Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_mirtron (289 loci)

block978856 [novel_lenNOK_mirtron]

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	0.221	no	no	0.63/0.68	19/19/0.00	1.0	1.0	2	0	1	0	27	2	3arm	1	1	0.16	2	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------CCGCAAU----------------------------------------	1	novel
seed	-------------------------------------------------------------GCAAUGU--------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------TCCGCAATGTCCGAGCTGC-----------------------------	19	1
	------------------------------------------------------------CGCAATGTCCGAGCTGCCC---------------------------	19	1
rat	cgcacagcttcacactgccgccggagccggttcctaagtgcatctgaggactcaacggTCCGCAATGTCCGAGCTGCCCggagaaagcaggatcccggacctgtgc
	**********************************************************************************************************
	............................................>>>>>>>>>>>>>>>>>>>>>+>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000057109 ENSRNOG00000037644 RGD1560818_predicted
rat	.((((((.(((...((((..((((.((.(((((......((((.((.(((((....))))).))))))..))))))))))).....))))......))).))))))	0.960 -37.70

rat

chromosome:1:83357050:83357155:1

Same_strand|Boundary_non-coding|ENSRNOT00000057109|ENSRNOG00000037644 ## ENSRNOG00000037644|pseudogene|RGD1560818_predicted|

block7696 [novel_lenNOK_mirtron]

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	0.358	no	no	0.61/0.63	18/19/0.00	0.5	0.0	2	0	2	0	22	1	5arm	3	0	0.21	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------GGCUUGC------------------------------------------------------------------------------------	1	novel
seed	------------------------GCUUGCC-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T3S1
	----------------------GGGCTTGCCTTCTGACCAG-------------------------------------------------------------------------	19	1	-
	-----------------------GGCTTGCCTTCTGACCAG-------------------------------------------------------------------------	18	-	1
rat	gtaccgttaagtcgcctctactGGGCTTGCCTTCTGACCAGgtccttcttccctctcttgtccctgtacctcttggtctttgaataaagcctgagtaggaagcagtctgtgtgc
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>................	ENSRNOT00000048977 ENSRNOG00000031686 LOC360504
rat	((((.....((..((.((((((((((((...(((.(((((((.............................)))))))...)))..)))))).))))))..))...))..))))	0.950 -27.35

rat

chromosome:10:15554898:15555011:-1

Same_strand|Intronic_non-coding|ENSRNOT00000048977|ENSRNOG00000031686 ## ENSRNOG00000031686|protein_coding|LOC360504|hemoglobin alpha 2 chain [Source:RefSeq_peptide;Acc:NP_001007723]

block424256 [novel_lenNOK_mirtron]

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	0.292	no	no	0.53/0.53	19/19/0.00	0.0	0.0	1	0	1	0	22	12	3arm	1	1	0.26	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------AGUGAGU---------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-------------------------------------------------------------------------GAGTGAGTGGGGTTTCTAC----------------------	19	1
rat	ggaccttgcggaaggaacggactgagtgacccacagttctcctgggtccggaaggcgacctcgcctgggaactGAGTGAGTGGGGTTTCTACgctaagatggtcgcgagtgcca
	******************************************************************************************************************
	..................................................................>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000005834 ENSRNOG00000004161 Mtif2
rat	((..(((((((.......((....((.(((((.((...(((((.(((((...(((((....))))).))).)).)).)))))))))).))...)).......)))))))..)).	0.870 -42.04

rat

chromosome:14:110538850:110538963:1

Same_strand|Boundary_non-coding|ENSRNOT00000056759|ENSRNOG00000004161 ## ENSRNOG00000004161|protein_coding|Mtif2|mitochondrial translational initiation factor 2 [Source:RefSeq_peptide;Acc:NP_001004254]

block440482 [novel_lenNOK_mirtron]

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	0.082	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	16	12	5arm	2	2	0.26	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------UCCCGUU------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	----------------ATCCCGTTTATCTGCTCCT-------------------------------------------------------------------------------	19	1
rat	ctcaccccaattttccATCCCGTTTATCTGCTCCTaggaggaacaggccaacaccaacctgtccaagttccgcaaggtgcagcacgagctggatgaggcagaggagagggcgga
	******************************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000023302 ENSRNOG00000025757 Myh6
rat	.((..(((..((((((((((.((((..((((.(((.(((((.(((((..........)))))))....)))...))).))))...)))).))))).....)))))..)))..))	0.750 -37.90

rat

chromosome:15:33045004:33045117:-1

Same_strand|Intronic_coding|ENSRNOT00000023302|ENSRNOG00000025757 ## ENSRNOG00000025757|protein_coding|Myh6|Myosin-6 (Myosin heavy chain 6) (Myosin heavy chain, cardiac muscle alpha isoform) (MyHC-alpha). [Source:UniProtKB/Swiss-Prot;Acc:P02563]

block443431 [novel_lenNOK_mirtron]

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	0.360	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	7	8	3arm	2	3	0.26	2	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------AGUUCUA------------------	1	novel
		len	cloning frequencies
			T3S1
	---------------------------------------------------GAGTTCTAGGGTGTGGACC-------	19	1
rat	ccagccatggcccaagaggaacctgggggctccaactcagtcctgaatggtGAGTTCTAGGGTGTGGACCagcagga
	*****************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++	ENSRNOT00000059475 ENSRNOG00000038908
rat	((.((..(((.(((......((((.((..(((....(((....))).....)))..)).)))).))).))))).)).	0.780 -23.40

rat

chromosome:15:38391752:38391828:-1

Same_strand|Intronic_coding|ENSRNOT00000059475|ENSRNOG00000038908 ## ENSRNOG00000038908|protein_coding||

block546613 [novel_lenNOK_mirtron]

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	0.062	no	no	0.58/0.58	19/19/0.00	0.0	0.0	1	0	1	0	19	15	3arm	1	3	0.26	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------CUUCCCC------------------------------	1	novel
		len	cloning frequencies
			T5S2
	-------------------------------------------------------------------TCTTCCCCCGTTTCCTCCT-------------------	19	1
rat	ggcgctcgcacttcacaagctgctggggggttgggggaaaggttctttcgccgaagtagcctgtcaaTCTTCCCCCGTTTCCTCCTcagggcgaccgagctgctc
	*********************************************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000020900 ENSRNOG00000015568 LOC683534
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000058498 ENSRNOG00000015568 LOC683534
rat	((((((((..........(((.((((((((.(((((((((((((((((....)))).))))).......))))))))...))))).))))))...))))).))).	0.950 -42.63

rat

chromosome:16:70728321:70728425:-1

Same_strand|Intronic_coding|ENSRNOT00000020900|ENSRNOG00000015568 ## ENSRNOG00000015568|protein_coding|LOC683534|similar to phosphatidic acid phosphatase type 2 domain containing 1A (LOC680466), mRNA [Source:RefSeq_dna;Acc:NM_001109411]

block751859 [novel_lenNOK_mirtron]

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	0.225	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	10	4	5arm	1	0	0.11	1	1	1	na	na

		reads	miRBase family seed
seed	-----------AUCAAUU------------------------------------------------------------	1	novel
		len	cloning frequencies
			T4S1
	----------GATCAATTTCCTTCCCAG--------------------------------------------------	18	1
rat	gtttacatctGATCAATTTCCTTCCCAGttgctgatgtgcggccttggtgatgtggacgtgaatgattggagacagca
	******************************************************************************
	+++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000023890 ENSRNOG00000017610 Q5U1Z5_RAT
rat	(((....((..((((((.(((.((((((((((......)))))..))).))...))).))...))))..))...))).	0.800 -20.90

rat

chromosome:18:61471679:61471756:1

Same_strand|Intronic_coding|ENSRNOT00000023890|ENSRNOG00000017610 ## ENSRNOG00000017610|protein_coding|Q5U1Z5_RAT|Nedd4l protein. [Source:UniProtKB/TrEMBL;Acc:Q5U1Z5]

block903359 [novel_lenNOK_mirtron]

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	0.130	no	no	0.58/0.60	19/20/0.50	0.2	0.2	4	0	2	0	22	5	3arm	1	0	0.25	3	4	2	na	na

		reads	miRBase family seed
seed	----------------------------------------------------------------CCCUCUU----------------------------------	3	novel
seed	---------------------------------------------------------------UCCCUCU-----------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2
	---------------------------------------------------------------TCCCTCTTCCTTCCCACAG-----------------------	19	2	-
	--------------------------------------------------------------GTCCCTCTTCCTTCCCACAG-----------------------	20	-	1
	---------------------------------------------------------------TCCCTCTTCCTTCCCACAGC----------------------	20	1	-
rat	ggtgagcaggccgtggtcctgatgtggggcaagggcttgctggggcgtttgaccgaccacacGTCCCTCTTCCTTCCCACAGCggtctaggttacattgctggct
	*********************************************************************************************************
	>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000024185 ENSRNOG00000017621 RGD1305613
rat	(((.((((((((.(((.((...(((((((..((((......(((((((.((......)).)))))))...)))))))))))..)).))))))....))))).)))	0.880 -42.80

rat

chromosome:1:185459439:185459543:-1

Same_strand|Boundary_coding|ENSRNOT00000024185|ENSRNOG00000017621 ## ENSRNOG00000017621|protein_coding|RGD1305613|Similar to spinster-like protein. [Source:UniProtKB/TrEMBL;Acc:Q2YDU8]

block1788354 [novel_lenNOK_mirtron]

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	0.283	no	no	0.53/0.53	19/19/0.00	0.0	0.0	3	0	1	0	22	16	5arm	1	1	0.26	3	3	1	na	na

		reads	miRBase family seed
seed	-----------------------UGAGUGU------------------------------------------------------------------------------------------	3	novel
		len	cloning frequencies
			T1S1
	----------------------GTGAGTGTGTGGGGAATCA-------------------------------------------------------------------------------	19	3
rat	tcctgttaggagcggacgcggaGTGAGTGTGTGGGGAATCAggcgggtggttgttacaatttggaagttacgagtcaggcctgagcctaccattttcagctaccagctttggcagcgggg
	************************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000017156 ENSRNOG00000012266 NP_001102737.1
rat	.((((((.(((((((..((.((..(((((.(((((...((((((...(((((((.((.........)).)))).))).)))))).)))))))))))).))..)).)))))...)))))).	0.620 -39.80

rat

chromosome:5:149388204:149388323:-1

Same_strand|Boundary_non-coding|ENSRNOT00000017156|ENSRNOG00000012266 ## ENSRNOG00000012266|protein_coding|NP_001102737.1|similar to PS1D protein (predicted) (RGD1565267_predicted), mRNA [Source:RefSeq_dna;Acc:NM_001109267]

novel_Multihit_shortStem (282 loci)

block14742 [novel_Multihit_shortStem]

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	0.426	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	1	16	3arm	17	nd	0.25	2	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------UGAAGAU-------------	1	novel
		len	cloning frequencies
			T3S2
	-------------------------------------------------------------------------------GTGAAGATGGTTCGCTACTC-	20	1
rat	ggattgggtactactgtctatactacagattaagaaagaaggtctcgttcctcttcctgtaagcggccagaggtgacctGTGAAGATGGTTCGCTACTCc
	****************************************************************************************************
rat	(((...(((...(((((((.(((................(((((.....(((((..(((....)))..))))).)))))))).)))))))..)))..)))	0.500 -25.69

rat

chromosome:10:34020857:34020956:-1

intergenic

Back to summary page

other hairpins:

Jump 10 pages back

Page 29190

Jump 10 pages forward

©2008 InteRNA Genomics B.V.