Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_shortStem_bulgeHIGH (2306 loci)

block1538353 [novel_lenNOK_shortStem_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	0.024	no	no	0.58/0.61	18/19/0.00	0.0	0.2	9	0	4	0	3	34	5arm	2	nd	0.26	4	9	4	na	na

		reads	miRBase family seed
seed	----AGCAGCA---------------------------------------------------------------------------------------------------------	9	miR-15b/16/195/322/497
		len	cloning frequencies
			T1S2	T4S1	T4S2	T5S1
	---CAGCAGCACAGACACTGC-----------------------------------------------------------------------------------------------	18	2	1	3	1
	---CAGCAGCACAGACACTGCA----------------------------------------------------------------------------------------------	19	-	-	2	-
rat	gagCAGCAGCACAGACACTGCAgtcctcagccctgctctagcggtaagacaatagcagagcttatgcatacgctggatgacgtcagggacactgcacagactgactgcgctgcttg
	********************************************************************************************************************
	------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000060641 ENSRNOG00000007474 ST7
	------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000010219 ENSRNOG00000007474 ST7
	------------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000042575 ENSRNOG00000007474 ST7
rat	(((((((.((((((....((((((......(((((.(((((((..........(((...)))........)))))))......)))))..))))))....)))..)))))))))).	0.760 -40.17

rat

chromosome:4:43408563:43408678:-1

Opposite_strand|Intronic_coding|ENSRNOT00000010219|ENSRNOG00000007474 ## ENSRNOG00000007474|protein_coding|ST7|suppression of tumorigenicity 7 isoform a [Source:RefSeq_peptide;Acc:NP_001004102]

block1662819 [novel_lenNOK_shortStem_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	0.019	no	no	0.48/0.53	19/23/0.33	1.0	0.3	3	0	1	0	1	30	5arm	2	nd	0.30	4	3	1	na	na

		reads	miRBase family seed
seed	-----GCAGCUA------------------------------------------------------------------------------------------	2	novel
seed	--GAAGCAG---------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	----AGCAGCTACAAAACCGAGG-------------------------------------------------------------------------------	19	2
	-TGAAGCAGCTACAAAACCGAGGA------------------------------------------------------------------------------	23	1
rat	cTGAAGCAGCTACAAAACCGAGGAacagtcatagctgcaaaaaccatcataagtagaggacttttttggtttttgttttgttttttggtgttagaaatttta
	******************************************************************************************************
rat	.(((((...(((....((((((((((((........((((((((((....((((.....))))...)))))))))).))))))))))))..)))...)))))	0.920 -26.20

rat

chromosome:4:102406797:102406898:1

intergenic

block1695823 [novel_lenNOK_shortStem_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	0.915	no	no	0.48/0.50	25/26/0.00	1.0	1.3	3	0	1	0	4	10	5arm	1	nd	0.23	4	3	1	na	na

		reads	miRBase family seed
seed	--------UCACCGU-------------------------------------------------------------------------------------	2	novel
seed	-----CCUUCAC----------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S1
	-------TTCACCGTTCAGGAAATCTCAGCTCC-------------------------------------------------------------------	26	2
	----TCCTTCACCGTTCAGGAAATCTCAG-----------------------------------------------------------------------	25	1
rat	ttctTCCTTCACCGTTCAGGAAATCTCAGCTCCttcagtattgaaacgacacttaggtaggacaaaaggcttcagggagggactggcagtgtgagcaaga
	****************************************************************************************************
rat	.((((.((((((.((.(((....(((((((((((..(((.(((...))).))).)))..........))))...))))....))))).))).))).))))	0.600 -18.90

rat

chromosome:4:164248015:164248114:1

intergenic

block1697139 [novel_lenNOK_shortStem_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	0.436	no	no	0.54/0.54	26/26/0.00	0.0	0.0	1	0	1	0	4	14	3arm	1	nd	0.27	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------GGGUUGU----------------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------------------------------------------TGGGTTGTTTCAGTAGGGGTTCAGGG----	26	1
rat	agactttcaaatgtccaaggaaaaagcaaccgtatgcctggctccgggtgggtactctTGGGTTGTTTCAGTAGGGGTTCAGGGtcta
	****************************************************************************************
rat	(((((((.((...(((...(((...(((((((((((((((....)))))..)))).....)))))))))....))).)).))))))).	0.890 -23.30

rat

chromosome:4:164708119:164708206:1

intergenic

block1700748 [novel_lenNOK_shortStem_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	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	4	9	5arm	1	nd	0.22	4	1	1	na	na

		reads	miRBase family seed
seed	-----UAAAAUG----------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	----CTAAAATGTCTTAGCCCT------------------------------------------------------------------	18	1
rat	tggcCTAAAATGTCTTAGCCCTgtactcgaaccccttcctctgcagttcctttagctcatatggtttcctcattttaaaatgggtcac
	****************************************************************************************
rat	((((((((((((....(((((((((...(((....)))...)))))................))))....))))).....))))))).	0.630 -14.79

rat

chromosome:4:170952090:170952177:1

intergenic

block911971 [novel_lenNOK_shortStem_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	0.200	no	no	0.61/0.61	18/18/0.00	0.4	0.4	5	0	3	0	0	29	5arm	1	nd	0.22	4	5	3	na	na

		reads	miRBase family seed
seed	-CCUGUGU-------------------------------------------------------------------------------------------------------	4	novel
seed	---UGUGUGA-----------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1	T5S2
	TCCTGTGTGAGGGCTGTG---------------------------------------------------------------------------------------------	18	2	1	1
	--CTGTGTGAGGGCTGTGGT-------------------------------------------------------------------------------------------	18	1	-	-
rat	TCCTGTGTGAGGGCTGTGGTgtgtgtgatgctggcacctggcgcttgggtctgtttcaggagtgtgcagggtcagaatttgtgcagggagcctttctcctgtgctgcaggg
	***************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000039677 ENSRNOG00000020857 NP_001099790.1
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000054858 ENSRNOG00000020857 NP_001099790.1
rat	.((((((((((((....(((.((..(((..(((((.((((((((((.((......))..)))))).)))))))))...)))..))....)))....)))).))).))))).	0.590 -39.20

rat

chromosome:1:204913710:204913820:-1

Same_strand|Intronic_coding|ENSRNOT00000039677|ENSRNOG00000020857 ## ENSRNOG00000020857|protein_coding|NP_001099790.1|protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 1 [Source:RefSeq_peptide;Acc:NP_001099790]

block1788190 [novel_lenNOK_shortStem_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	0.117	no	no	0.67/0.67	18/18/0.00	0.0	0.0	1	0	1	0	0	29	3arm	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------------GUCCUGU----------	1	novel
		len	cloning frequencies
			T5S1
	-------------------------------------------------------------------------------------GGTCCTGTCCATGCTGGG	18	1
rat	gcccatttagggaaaggaattcgtgtggcctgagctgcagtgcgggccagtccttgggactaagcactggctcattagctctccgGGTCCTGTCCATGCTGGG
	*******************************************************************************************************
rat	.((((.....(((.(((.(((((...(((.(((((..((((((.....(((((...)))))..)))))))))))...)))...)))))))).)))....))))	0.770 -39.70

rat

chromosome:5:149193574:149193676:-1

intergenic

block1911791 [novel_lenNOK_shortStem_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	0.137	no	no	0.64/0.64	25/25/0.00	0.0	0.0	1	0	1	0	1	24	3arm	2	nd	0.20	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------CGGGUGG------------------	1	novel
		len	cloning frequencies
			T4S1
	--------------------------------------------------------------------------CCGGGTGGCTACCCTGACAAGTCTG-	25	1
rat	gtgggcggggcgagggggccctcatgctcgggttggcgggccttgaaattgggcctgcggaaagcagttgagatCCGGGTGGCTACCCTGACAAGTCTGc
	****************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<................................................................................	ENSRNOT00000021923 ENSRNOG00000016134 Msh6
rat	((((((....((.(((((((.....(((((((((.((((((((.......)))))))).............))))))))))))).)))))....))))))	0.410 -40.94

rat

chromosome:6:11524998:11525097:-1

intergenic

novel_shortStem_nonpairedHIGH (1938 loci)

block102 [novel_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	0.110	no	no	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	1	4	5arm	2	nd	0.33	3	1	1	na	na

		reads	miRBase family seed
seed	--GUGACCA------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2
	-TGTGACCAAGCTCTAACTTCCAGT--------------------------------------	24	1
rat	cTGTGACCAAGCTCTAACTTCCAGTttgaacacagaattaaattaggatgggggggaaacgga
	***************************************************************
rat	((((..((...(((((...((((((((((........))))))).)))))))).))..)))).	1.000 -14.70

rat

chromosome:10:199229:199291:-1

intergenic

block1676 [novel_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	0.024	no	no	0.62/0.62	24/24/1.00	0.0	0.0	1	0	1	0	4	7	5arm	2	nd	0.38	3	1	1	na	na

		reads	miRBase family seed
seed	-----AGCCACU-----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S2
	----GAGCCACTGCAGCCATTAGCACCC-------------------------------------------------------	24	1
rat	gtaaGAGCCACTGCAGCCATTAGCACCCcccttgcacacacacaattacaggtaagggcactgatgtgtctgcctgtgtctta
	***********************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000003150 ENSRNOG00000002294 LOC687335
rat	....(((.(((.((((.(((...((...(((((((................)))))))...))..))).))))..))).))).	0.750 -22.89

rat

chromosome:10:3770254:3770336:-1

Same_strand|Intronic_coding|ENSRNOT00000003150|ENSRNOG00000002294 ## ENSRNOG00000002294|protein_coding|LOC687335|similar to kinesin-like motor protein C20orf23 (LOC689142), mRNA [Source:RefSeq_dna;Acc:NM_001109526]

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