Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_5varHIGH_bulgeHIGH (15 loci)

block1403433 [novel_lenNOK_shortStem_5varHIGH_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	0.814	no	no	0.37/0.42	19/21/0.60	3.2	4.0	5	0	3	0	0	7	5arm	1	nd	0.30	4	5	3	na	na

		reads	miRBase family seed
seed	-UAAGGAC----------------------------------------------------------------------	2	novel
seed	-------CCAAUAA----------------------------------------------------------------	1	novel
seed	--------CAAUAAA---------------------------------------------------------------	1	novel
seed	----GGACCAA-------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1
	CTAAGGACCAATAAACTGT-----------------------------------------------------------	19	1	-	-
	---AGGACCAATAAACTGTCAC--------------------------------------------------------	19	-	1	-
	-------CCAATAAACTGTCACTCAAC---------------------------------------------------	20	1	-	-
	CTAAGGACCAATAAACTGTC----------------------------------------------------------	20	-	-	1
	------ACCAATAAACTGTCACTCAAC---------------------------------------------------	21	-	1	-
rat	CTAAGGACCAATAAACTGTCACTCAACaagctgcctctgtctctacctgtcccccagtgtccctagtgtggctttgga
	******************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000028839 ENSRNOG00000021234 Slc4a11
rat	((((((.(((....((((.((((..(((((..((....))..))...))).....))))....)))).))))))))).	0.510 -11.90

rat

chromosome:3:118332681:118332758:-1

Same_strand|Boundary_non-coding|ENSRNOT00000039716|ENSRNOG00000021234 ## Same_strand|Intronic_non-coding|ENSRNOT00000028839|ENSRNOG00000021234 ## ENSRNOG00000021234|protein_coding|Slc4a11|solute carrier family 4, sodium bicarbonate transporter-like, member 11 Gene [Source:MGI (curated);Acc:Slc4a11-001]

block1414110 [novel_lenNOK_shortStem_5varHIGH_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	0.027	no	no	0.39/0.45	18/21/0.67	1.3	1.0	3	0	3	0	0	19	5arm	4	nd	0.30	4	3	3	na	na

		reads	miRBase family seed
seed	-CCUUCCA-------------------------------------------------------------------------------------	2	novel
seed	-----CCACUUU---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T4S2	T5S1
	TCCTTCCACTTTGTGTTCCA-------------------------------------------------------------------------	20	-	-	1
	TCCTTCCACTTTGTGTTCCAA------------------------------------------------------------------------	21	-	1	-
	----TCCACTTTGTGTTCCAAA-----------------------------------------------------------------------	18	1	-	-
rat	TCCTTCCACTTTGTGTTCCAAAaccatataaagttttttgttgataatgtgcaaaagattaatgatatgaatgtggtgtagagtttatgaagg
	*********************************************************************************************
rat	.(((((.((((((....(((....(((((..((((((((((.........))))))))))....)))))....)))..))))))....)))))	1.000 -20.40

rat

chromosome:3:141689953:141690045:-1

intergenic

block1606106 [novel_lenNOK_shortStem_5varHIGH_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	0.264	no	no	0.50/0.50	18/22/0.33	1.3	0.0	3	0	1	0	2	19	5arm	1	nd	0.28	4	3	1	na	na

		reads	miRBase family seed
seed	-------AGAGCCU--------------------------------------------------------------------------------	2	novel
seed	---AUGGAGA------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	------GAGAGCCTCACTAGAATG----------------------------------------------------------------------	18	2
	--CATGGAGAGCCTCACTAGAATG----------------------------------------------------------------------	22	1
rat	agCATGGAGAGCCTCACTAGAATGaagtcctttgtgccttcagtcagcttcggggattatacagggaaggctctgggagctgttttcctggctg
	**********************************************************************************************
rat	(((..((((((((((.(((((......(((((.((.(((..((....))..))).)).....)))))....))))))))..)))))))..))).	0.620 -27.50

rat

chromosome:4:173474746:173474839:-1

intergenic

block1696401 [novel_lenNOK_shortStem_5varHIGH_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	0.058	no	no	0.30/0.31	23/26/0.50	1.5	0.0	2	0	1	0	4	3	5arm	1	nd	0.23	4	2	1	na	na

		reads	miRBase family seed
seed	-----CAUGAAA----------------------------------------------------------	1	novel
seed	--------GAAAGUU-------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------TGAAAGTTGTTCATTTGGTTCAA----------------------------------------	23	1
	----TCATGAAAGTTGTTCATTTGGTTCAA----------------------------------------	26	1
rat	gtttTCATGAAAGTTGTTCATTTGGTTCAAtggcacgccattgaaatgcacagtgttgcaatatgtagac
	**********************************************************************
rat	((((.(((....(((((.((((((.((((((((....))))))))...)).))))..)))))))).))))	0.900 -17.10

rat

chromosome:4:164270213:164270282:1

intergenic

block2311410 [novel_lenNOK_shortStem_5varHIGH_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	0.137	no	no	0.43/0.48	23/25/0.50	1.5	0.5	2	0	1	0	0	4	5arm	1	nd	0.24	4	2	1	na	na

		reads	miRBase family seed
seed	----CAUCAAU------------------------------------------------------	1	novel
seed	-CACCAUC---------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	---CCATCAATTCTTGCTCTGGTTCA---------------------------------------	23	1
	GCACCATCAATTCTTGCTCTGGTTC----------------------------------------	25	1
rat	GCACCATCAATTCTTGCTCTGGTTCAtttctaagatggagaatcagggtagctggtttacagggc
	*****************************************************************
rat	((.((((((....((((((((((((..(((......))))))))))))))).)))).....))))	0.440 -16.20

rat

chromosome:8:57715446:57715510:-1

intergenic

block209076 [novel_lenNOK_shortStem_5varHIGH_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	0.346	no	no	0.45/0.57	19/23/0.60	1.6	2.2	5	0	3	0	2	19	3arm	1	nd	0.30	4	5	3	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------CGAUUUC-----------------	4	novel
seed	------------------------------------------------------------------------------AUCGAUU-------------------	1	novel
		len	cloning frequencies
			T2S1	T4S1	T5S1
	-------------------------------------------------------------------------------TCGATTTCTGAGCGTCTCC------	19	1	-	1
	-------------------------------------------------------------------------------TCGATTTCTGAGCGTCTCCCTG---	22	-	-	1
	-----------------------------------------------------------------------------TATCGATTTCTGAGCGTCTC-------	20	-	-	1
	-------------------------------------------------------------------------------TCGATTTCTGAGCGTCTCCCTGG--	23	-	1	-
rat	gccctggctgccaggagacgatacgtacactaccattctgaggctttgctgaaggatcctttgagccctgggctgctTATCGATTTCTGAGCGTCTCCCTGGgt
	********************************************************************************************************
rat	((((.((.(((((((((.(((((.(((.....(((......(((((....((((....))))))))).)))..))).))))).)))))).)))....)).))))	0.800 -31.70

rat

chromosome:12:5616961:5617064:1

intergenic

block1311113 [novel_lenNOK_shortStem_5varHIGH_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	0.064	no	no	0.67/0.70	18/23/0.50	2.5	0.0	2	0	1	0	0	7	5arm	1	nd	0.28	4	2	1	na	na

		reads	miRBase family seed
seed	------UCCACAG-----------------------------------------------------------	1	novel
seed	-CCACCUC----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	-----CTCCACAGCCTGACCTGC-------------------------------------------------	18	1
	CCCACCTCCACAGCCTGACCTGC-------------------------------------------------	23	1
rat	CCCACCTCCACAGCCTGACCTGCtgcagctggaggagctaaggaagctgagcgtggtggggaggggagcggg
	************************************************************************
rat	(((..((((....(((.(((((((.(((((..............))))))))).))).)))...)))).)))	1.000 -31.04

rat

chromosome:2:181264108:181264179:1

intergenic

block1060594 [novel_lenNOK_shortStem_5varHIGH_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	0.141	no	no	0.52/0.55	19/22/0.57	1.6	2.9	7	0	1	0	4	11	5arm	1	nd	0.29	6	7	1	na	na

		reads	miRBase family seed
seed	-----CCGAAGC------------------------------------------------------------------------------	4	novel
seed	--------AAGCAGG---------------------------------------------------------------------------	2	novel
seed	----------GCAGGGA-------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------GAAGCAGGGACTAGAAAGCTG--------------------------------------------------------------	21	2
	----TCCGAAGCAGGGACTAGAA-------------------------------------------------------------------	19	2
	----TCCGAAGCAGGGACTAGAAAGC----------------------------------------------------------------	22	1
	----TCCGAAGCAGGGACTAGAAAG-----------------------------------------------------------------	21	1
	---------AGCAGGGACTAGAAAGCTG--------------------------------------------------------------	19	1
rat	cagcTCCGAAGCAGGGACTAGAAAGCTGccaggtgagcattttgagaccattgcagaacacagtcccaaaccaaagtgtcttgggatctg
	******************************************************************************************
rat	(((.(((.(((((((((((......((((..(((...((...))..)))...)))).....)))))).........)).))).))).)))	0.590 -24.60

rat

chromosome:20:5510388:5510477:-1

intergenic

block1887941 [novel_lenNOK_shortStem_5varHIGH_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	0.095	no	no	0.76/0.80	18/21/0.40	1.4	1.2	5	0	4	0	0	13	3arm	1	nd	0.30	4	5	4	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------GGCUUCG------------	2	novel
seed	----------------------------------------------------------CGCCGGC----------------	1	novel
seed	------------------------------------------------------------CCGGCUU--------------	1	novel
seed	-------------------------------------------------------------CGGCUUC-------------	1	novel
		len	cloning frequencies
			T1S1	T2S2	T3S1	T4S2
	-------------------------------------------------------------CGGCTTCGCGAGCAGCGC--	18	-	-	2	-
	---------------------------------------------------------GCGCCGGCTTCGCGAGCAGC----	20	-	-	-	1
	------------------------------------------------------------CCGGCTTCGCGAGCAGCGCTG	21	-	1	-	-
	-----------------------------------------------------------GCCGGCTTCGCGAGCAGC----	18	1	-	-	-
rat	cagcgggctgacagagccgggcgagcgctggcagttccgtggtggggatggtgaggaGCGCCGGCTTCGCGAGCAGCGCTG
	*********************************************************************************
rat	(((((.(((....(((((.((((....((.((.(((((......))))).)).))...)))))))))....)))..)))))	0.480 -34.80

rat

chromosome:5:152639903:152639983:1

intergenic

novel_multiarm_DicerNOK_5varHIGH (15 loci)

sblock1070 [novel_multiarm_DicerNOK_5varHIGH]

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	0.017	no	no	0.50/0.70	18/23/0.83	0.0 1.8	0.0 0.8	1 5	0 0	1 3	0 0	24 26	8 2	5arm 3arm	1 1	nd nd	0.11 0.15	1 1	6	3	-5	0

		reads	miRBase family seed
seed	------------------------------------------------------------CUGCAGA----------------------------------------	3	novel
seed	---------------------------------------------------------CUGCUGC-------------------------------------------	2	novel
seed	-------------------------UCACACC---------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1	T5S1
	-----------------------------------------------------------GCTGCAGACCCCGGTGTGACAA--------------------------	22	-	-	2
	--------------------------------------------------------ACTGCTGCAGACCCCGGTGTGAC----------------------------	23	2	-	-
	------------------------ATCACACCGGTGTTTGCA-----------------------------------------------------------------	18	-	1	-
	-----------------------------------------------------------GCTGCAGACCCCGGTGTGAC----------------------------	20	-	1	-
rat	tgcacacggcggggagcctgacttATCACACCGGTGTTTGCAtacatcccggaaggACTGCTGCAGACCCCGGTGTGACAAtgttacacaatgcccggggaaagcag
	***********************************************************************************************************
rat	(((......((((.....((((((.(((((((((.(((((((..((..((....))..)).))))))).))))))))).)).)))).......))))......))).	0.500 -41.10

rat

chromosome:1:245996317:245996423:-1

intergenic

Back to summary page

other hairpins:

Jump 10 pages back

Page 30895

Jump 10 pages forward

©2008 InteRNA Genomics B.V.