Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_Multihit_loopOverlap_nonpairedHIGH (175 loci)

novel_Multihit_shortStem_nonpairedHIGH_bulgeHIGH (172 loci)

block24711 [novel_Multihit_shortStem_nonpairedHIGH_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	0.209	no	no	0.55/0.55	22/22/1.00	0.0	0.0	1	0	1	0	2	3	3arm	20	nd	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------ACUCGGG----------------	1	novel
		len	cloning frequencies
			T1S2
	---------------------------------AACTCGGGCCCATGGAAACAGT--	22	1
rat	cagtgactcctggaagagtgatctggggaaagtAACTCGGGCCCATGGAAACAGTgg
	*********************************************************
rat	((.((..((((((..((((...((......))..))))....))).)))..)).)).	0.710 -15.00

rat

chromosome:10:55909456:55909512:-1

intergenic

block32854 [novel_Multihit_shortStem_nonpairedHIGH_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	0.718	no	no	0.59/0.59	22/22/1.00	0.0	0.0	1	0	1	0	4	3	3arm	112	nd	0.36	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------UCAGUUG------------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------------------------CTCAGTTGCTGAGGAGTCCCCA----	22	1
rat	ggatcacccaccccagcccagtgagaatctgagagcaagagagaggccCTCAGTTGCTGAGGAGTCCCCAtccc
	**************************************************************************
rat	((((.....((((((((...........(((((.((.........)).)))))..)))).)).))....)))).	0.650 -17.12

rat

chromosome:10:72029887:72029960:-1

intergenic

block73212 [novel_Multihit_shortStem_nonpairedHIGH_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	0.493	no	no	0.60/0.60	20/20/1.00	0.0	0.0	1	0	1	0	2	14	3arm	106	nd	0.35	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------CAUCCUG--------------	1	novel
		len	cloning frequencies
			T4S1
	----------------------------------------------------------GCATCCTGCACCACCAACTG--	20	1
rat	gtttgtgatgtgtgtgaaccatgagaaatatgacaactccctcaagattgtcagcaatGCATCCTGCACCACCAACTGct
	********************************************************************************
rat	((..((...(((.(((....(((.......((((((((......)).))))))......)))....))))))..)).)).	0.910 -14.62

rat

chromosome:10:45104224:45104303:1

intergenic

block79011 [novel_Multihit_shortStem_nonpairedHIGH_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	0.075	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	2	26	3arm	35	nd	0.32	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------ACCUUCC----------------	1	novel
		len	cloning frequencies
			T2S1
	-------------------------------------------------------------------------AACCTTCCTGCAAAGGCCATTG--	22	1
rat	ccagagtggtctggggaaaagtaactgggacccacagaaacagtgatgcggtttttgtgccaaattccaaagcAACCTTCCTGCAAAGGCCATTGga
	*************************************************************************************************
	-----------------------------------------------------------------------------------------------------------	ENSRNOT00000032926 ENSRNOG00000026647 Cxcl16
rat	(((..(((((((.(((((.......(((((..(((((((((.((...)).))))))))).....)))))........)))))....)))))))))).	0.950 -27.86

rat

chromosome:10:57299101:57299197:1

Opposite_strand|Intronic_coding|ENSRNOT00000032926|ENSRNOG00000026647 ## ENSRNOG00000026647|protein_coding|Cxcl16|similar to chemokine (C-X-C motif) ligand 16 (Cxcl16), mRNA [Source:RefSeq_dna;Acc:NM_001017478]

block103957 [novel_Multihit_shortStem_nonpairedHIGH_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	0.434	no	no	0.55/0.55	20/20/1.00	0.0	0.0	1	0	1	0	2	14	5arm	27	nd	0.40	4	1	1	na	na

		reads	miRBase family seed
seed	---GGUACAG----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	--TGGTACAGTCTGGGGGTTGT----------------------------------------------------------------	20	1
rat	ccTGGTACAGTCTGGGGGTTGTaaattggcatggaaattaaagcaggttcttgttggtgcacagcacaaattagttatatatgggg
	**************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000005035 ENSRNOG00000003673 Pcnt1
	------------------------------------------------------------------------------------------------	ENSRNOT00000005347 ENSRNOG00000003990 Grb2
	------------------------------------------------------------------------------------------------	ENSRNOT00000043473 ENSRNOG00000003990 Grb2
rat	(((.(((....((((..(((((..((..(((.((((...........)))))))..))..))))).....)))).....))).)))	0.830 -17.50

rat

chromosome:10:105806142:105806227:1

Opposite_strand|Intronic_coding|ENSRNOT00000043473|ENSRNOG00000003990 ## Same_strand|Intronic_non-coding|ENSRNOT00000005035|ENSRNOG00000003673 ## ENSRNOG00000003990|protein_coding|Grb2|Growth factor receptor-bound protein 2 (Adapter protein GRB2) (SH2/SH3 adapter GRB2) (Protein Ash). [Source:UniProtKB/Swiss-Prot;Acc:P62994] ## ENSRNOG00000003673|protein_coding|Pcnt1|pericentrin 1 [Source:RefSeq_peptide;Acc:NP_001020572]

block119861 [novel_Multihit_shortStem_nonpairedHIGH_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	0.531	no	no	0.50/0.52	20/21/1.00	0.0	0.0	6	0	1	0	4	7	5arm	44	nd	0.38	4	7	1	na	na

		reads	miRBase family seed
seed	-----GCCUUCA--------------------------------------------------------	7	novel
		len	cloning frequencies
			T5S1
	----TGCCTTCACACAGGTGAACTC-------------------------------------------	21	6
	----TGCCTTCACACAGGTGAACT--------------------------------------------	20	1
rat	ctgtTGCCTTCACACAGGTGAACTCggaagacaagggtgctctggctaagctggtggaagctattagg
	********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000033486 ENSRNOG00000028248 LOC498065
rat	(((..((.(((((...(((....(((((..((....))..)))))....))).))))).))...))).	0.790 -16.40

rat

chromosome:11:36471806:36471873:-1

Same_strand|Intronic_coding|ENSRNOT00000033486|ENSRNOG00000028248 ## ENSRNOG00000028248|protein_coding|LOC498065|

block137082 [novel_Multihit_shortStem_nonpairedHIGH_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	0.329	no	no	0.75/0.75	20/20/1.00	0.0	0.0	1	0	1	0	0	3	3arm	13	nd	0.37	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------CCGGCAG------------	1	novel
		len	cloning frequencies
			T3S1
	-----------------------------------------------CCCGGCAGAATGGCTCCCGC	20	1
rat	gcgactttccatcccacaatccctcgcgcccttccttccaacttgggCCCGGCAGAATGGCTCCCGC
	*******************************************************************
rat	(((.....((((.......((..(((.((((.............)))).)))..))))))....)))	0.950 -13.23

rat

chromosome:11:80307889:80307955:-1

intergenic

block139233 [novel_Multihit_shortStem_nonpairedHIGH_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	0.063	no	no	0.52/0.52	21/21/1.00	0.0	0.0	1	0	1	0	1	37	5arm	44	nd	0.48	5	1	1	na	na

		reads	miRBase family seed
seed	--CUCUGCU-------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-CCTCTGCTTCTTCTCCTGCTT------------------------------------------------------------------------------------	21	1
rat	gCCTCTGCTTCTTCTCCTGCTTtgtctctggcctgtatttgtgggcaagcttaagcagctgagtcgctgtttgcctgtgcagggcctgggggaactggttaatggc
	**********************************************************************************************************
rat	(((...(((..(((((((...........(((((((((....((((((......(((((......)))))))))))))))))).)).)))))))..)))....)))	0.710 -37.50

rat

chromosome:11:82935677:82935782:-1

intergenic

block217592 [novel_Multihit_shortStem_nonpairedHIGH_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	0.016	no	no	0.62/0.62	21/21/1.00	0.0	0.0	1	0	1	0	1	27	3arm	16	nd	0.43	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CUGCUGA--------------	1	novel
		len	cloning frequencies
			T3S1
	------------------------------------------------------------------------ACTGCTGAGTGCCCCAGTGTC-	21	1
rat	ggtcctgctcaactcagtcctccacttgagaatatctgagcatctgtttttatttatcctgattctctcgggACTGCTGAGTGCCCCAGTGTCc
	**********************************************************************************************
rat	((..(((....(((((((..(((....((((((....((((....))))............))))))...)))..)))))))....)))..)).	0.960 -24.99

rat

chromosome:12:17981665:17981758:1

intergenic

block218764 [novel_Multihit_shortStem_nonpairedHIGH_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	0.054	no	no	0.62/0.62	21/21/1.00	0.0	0.0	1	0	1	0	1	27	3arm	16	nd	0.43	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------CUGCUGA--------------	1	novel
		len	cloning frequencies
			T3S1
	------------------------------------------------------------------------ACTGCTGAGTGCCCCAGTGTC-	21	1
rat	ggtcctgctcaattcagtcttccccttgagaatgtctgagcatgtgtttttatttaccctgattctctcgggACTGCTGAGTGCCCCAGTGTCc
	**********************************************************************************************
rat	((..(((....(((((((..((((...((((((((..((((....))))..))........))))))..))))..)))))))....)))..)).	0.880 -25.00

rat

chromosome:12:20157036:20157129:1

intergenic

Back to summary page

other hairpins:

Jump 10 pages back

Page 29796

Jump 10 pages forward

©2008 InteRNA Genomics B.V.