Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_5varHIGH_randfoldOK_nonpairedHIGH (4 loci)

block1675575 [novel_lenNOK_5varHIGH_randfoldOK_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	0.001	no	no	0.47/0.47	19/19/0.00	1.5	1.5	2	0	2	0	10	28	5arm	1	nd	0.37	3	2	2	na	na

		reads	miRBase family seed
seed	-----------CACCCUU---------------------------------------------------------------------------------------------------	1	miR-336
seed	--------------CCUUUGU------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T4S2
	----------TCACCCTTTGTATTCCCCA----------------------------------------------------------------------------------------	19	1	-
	-------------CCCTTTGTATTCCCCATAG-------------------------------------------------------------------------------------	19	-	1
rat	cttcttaaccTCACCCTTTGTATTCCCCATAGctagttctgtctctctgtaaatggcaagcctgtatcatttgccgttaatgccaaggggcagggggacaaagggcacccatgaaga
	*********************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000012875 ENSRNOG00000009019 Slc6a6
rat	((((.........(((((((...(((((..........((((((((..((((((((((((.........)))))))))..)))..)))))))))))))))))))).......)))).	0.900 -39.19

rat

chromosome:4:125914521:125914637:1

Same_strand|Intronic_coding|ENSRNOT00000012875|ENSRNOG00000009019 ## ENSRNOG00000009019|protein_coding|Slc6a6|Sodium- and chloride-dependent taurine transporter. [Source:UniProtKB/Swiss-Prot;Acc:P31643]

block105398 [novel_lenNOK_5varHIGH_randfoldOK_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	0.010	no	no	0.57/0.63	19/25/0.20	3.5 0.0	1.5 0.0	4 1	0 0	3 1	0 0	25 18	10 26	3arm 3arm	1 1	nd nd	0.32 0.37	3 3	5	4	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------UCGUGUG------------------------------------	2	novel
seed	------------------------------------------------------------------------UGACAUC-----------------------------------------	1	novel
seed	------------------------------------------------------------------------------------UGCGCAA-----------------------------	1	let-7i*
seed	--------------------------------------------------------------------UGCCUGA---------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S1	T3S2	T5S1
	----------------------------------------------------------------------------ATCGTGTGTGCGCAAGCCT-------------------------	19	-	-	-	2
	-----------------------------------------------------------------------------------GTGCGCAAGCCTAGTGTGC------------------	19	1	-	-	-
	-------------------------------------------------------------------GTGCCTGACATCGTGTGTGCGCAAG----------------------------	25	-	1	-	-
	-----------------------------------------------------------------------CTGACATCGTGTGTGCGCAAG----------------------------	21	-	-	1	-
rat	gctgacccagctgcggcctggcgtggttcccgcgatgtacgtgggtggcgtcacttccgcctcctgcGTGCCTGACATCGTGTGTGCGCAAGCCTAGTGTGCtgcggctaggggctcagc
	************************************************************************************************************************
rat	((((((((((((((((((((((.((((...(((((((((((..((.((((.......)))).))..))).....))))))))...)).)).))).))...)))))))))..))).)))))	0.980 -61.80

rat

chromosome:10:108296499:108296618:1

intergenic

block1848496 [novel_lenNOK_5varHIGH_randfoldOK_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	0.004	no	no	0.45/0.47	19/24/0.67	1.7	2.7	3	0	2	0	8	27	3arm	1	nd	0.32	2	3	2	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------AGGAUAC------------------------	2	novel
seed	-----------------------------------------------------------------------------------------ACUGUGG-------------------	1	miR-881
		len	cloning frequencies
			T1S2	T5S1
	----------------------------------------------------------------------------------------TACTGTGGAGTCAGTTGTG--------	19	1	-
	-----------------------------------------------------------------------------------AAGGATACTGTGGAGTCAGT------------	20	1	-
	-----------------------------------------------------------------------------------AAGGATACTGTGGAGTCAGTTGTG--------	24	-	1
rat	gccttcccaccatacaccacagagccagaatcctcctctctcctgtcctggtggacaccaggcacagggagagctgaggcctgAAGGATACTGTGGAGTCAGTTGTGccctaggc
	*******************************************************************************************************************
rat	((((...(((.((((.((((((..((.....(((((((((.(((((((((((....)))))).))))))))))..))))......))...)))))).))..)).)))....))))	0.910 -49.90

rat

chromosome:5:79246003:79246117:1

intergenic

novel_lenNOK_Multihit_5varHIGH_loopOverlap_randfoldOK (4 loci)

block958367 [novel_lenNOK_Multihit_5varHIGH_loopOverlap_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	0.59/0.61	18/22/0.50	2.0	0.0	2	0	2	0	17	-5	3arm	25	nd	0.22	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------AGCUGCC-------------------------------	1	miR-22
seed	---------------------------------------------------GCCUCUU---------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	----------------------------------------------AAGCTGCCTCTTCTGACACCCC-----------------	22	-	1
	--------------------------------------------------TGCCTCTTCTGACACCCC-----------------	18	1	-
rat	atgtgactgttagcccatatctgtgattcactgtcattaggaggctAAGCTGCCTCTTCTGACACCCCacagtgggccggataca
	*************************************************************************************
rat	.((((.(((...(((((...(((((......(((((..(((((((......))))))).)))))...))))))))))))).))))	1.000 -32.20

rat

chromosome:1:47726066:47726150:1

intergenic

block842450 [novel_lenNOK_Multihit_5varHIGH_loopOverlap_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	0.001	no	no	0.59/0.61	18/22/0.50	2.0	0.0	2	0	2	0	19	-5	3arm	25	nd	0.22	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------AGCUGCC---------------------------------	1	miR-22
seed	---------------------------------------------------GCCUCUU-----------------------------	1	novel
		len	cloning frequencies
			T2S1	T5S1
	----------------------------------------------AAGCTGCCTCTTCTGACACCCC-------------------	22	-	1
	--------------------------------------------------TGCCTCTTCTGACACCCC-------------------	18	1	-
rat	atgtgactattagcccatatctgtgattcactgtcattaggaggctAAGCTGCCTCTTCTGACACCCCacagtgggccggatacaca
	***************************************************************************************
rat	.((((..((((.(((((...(((((......(((((..(((((((......))))))).)))))...))))))))))..))))))))	1.000 -32.10

rat

chromosome:1:48366137:48366223:-1

intergenic

block843198 [novel_lenNOK_Multihit_5varHIGH_loopOverlap_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	0.001	no	no	0.59/0.61	18/22/0.50	2.0	0.0	2	0	2	0	19	-5	3arm	25	nd	0.11	1	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------GCCUCUU-----------------------------	1	novel
seed	-------------------------------------------------AGCUGCC---------------------------------	1	miR-22
		len	cloning frequencies
			T2S1	T5S1
	------------------------------------------------AAGCTGCCTCTTCTGACACCCC-------------------	22	-	1
	----------------------------------------------------TGCCTCTTCTGACACCCC-------------------	18	1	-
rat	ctatgtgactgttagcccatatctgggattgactgtcattaagaggctAAGCTGCCTCTTCTGACACCCCacattgggcaggatacata
	*****************************************************************************************
rat	.((((((.((....(((((....((((......(((((..(((((((......))))))).))))).))))...))))).)).))))))	0.950 -33.30

rat

chromosome:1:49043682:49043770:-1

intergenic

block1685066 [novel_lenNOK_Multihit_5varHIGH_loopOverlap_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	0.007	no	no	0.40/0.44	18/20/0.50	1.5	0.5	2	0	2	0	35	-18	3arm_loop	18	nd	0.28	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------GUCACAG------------------------------------------------	1	novel
seed	------------------------------------------------------------ACAGAAU---------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T2S2
	-----------------------------------------------------------CACAGAATTTTGAGACCC-----------------------------------	18	1	-
	--------------------------------------------------------TGTCACAGAATTTTGAGACC------------------------------------	20	-	1
rat	aagttattagttttcaaaatcagtactttttaatggaaacaacttgatcaaaaatcTGTCACAGAATTTTGAGACCCattaaaacaagtttaatgagaaaaaagataaactt
	****************************************************************************************************************
rat	((((((((..(((((....(((..((((((((((((...........((((((.((((...)))).))))))...)))))))))..)))....))))))))..))))).)))	0.410 -19.74

rat

chromosome:4:147807604:147807715:1

intergenic

novel_lenNOK_Multihit_shortStem_loopOverlap_bulgeHIGH (4 loci)

block1428822 [novel_lenNOK_Multihit_shortStem_loopOverlap_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	0.58/0.58	26/26/0.00	0.0	0.0	3	0	1	0	0	-2	3arm_loop	12	nd	0.28	4	3	1	na	na

		reads	miRBase family seed
seed	----------------------------------UGUACCU------------------	3	novel
		len	cloning frequencies
			T1S1
	---------------------------------TTGTACCTGGAAGAGCCACCTCCTCC	26	3
rat	gaggggctgagttcccaaaggaagttgctgaccTTGTACCTGGAAGAGCCACCTCCTCC
	***********************************************************
rat	((((((.((.((((....(((....(((.......))))))....)))))).)))))).	0.600 -17.20

rat

chromosome:3:165404920:165404978:-1

intergenic

block1428910 [novel_lenNOK_Multihit_shortStem_loopOverlap_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	0.58/0.58	26/26/0.00	0.0	0.0	3	0	1	0	0	-2	3arm_loop	12	nd	0.28	4	3	1	na	na

		reads	miRBase family seed
seed	----------------------------------UGUACCU------------------	3	novel
		len	cloning frequencies
			T1S1
	---------------------------------TTGTACCTGGAAGAGCCACCTCCTCC	26	3
rat	gaggggctgagttcccaaaggaagttgctgaccTTGTACCTGGAAGAGCCACCTCCTCC
	***********************************************************
rat	((((((.((.((((....(((....(((.......))))))....)))))).)))))).	0.600 -17.20

rat

chromosome:3:165670395:165670453:-1

intergenic

block1515600 [novel_lenNOK_Multihit_shortStem_loopOverlap_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	0.58/0.58	26/26/0.00	0.0	0.0	3	0	1	0	0	-2	3arm_loop	12	nd	0.28	4	3	1	na	na

		reads	miRBase family seed
seed	----------------------------------UGUACCU------------------	3	novel
		len	cloning frequencies
			T1S1
	---------------------------------TTGTACCTGGAAGAGCCACCTCCTCC	26	3
rat	gaggggctgagttcccaaaggaagttgctgaccTTGTACCTGGAAGAGCCACCTCCTCC
	***********************************************************
rat	((((((.((.((((....(((....(((.......))))))....)))))).)))))).	0.600 -17.20

rat

chromosome:3:167131607:167131665:1

intergenic

Back to summary page

other hairpins:

Jump 10 pages back

Page 31095

Jump 10 pages forward

©2008 InteRNA Genomics B.V.