Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_shortStem_loopOverlap_nonpairedHIGH (164 loci)

block2570338 [novel_shortStem_loopOverlap_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	0.113	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	4	-3	3arm_loop	1	nd	0.50	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------CCUUUGG----------------	1	novel
		len	cloning frequencies
			T4S2
	-------------------------TCCTTTGGGGGACAAATTGA----	20	1
rat	taaagcatgtgacccctggaacttgTCCTTTGGGGGACAAATTGAtttg
	*************************************************
rat	.....((..((.((((..((........))..)))).))...)).....	0.990 -12.40

rat

chromosome:9:13054690:13054738:1

intergenic

block2615005 [novel_shortStem_loopOverlap_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	0.650	no	no	0.62/0.62	24/24/1.00	0.0	0.0	1	0	1	0	2	-1	3arm	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------GCACUCU------------------	1	novel
		len	cloning frequencies
			T2S2
	-------------------------------------------------AGCACTCTGGGGATGTGTGCAGGC--	24	1
rat	acttttgcaattttcagtatgtcatcatcaaacaatgtttacaaaactcAGCACTCTGGGGATGTGTGCAGGCgt
	***************************************************************************
rat	((.(((((((((..(((..(((............................)))..)))..)))...)))))).))	0.410 -11.49

rat

chromosome:9:70926079:70926153:1

intergenic

block2644581 [novel_shortStem_loopOverlap_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	0.246	no	no	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	4	-3	3arm_loop	2	nd	0.41	3	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------CAGGUUG------------------	1	novel
		len	cloning frequencies
			T4S2
	-----------------------------------------CCAGGTTGTAGTAACATCAAAG----	22	1
rat	ctgatgtcgtgcactacaccattttaacttcattacctcatCCAGGTTGTAGTAACATCAAAGcagg
	*******************************************************************
rat	(((.((..((..((((((((........................))).))))).))..))...))).	0.820 -11.06

rat

chromosome:9:105174210:105174276:1

intergenic

block2707463 [novel_shortStem_loopOverlap_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	0.729	no	no	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	4	-4	3arm_loop	1	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------ACUCUGG--------------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------AACTCTGGACCTGTATGACTTTCC----	24	1
rat	agagggactggaatcaatagaagcggcgAACTCTGGACCTGTATGACTTTCCcctt
	********************************************************
rat	.(((((...(((((((((((...(((......)))...)))).))).)))))))))	0.990 -10.30

rat

chromosome:X:55459954:55460009:-1

intergenic

block3134100 [novel_shortStem_loopOverlap_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	0.066	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	3	-2	5arm_loop	1	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	----AUGGUAG-------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	---TATGGTAGTTTTTCTTCCCT-------------------------	20	1
rat	catTATGGTAGTTTTTCTTCCCTccggctggtacttaccatttcatga
	************************************************
rat	(((.((((((((...((..((....))..)).))).)))))...))).	1.000 -8.50

rat

chromosome:X:146655937:146655984:1

intergenic

block3193898 [novel_shortStem_loopOverlap_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	0.41/0.41	22/22/1.00	0.0	0.0	1	0	1	0	4	-3	3arm_loop	1	nd	0.32	2	1	1	na	na

		reads	miRBase family seed
seed	----------------------------AGGACCU------------------	1	novel
		len	cloning frequencies
			T4S2
	---------------------------TAGGACCTTGCACTAGAAACTT----	22	1
rat	ttcaaggttttctcttgcattgagttcTAGGACCTTGCACTAGAAACTTgaga
	*****************************************************
rat	((((((...((((..((((....(((....)))..))))..)))).)))))).	0.980 -13.50

rat

chromosome:X:159244236:159244288:1

intergenic

block1034190 [novel_shortStem_loopOverlap_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	0.633	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	4	-4	3arm_loop	1	nd	0.40	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------CCAAGGU----------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------TCCAAGGTGCAAGTACCCCC----	20	1
rat	ggcgggcggcgctccttttgtgtgtttcttTCCAAGGTGCAAGTACCCCCcacc
	******************************************************
rat	((.(((.((..((.......((..(((.......)))..))))..)).))).))	0.810 -12.51

rat

chromosome:1:213124659:213124712:1

intergenic

block366517 [novel_shortStem_loopOverlap_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	0.085	no	no	0.64/0.64	22/22/1.00	0.0	0.0	1	0	1	0	4	-2	3arm_loop	1	nd	0.32	2	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------AGCAGGG------------------	1	novel
		len	cloning frequencies
			T5S1
	-----------------------------------GAGCAGGGCCATCAGAAGGGAC----	22	1
rat	aggcagaccgactgaggagggcctggggggcaggaGAGCAGGGCCATCAGAAGGGACtcct
	*************************************************************
	-----------------------------------------------------------------------	ENSRNOT00000024813 ENSRNOG00000018319 LOC683500
rat	(((.((.((..((((....(((((.....((......)).))))).))))..))..)))))	1.000 -22.00

rat

chromosome:14:83733503:83733563:-1

Opposite_strand|Intronic_coding|ENSRNOT00000024813|ENSRNOG00000018319 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000057779|ENSRNOG00000018319 ## ENSRNOG00000018319|protein_coding|LOC683500|

block1167435 [novel_shortStem_loopOverlap_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	0.448	no	no	0.39/0.39	23/23/1.00	0.0	0.0	1	0	1	0	3	-1	5arm_loop	1	nd	0.39	3	1	1	na	na

		reads	miRBase family seed
seed	----GACCAAG---------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	---TGACCAAGTGTGATTAGTTTGCT------------------------------	23	1
rat	tcaTGACCAAGTGTGATTAGTTTGCTgatgttgtgaatattttacctgaatcctga
	********************************************************
rat	(((.((...((.((((...((((((.......))))))...))))))...)).)))	0.970 -8.30

rat

chromosome:2:105759781:105759836:-1

intergenic

novel_lenNOK_cloningOK_shortStem_nonpairedHIGH (163 loci)

block4018 [novel_lenNOK_cloningOK_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	0.228	no	no	0.26/0.28	18/19/0.00	0.0	0.0	27	0	2	0	0	29	5arm	2	nd	0.39	3	30	2	na	na

		reads	miRBase family seed
seed	-GGAAUGA--------------------------------------------------------------------------------------------	30	novel
		len	cloning frequencies
			T4S1	T4S2
	TGGAATGATTTCTTTCAA----------------------------------------------------------------------------------	18	10	17
	TGGAATGATTTCTTTCAAA---------------------------------------------------------------------------------	19	1	2
rat	TGGAATGATTTCTTTCAAagaataaatgtgtgtgttaaatatcagaaattgttataatccttctgcgtaaactaactcattatttctttcagttcttcca
	****************************************************************************************************
rat	.((((.((...((...((((((..((((.((..(((...((((((((.............))))).))))))..)).))))..)))))).)).)))))).	0.900 -14.72

rat

chromosome:10:8768304:8768403:-1

intergenic

Back to summary page

other hairpins:

Jump 10 pages back

Page 29897

Jump 10 pages forward

©2008 InteRNA Genomics B.V.