Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_loopOverlap_bulgeHIGH (21 loci)

novel_lenNOK_Multihit_loopOverlap_randfoldOK (21 loci)

block19963 [novel_lenNOK_Multihit_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	0.008	no	no	0.68/0.68	19/19/0.00	0.0	0.0	1	0	1	0	33	-1	3arm	13	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------GGGACGU--------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------------------CGGGACGTGATGGTCGAGC---------------------------------	19	1
rat	gcttggccagctccccaggcagcagcaggcgcacggccgtctgcacctcgCGGGACGTGATGGTCGAGCgcttgttgtaatgagccaggcgggaggcctcgc
	******************************************************************************************************
	----------------------------------------------------------------------------------------------------------------	ENSRNOT00000033866 ENSRNOG00000022983 Trim17
	----------------------------------------------------------------------------------------------------------------	ENSRNOT00000048642 ENSRNOG00000022983 Trim17
	----------------------------------------------------------------------------------------------------------------	ENSRNOT00000033894 ENSRNOG00000022983 Trim17
	----------------------------------------------------------------------------------------------------------------	ENSRNOT00000058453 ENSRNOG00000022983 Trim17
rat	((..((((..(((.((.(((.(((((((((((.((((((((((..((....))..)).)))))))).))))))))))).....))).)).))).))))..))	0.970 -53.90

rat

chromosome:10:45238379:45238480:-1

Opposite_strand|Intronic_coding|ENSRNOT00000058453|ENSRNOG00000022983 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000003885|ENSRNOG00000022983 ## ENSRNOG00000022983|protein_coding|Trim17|Tripartite motif-containing protein 17 (Testis RING finger protein). [Source:UniProtKB/Swiss-Prot;Acc:Q9WV59]

block251037 [novel_lenNOK_Multihit_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	0.009	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	20	-2	3arm_loop	14	nd	0.06	1	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------GAGGGCU------------------------------	1	novel
		len	cloning frequencies
			T4S2
	---------------------------------------TGAGGGCTTAGGAAAATT--------------------	18	1
rat	tggaggaccttcttagttaggttttcttgggatcctaatTGAGGGCTTAGGAAAATTctgagagctggtgggccttt
	*****************************************************************************
rat	.(((((.(((((((((...((((((((((((.((((.....))))))))))))))))))))))......))))))))	0.900 -25.60

rat

chromosome:13:30540772:30540848:-1

intergenic

block285079 [novel_lenNOK_Multihit_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	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	20	-3	3arm_loop	14	nd	0.11	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------GAGGGCU------------------------------	1	novel
		len	cloning frequencies
			T4S2
	--------------------------------------TGAGGGCTTAGGAAAATT--------------------	18	1
rat	ggaggactttcttagttaggttttcctgggatcccaacTGAGGGCTTAGGAAAATTctgagagcaggtgggcctct
	****************************************************************************
rat	(((((.(((((((((...((((((((((((..(((......)))))))))))))))))))))).)).....)))))	0.990 -28.90

rat

chromosome:13:283335:283410:1

intergenic

block353695 [novel_lenNOK_Multihit_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	0.005	no	no	0.42/0.42	19/19/0.00	0.0	0.0	1	0	1	0	34	-2	3arm_loop	28	nd	0.26	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------CCUAGAA---------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------------ACCTAGAATACCATGTGGA----------------------------------	19	1
rat	cattgtagctgggtctgaatctgagttcaagaatggtatgagcaACCTAGAATACCATGTGGAttccttctggagaacatgcccagaattgtggtga
	*************************************************************************************************
	-----------------------------------------------------------------------------------------------------------	ENSRNOT00000049147 ENSRNOG00000032644
rat	(((..((.((((((.((..((((((((((...(((((((.((....))...))))))).))))))).....)))...)).))))))...))..))).	0.820 -31.40

rat

chromosome:14:49183103:49183199:-1

Opposite_strand|Intronic_coding|ENSRNOT00000049147|ENSRNOG00000032644 ## ENSRNOG00000032644|protein_coding||

block400590 [novel_lenNOK_Multihit_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	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	13	-3	3arm_loop	19	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------GACUAGA------------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------AGACTAGATGTGATAAAGT-------------	19	1
rat	acacttgcacatgctttaacatctagagAGACTAGATGTGATAAAGTaggatgcccttgt
	************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000043791 ENSRNOG00000032207 LOC690700
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000045975 ENSRNOG00000032207 LOC690700
rat	(((...(((..(((((((((((((((.....))))))))..)))))))...)))...)))	0.990 -17.70

rat

chromosome:14:49687757:49687816:1

Same_strand|Boundary_non-coding|ENSRNOT00000050021|ENSRNOG00000032207 ## Same_strand|Intronic_coding|ENSRNOT00000045975|ENSRNOG00000032207 ## Same_strand|Intronic_non-coding|ENSRNOT00000043791|ENSRNOG00000032207 ## ENSRNOG00000032207|protein_coding|LOC690700|LOC501224 protein. [Source:UniProtKB/TrEMBL;Acc:Q0P5Q7]

block400776 [novel_lenNOK_Multihit_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	0.006	no	no	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	23	-3	3arm_loop	19	nd	0.21	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------GACUAGA----------------------------------	1	novel
		len	cloning frequencies
			T5S2
	------------------------------------AGACTAGATGTGATAAAGT-----------------------	19	1
rat	ctgtgtttacacttgcacatgctttaacatctagagAGACTAGATGTGATAAAGTaggatgcccttgtcgtttacata
	******************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000046075 ENSRNOG00000038676 LOC367617
rat	.(((((..((((..(((..(((((((((((((((.....))))))))..)))))))...)))....)).))..)))))	0.980 -22.20

rat

chromosome:14:49795178:49795255:1

Same_strand|Intronic_non-coding|ENSRNOT00000046075|ENSRNOG00000038676 ## ENSRNOG00000038676|protein_coding|LOC367617|

block773675 [novel_lenNOK_Multihit_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	0.009	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	41	-2	3arm_loop	13	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------UUUUUAU---------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------------------------GTTTTTATAGGTGCTGTT-----------------------------------------	18	1
rat	cagcatcagtattaaaccacagagataatgaccagcaacgtcattttgggaaatagGTTTTTATAGGTGCTGTTtcacttgatcattcatttgctgtgttttttattgttgctga
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000041121 ENSRNOG00000029942 LOC684084
rat	(((((.(((((..(((.((((((((((((((.(((.((((.(((((...((((.....))))..))))).))))....))).))))).)))).))))))))..))))).))))).	0.560 -30.30

rat

chromosome:19:23330398:23330512:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000041121|ENSRNOG00000029942 ## ENSRNOG00000029942|protein_coding|LOC684084|

block773852 [novel_lenNOK_Multihit_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	0.009	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	41	-2	3arm_loop	13	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------UUUUUAU---------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------------------------GTTTTTATAGGTGCTGTT-----------------------------------------	18	1
rat	cagcatcagtattaaaccacagagataatgaccagcaacgtcattttgggaaatagGTTTTTATAGGTGCTGTTtcacttgatcattcatttgctgtgttttttattgttgctga
	*******************************************************************************************************************
rat	(((((.(((((..(((.((((((((((((((.(((.((((.(((((...((((.....))))..))))).))))....))).))))).)))).))))))))..))))).))))).	0.560 -30.30

rat

chromosome:19:23552771:23552885:-1

intergenic

block803870 [novel_lenNOK_Multihit_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	0.003	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	41	-2	3arm_loop	13	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------UUUUUAU---------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	--------------------------------------------------------GTTTTTATAGGTGCTGTT-----------------------------------------	18	1
rat	cagcatcagtattaaaccacagatataatgatcagcaacgtcattttgggaaatagGTTTTTATAGGTGCTGTTtcacttgatcattcatttgctgtgttttttattgttgctga
	*******************************************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000050888 ENSRNOG00000034204 LOC685424
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000051707 ENSRNOG00000034204 LOC685424
rat	(((((.(((((..(((.(((((..(((((((((((.((((.(((((...((((.....))))..))))).))))....))))))))).))...))))))))..))))).))))).	0.700 -33.20

rat

chromosome:19:24576494:24576608:1

Opposite_strand|Boundary_non-coding|ENSRNOT00000047525|ENSRNOG00000034204 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000051707|ENSRNOG00000034204 ## ENSRNOG00000034204|protein_coding|LOC685424|

block962304 [novel_lenNOK_Multihit_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	0.003	no	no	0.15/0.16	19/20/0.67	0.0	0.7	3	0	2	0	20	-3	3arm_loop	26	nd	0.30	3	3	2	na	na

		reads	miRBase family seed
seed	--------------------------------------AUGAUUA--------------------------------	3	novel
		len	cloning frequencies
			T3S2	T5S2
	-------------------------------------AATGATTATTTATAAAGTCT--------------------	20	1	1
	-------------------------------------AATGATTATTTATAAAGTC---------------------	19	-	1
rat	ttgggtcagaaaatgtccatagacttggaatactcaaAATGATTATTTATAAAGTCTaaaacagctgcaaatctaaa
	*****************************************************************************
rat	(((((((((....(((...(((((((.(((((.((.....)).)))))...)))))))..))).)))...)))))).	0.980 -17.10

rat

chromosome:1:51398764:51398840:1

intergenic

Back to summary page

other hairpins:

Jump 10 pages back

Page 30819

Jump 10 pages forward

©2008 InteRNA Genomics B.V.