Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_cloningOK_multiarm_loopOverlap (10 loci)

novel_lenNOK_5varHIGH_loopOverlap_randfoldOK (10 loci)

block158306 [novel_lenNOK_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	0.52/0.63	19/23/0.40	2.0	3.6	5	0	3	0	14	-5	3arm_loop	6	nd	0.09	2	5	3	na	na

		reads	miRBase family seed
seed	---------------------------------------------GCCCGCA---------------------------------	2	novel
seed	-------------------------------------------------GCAGGCU-----------------------------	2	novel
seed	-----------------------------------------------CCGCAGG-------------------------------	1	novel
		len	cloning frequencies
			T3S1	T3S2	T4S1
	------------------------------------------------CGCAGGCTTCTGAATAGGTTTGG--------------	23	2	-	-
	--------------------------------------------GGCCCGCAGGCTTCTGAAT----------------------	19	-	-	2
	----------------------------------------------CCCGCAGGCTTCTGAATAG--------------------	19	-	1	-
rat	ggtctgacaaactatgctgcagcctattgcactggcctgctgctGGCCCGCAGGCTTCTGAATAGGTTTGGcatggacaagatct
	*************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000039254 ENSRNOG00000027772 RGD1310935_predicted
rat	(((((......((((((((.((((((((.((..(((((((.........)))))))..))))))))))))))))))...))))).	1.000 -36.40

rat

chromosome:11:44447755:44447839:1

Same_strand|Intronic_non-coding|ENSRNOT00000039254|ENSRNOG00000027772 ## ENSRNOG00000027772|protein_coding|RGD1310935_predicted|

block601332 [novel_lenNOK_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	0.010	no	no	0.38/0.55	20/26/0.67	4.0 0.0	1.0 0.0	2 1	0 0	1 1	0 0	10 5	-22 5	3arm 3arm	1 1	nd nd	0.40 0.30	3 3	3	1	na	na

		reads	miRBase family seed
seed	------------------------------------UGUCACU-----------------	1	novel
seed	-------------------------------UCAAAUG----------------------	1	novel
seed	-----------------------GAAGUCA------------------------------	1	novel
		len	cloning frequencies
			T5S1
	------------------------------TTCAAATGTCACTGAACCGA----------	20	1
	-----------------------------------ATGTCACTGAACCGACCCTG-----	20	1
	----------------------TGAAGTCATTCAAATGTCACTGAACC------------	26	1
rat	ctccataggctcaattaatgcaTGAAGTCATTCAAATGTCACTGAACCGACCCTGtggag
	************************************************************
rat	(((((((((.((..(((.((((((((....))))..)).)).)))...)).)))))))))	0.890 -17.50

rat

chromosome:17:17535406:17535465:-1

intergenic

block910167 [novel_lenNOK_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	0.72/0.74	18/19/0.00	1.5	1.0	2	0	2	0	12	-1	5arm_loop	1	nd	0.16	2	2	2	na	na

		reads	miRBase family seed
seed	-------------CUGGGCC--------------------------------------------------	1	novel
seed	----------------GGCCCUU-----------------------------------------------	1	novel
		len	cloning frequencies
			T3S1	T5S1
	---------------GGGCCCTTCCCGTGGATG-------------------------------------	18	-	1
	------------GCTGGGCCCTTCCCGTGGA---------------------------------------	19	1	-
rat	gctgagaccagaGCTGGGCCCTTCCCGTGGATGgggcggggtgtatgtggaagggtggggtgggggtagg
	**********************************************************************
	--------------------------------------------------------------------------------	ENSRNOT00000023219 ENSRNOG00000017109 NP_001099787.1
rat	.(((...((...(((..((((((((((((.((........)).)))).))))))))..)))..)).))).	1.000 -26.60

rat

chromosome:1:201412629:201412698:-1

Opposite_strand|Intronic_coding|ENSRNOT00000023219|ENSRNOG00000017109 ## ENSRNOG00000017109|protein_coding|NP_001099787.1|Ras association (RalGDS/AF-6) domain family 7 [Source:RefSeq_peptide;Acc:NP_001099787]

block1009426 [novel_lenNOK_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	0.52/0.61	18/23/0.40	1.4	1.4	5	0	4	0	11	-1	3arm	1	nd	0.14	3	5	4	na	na

		reads	miRBase family seed
seed	---------------------------------------------------CCGCAGA--------------------------	3	novel
seed	-------------------------------------------------AUCCGCA----------------------------	1	novel
seed	--------------------------------------------------UCCGCAG---------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T3S2	T4S1
	-------------------------------------------------ATCCGCAGACACAAAGGC-----------------	18	-	-	1	-
	------------------------------------------------TATCCGCAGACACAAAGGCCA---------------	21	-	1	-	-
	--------------------------------------------------TCCGCAGACACAAAGGCCA---------------	19	1	-	-	-
	--------------------------------------------------TCCGCAGACACAAAGGCC----------------	18	-	-	1	-
	--------------------------------------------------TCCGCAGACACAAAGGCCAGTCC-----------	23	-	-	-	1
rat	gcgccgctgaggctgggccttggagtctgcggattttccgcttgcatcTATCCGCAGACACAAAGGCCAGTCCtggcttgcgcg
	************************************************************************************
rat	((((.(((..((((.((((((...((((((((((...............))))))))))...))))))))))..)))..)))).	1.000 -44.86

rat

chromosome:1:156871018:156871101:1

intergenic

block1105757 [novel_lenNOK_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	0.006	no	no	0.36/0.37	19/22/0.50	3.0	1.5	4	0	1	0	13	-20	3arm_loop	1	nd	0.26	2	4	1	na	na

		reads	miRBase family seed
seed	-----------------------------------UUUGCAC------------------------	2	novel
seed	-----------------------------AUAGUUU------------------------------	2	novel
		len	cloning frequencies
			T4S2
	----------------------------------TTTTGCACATAGGTTGCTT-------------	19	2
	----------------------------CATAGTTTTTGCACATAGGTTG----------------	22	2
rat	agactgccttgtcctaagtcacaatgtgCATAGTTTTTGCACATAGGTTGCTTagcttaagctatc
	******************************************************************
rat	.((..((.(((..((((((.((.(((((((.......)))))))..)).))))))..)))))..))	0.990 -19.70

rat

chromosome:20:24627462:24627527:1

intergenic

block2523204 [novel_lenNOK_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	0.010	no	no	0.46/0.47	19/24/0.50	2.0	0.5	2	0	1	0	35	-1	3arm	1	11	0.08	1	2	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------CCUUUAC-----------------------------------------------	1	novel
seed	--------------------------------------------------------------AGUCCCU---------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------CAGTCCCTTTACTAATGACCCCTT-----------------------------------	24	1
	-----------------------------------------------------------------CCCTTTACTAATGACCCCT------------------------------------	19	1
rat	gggtaggtgggtagatgggtgggtggataggtgggtgggcggatggatggaggggactacaCAGTCCCTTTACTAATGACCCCTTattcctcgcagatatgtgcactacttcagcggcct
	************************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	ENSRNOT00000035277 ENSRNOG00000014182 Tns
rat	(((((((((((((.(((.(((((.(((((((.((((...((..(((...(((((((((....))))))))).))).))))))))))))))))))...))).))).)))))).....))))	0.990 -45.90

rat

chromosome:9:73306655:73306774:-1

Same_strand|Boundary_non-coding|ENSRNOT00000019092|ENSRNOG00000014182 ## Same_strand|Intronic_coding|ENSRNOT00000035277|ENSRNOG00000014182 ## ENSRNOG00000014182|protein_coding|Tns|Tensin (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q62783]

block3002688 [novel_lenNOK_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	0.003	no	no	0.37/0.42	19/19/0.00	1.5	1.5	2	0	2	0	11	-1	3arm	1	nd	0.21	3	2	2	na	na

		reads	miRBase family seed
seed	---------------------------------------------UGACCUG-------------------------	1	novel
seed	------------------------------------------------CCUGUGA----------------------	1	novel
		len	cloning frequencies
			T5S1	T5S2
	--------------------------------------------CTGACCTGTGAATTCTGTA--------------	19	1	-
	-----------------------------------------------ACCTGTGAATTCTGTACTT-----------	19	-	1
rat	cacatataaatgattatacagaagacagagttcatttcacttccCTGACCTGTGAATTCTGTACTTatcctatatgt
	*****************************************************************************
rat	.(((((((...(((.......((((((((((((((.(((......)))...))))))))))).)))))).)))))))	0.670 -18.51

rat

chromosome:X:77639670:77639746:1

intergenic

block997591 [novel_lenNOK_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	0.005	no	no	0.33/0.44	19/25/0.40	3.2	5.8	5	0	2	0	11	-22	3arm_loop	2	nd	0.12	1	5	2	na	na

		reads	miRBase family seed
seed	------------------------------------------CCAGAAA------------------------------------	3	novel
seed	--------------------------------------------------AGAGAGU----------------------------	2	novel
		len	cloning frequencies
			T1S1	T5S1
	-------------------------------------------------TAGAGAGTTTGAACAGACTTGGGAG-----------	25	-	1
	-------------------------------------------------TAGAGAGTTTGAACAGACT-----------------	19	1	-
	-----------------------------------------TCCAGAAATAGAGAGTTTGAA-----------------------	21	-	1
	-----------------------------------------TCCAGAAATAGAGAGTTTG-------------------------	19	-	1
	-----------------------------------------TCCAGAAATAGAGAGTTTGAACAG--------------------	24	-	1
rat	ggtacagatggtattctcaaggaaattctgtcagccttctcTCCAGAAATAGAGAGTTTGAACAGACTTGGGAGtcctcgtgcca
	*************************************************************************************
rat	(((((.((.((.(((((((((.....((((((((....(((((........))))).)))).)))))))))))))))))))))).	1.000 -31.70

rat

chromosome:1:128262459:128262543:1

intergenic

block770022 [novel_lenNOK_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	0.004	no	no	0.36/0.48	19/22/0.67	5.0	3.7	3	0	2	0	25	-19	3arm	1	nd	0.29	3	3	2	na	na

		reads	miRBase family seed
seed	---------------------------------GUUUUUA---------------------------------------------	1	novel
seed	------------------------------------------GUUGGUU------------------------------------	1	novel
seed	---------------------------------------ACAGUUG---------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1
	--------------------------------------TACAGTTGGTTCTGTGGCTCT--------------------------	21	-	1
	-----------------------------------------AGTTGGTTCTGTGGCTCTT-------------------------	19	-	1
	--------------------------------TGTTTTTACAGTTGGTTCTGTG-------------------------------	22	1	-
rat	tcgaatcttttgttgacttgagctattgaaccTGTTTTTACAGTTGGTTCTGTGGCTCTTttcatgagttccaataaatcttgac
	*************************************************************************************
rat	((((....((((((((((((((((((.((((((((....)))...))))).))))))).......))))..)))))))..)))).	0.940 -21.71

rat

chromosome:19:15927996:15928080:-1

intergenic

block1094155 [novel_lenNOK_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	0.005	no	no	0.55/0.62	18/21/0.67	1.3	1.8	6	0	1	0	18	-5	3arm	1	nd	0.22	3	6	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------GAGCCAA--------------------------------	2	novel
seed	------------------------------------------AGCCAAA-------------------------------	2	novel
seed	-------------------------------------GGCUGAG------------------------------------	1	novel
seed	-------------------------------------------GCCAAAG------------------------------	1	novel
		len	cloning frequencies
			T5S1
	----------------------------------------TGAGCCAAAGCAGGGAGA----------------------	18	2
	-----------------------------------------GAGCCAAAGCAGGGAGATAG-------------------	20	2
	------------------------------------------AGCCAAAGCAGGGAGATAGG------------------	20	1
	------------------------------------TGGCTGAGCCAAAGCAGGGAG-----------------------	21	1
rat	gtagatagtgtgtgactctggtgtcccctgctgctcTGGCTGAGCCAAAGCAGGGAGATAGGcccagtctggtgtctaca
	********************************************************************************
rat	(((((((.((...((((..(((((((((((((((((.....))))...))))))).)))..))).)))))).))))))).	0.990 -34.40

rat

chromosome:20:5561474:5561553:1

intergenic

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