247846:79247923:1

intergenic

block958697 [novel_cloningOK_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	0.180	no	no	0.35/0.42	19/24/0.87	0.0	0.0	9	0	3	0	8	27	3arm	2	nd	0.35	2	15	3	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------GAGGAUG--------------------	9	novel
seed	-----------------------------------------------------------------------------------CUGAGGA----------------------	2	novel
seed	----------------------------------------------------------------------------------UCUGAGG-----------------------	2	novel
seed	---------------------------------------------------------------------------------CUCUGAG------------------------	1	novel
seed	------------------------------------------------------------------------------------UGAGGAU---------------------	1	novel
		len	cloning frequencies
			T2S2	T3S2	T5S1
	------------------------------------------------------------------------------------TGAGGATGATTGTTGAATGA--------	20	-	-	9
	--------------------------------------------------------------------------------TCTCTGAGGATGATTGTTGAATGA--------	24	-	1	-
	-----------------------------------------------------------------------------------CTGAGGATGATTGTTGAATGA--------	21	-	-	1
	----------------------------------------------------------------------------------TCTGAGGATGATTGTTGAATGAA-------	23	-	-	1
	---------------------------------------------------------------------------------CTCTGAGGATGATTGTTGAA-----------	20	-	-	1
	---------------------------------------------------------------------------------CTCTGAGGATGATTGTTGA------------	19	1	-	-
	----------------------------------------------------------------------------------TCTGAGGATGATTGTTGAA-----------	19	-	-	1
rat	gccatgtgggttgagcattaccactgataccagagcatagcaggaatttgcattcctgtgttctcattgctgttgtgttctctcTGAGGATGATTGTTGAATGAattcaggc
	****************************************************************************************************************
rat	(((..((..(((.(((((((((...((....((((((((((((.(((..((((....))))....))).)))))))))))).))...)).)))).))).)))..))...)))	0.700 -30.20

rat

chromosome:1:47745227:47745338:1

intergenic

novel_lenNOK_Multihit_shortStem_5varHIGH_loopOverlap (12 loci)

block843775 [novel_lenNOK_Multihit_shortStem_5varHIGH_loopOverlap]

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	0.169	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	2	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG-------------	3	novel
seed	---------------------------------CCAUUCU------------------	2	novel
seed	-------------------------------------UCUCACA--------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG--	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG--	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG--	20	-	1
rat	gtacttccaggttcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGcg
	**********************************************************
rat	(((((...(((((.....((((....((((......)))).)))))))))..))))).	0.730 -12.00

rat

chromosome:1:49951170:49951227:-1

intergenic

block844338 [novel_lenNOK_Multihit_shortStem_5varHIGH_loopOverlap]

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	0.324	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	2	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG-------------	3	novel
seed	---------------------------------CCAUUCU------------------	2	novel
seed	-------------------------------------UCUCACA--------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG--	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG--	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG--	20	-	1
rat	gtacttccagtgtcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGcg
	**********************************************************
	--------------------------------------------------------------------	ENSRNOT00000041575 ENSRNOG00000031160 LOC685793
rat	(((((...((.(((....((((....((((......)))).)))))))))..))))).	0.690 -10.20

rat

chromosome:1:50179232:50179289:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000049496|ENSRNOG00000031160 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041575|ENSRNOG00000031160 ## ENSRNOG00000031160|protein_coding|LOC685793|

block844592 [novel_lenNOK_Multihit_shortStem_5varHIGH_loopOverlap]

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	0.408	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	1	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG------------	3	novel
seed	---------------------------------CCAUUCU-----------------	2	novel
seed	-------------------------------------UCUCACA-------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG-	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG-	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG-	20	-	1
rat	gtacttccagtgtcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGc
	*********************************************************
	-------------------------------------------------------------------	ENSRNOT00000041575 ENSRNOG00000031160 LOC685793
rat	(((((...((.(((....((((....((((......)))).)))))))))..)))))	0.640 -8.50

rat

chromosome:1:50292025:50292081:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000049496|ENSRNOG00000031160 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000041575|ENSRNOG00000031160 ## ENSRNOG00000031160|protein_coding|LOC685793|

block845584 [novel_lenNOK_Multihit_shortStem_5varHIGH_loopOverlap]

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	0.408	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	1	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG------------	3	novel
seed	---------------------------------CCAUUCU-----------------	2	novel
seed	-------------------------------------UCUCACA-------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG-	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG-	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG-	20	-	1
rat	gtacttccagtgtcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGc
	*********************************************************
rat	(((((...((.(((....((((....((((......)))).)))))))))..)))))	0.640 -8.50

rat

chromosome:1:50783933:50783989:-1

intergenic

block845630 [novel_lenNOK_Multihit_shortStem_5varHIGH_loopOverlap]

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	0.408	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	1	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG------------	3	novel
seed	---------------------------------CCAUUCU-----------------	2	novel
seed	-------------------------------------UCUCACA-------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG-	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG-	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG-	20	-	1
rat	gtacttccagtgtcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGc
	*********************************************************
rat	(((((...((.(((....((((....((((......)))).)))))))))..)))))	0.640 -8.50

rat

chromosome:1:50785748:50785804:-1

intergenic

block845804 [novel_lenNOK_Multihit_shortStem_5varHIGH_loopOverlap]

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	0.408	no	no	0.54/0.58	19/24/0.50	1.8	0.0	6	0	2	0	1	-4	3arm	27	nd	0.15	2	6	2	na	na

		reads	miRBase family seed
seed	--------------------------------------CUCACAG------------	3	novel
seed	---------------------------------CCAUUCU-----------------	2	novel
seed	-------------------------------------UCUCACA-------------	1	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------TCTCACAGGACCTCCAGTG-	19	-	3
	--------------------------------TCCATTCTCACAGGACCTCCAGTG-	24	1	1
	------------------------------------TTCTCACAGGACCTCCAGTG-	20	-	1
rat	gtacttccagtgtcacagctgttataagaaccTCCATTCTCACAGGACCTCCAGTGc
	*********************************************************
rat	(((((...((.(((....((((....((((......)))).)))))))))..)))))	0.640 -8.50

rat

chromosome:1:50835193:50835249:-1

intergenic

block922387 [novel_lenNOK_Multihit_shortStem_5varHIGH_loopOverlap]

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	0.485	no	no	0.55/0.58	19/22/0.50	1.5	0.0	2	0	2	0	2	-4	3arm	129	nd	0.26	2	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------GCACAGU-------------	1	novel
seed	------------------------------------ACGGCAC----------------	1	novel
		len	cloning frequencies
			T3S1	T4S2
	--------------------------------------GGCACAGTCAAGGCTGAGA--	19	1	-
	-----------------------------------AACGGCACAGTCAAGGCTGAGA--	22	-	1
rat	gttccagtatgactctaactaaccatggcaaattcAACGGCACAGTCAAGGCTGAGAat
	***********************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000020763 ENSRNOG00000015406 Pgm5_predicted
rat	((((((((.(((((.............((..........))..)))))..)))).))))	0.980 -8.86

rat

chromosome:1:228113234:228113292:-1

Same_strand|Boundary_non-coding|ENSRNOT00000034973|ENSRNOG00000015406 ## Same_strand|Intronic_coding|ENSRNOT00000020763|ENSRNOG00000015406 ## ENSRNOG00000015406|protein_coding|Pgm5_predicted|

Back to summary page

other hairpins:

Jump 10 pages back

Page 30940

Jump 10 pages forward

©2008 InteRNA Genomics B.V.