Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_cloningOK_nonpairedHIGH (528 loci)

block1767237 [novel_lenNOK_cloningOK_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	0.247	no	no	0.47/0.47	19/19/0.00	0.0	0.0	7	0	4	0	6	6	5arm	1	nd	0.32	3	11	4	na	na

		reads	miRBase family seed
seed	-------GGCUGGC-------------------------------------------------	11	novel
		len	cloning frequencies
			T1S1	T1S2	T4S1	T5S1
	------TGGCTGGCTTTCAAGGAAT--------------------------------------	19	1	2	1	7
rat	agcccaTGGCTGGCTTTCAAGGAATatttggtctacttaatgattaagatagtggctgagggt
	***************************************************************
rat	.((((.(((((.(((.((...((.((((.((....)).)))).))..)).)))))))).))))	0.430 -13.90

rat

chromosome:5:114564312:114564374:-1

intergenic

block1889603 [novel_lenNOK_cloningOK_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	0.209	no	no	0.36/0.46	19/24/0.60	0.0 0.9	0.0 0.8	1 9	0 0	1 4	0 0	19 26	14 0	5arm 5arm	1 1	nd nd	0.55 0.40	10 3	10	5	na	na

		reads	miRBase family seed
seed	------------------------------CCUUGAC-----------------------------------------------------------------------	5	novel
seed	----------------------------UUCCUUG-------------------------------------------------------------------------	2	novel
seed	--------------------CACUUCA---------------------------------------------------------------------------------	1	novel
seed	-------------------------------CUUGACU----------------------------------------------------------------------	1	novel
seed	---------------------------GUUCCUU--------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T3S1	T4S1	T4S2	T5S1
	-----------------------------TCCTTGACTCTTACTTACT------------------------------------------------------------	19	1	-	-	-	3
	---------------------------GTTCCTTGACTCTTACTTACT------------------------------------------------------------	21	-	-	-	-	2
	-------------------TCACTTCAGTTCCTTGACTC---------------------------------------------------------------------	20	-	-	-	1	-
	--------------------------AGTTCCTTGACTCTTACTTACT------------------------------------------------------------	22	-	1	-	-	-
	-----------------------------TCCTTGACTCTTACTTACTAGCCC-------------------------------------------------------	24	-	-	-	-	1
	------------------------------CCTTGACTCTTACTTACTAG----------------------------------------------------------	20	-	-	1	-	-
rat	gtccaaagcttagaggcctTCACTTCAGTTCCTTGACTCTTACTTACTAGCCCaagtaacgggctcatacgaggtcatttccaacctgtgggccctgcgttgttagct
	************************************************************************************************************
rat	((....(((.(((.((((..(((..........((((.(((...((..(((((.......)))))..)).)))))))..........)))))))))).)))....)).	0.640 -26.95

rat

chromosome:5:154401191:154401298:1

intergenic

block1943367 [novel_lenNOK_cloningOK_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	0.405	no	no	0.61/0.65	18/20/0.04	0.0	0.2	22	0	3	0	14	15	5arm	1	nd	0.32	2	25	3	na	na

		reads	miRBase family seed
seed	---------------GGAAUGG-------------------------------------------------------------------------------------------	25	novel
		len	cloning frequencies
			T2S1	T4S1	T4S2
	--------------TGGAATGGCCCTGGGTTG---------------------------------------------------------------------------------	18	1	9	8
	--------------TGGAATGGCCCTGGGTTGG--------------------------------------------------------------------------------	19	-	1	5
	--------------TGGAATGGCCCTGGGTTGGG-------------------------------------------------------------------------------	20	-	-	1
rat	gggctgggggcgggTGGAATGGCCCTGGGTTGGgggtggagcaggtggaatggccctatcactgggaatacaccctccttctggaatattctgtccttggtggttccttgctt
	*****************************************************************************************************************
rat	.(((.(((((((((..(((((..((.(((..(((((((.....(((((..........))))).......)))))))..)))))..)))))..)))......)))))).))).	0.430 -39.60

rat

chromosome:6:72592995:72593107:-1

intergenic ## {Repeats: trf 24 44 0 class=trf}

novel_shortStem_randfoldOK (487 loci)

block4231 [novel_shortStem_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	0.58/0.58	24/24/1.00	0.0	0.0	2	0	1	0	4	10	3arm	1	nd	0.21	3	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------GCCUCCA--------------------	2	novel
		len	cloning frequencies
			T3S1
	-------------------------------------------------------------TGCCTCCAGGTCTCCCAACTCTCT----	24	2
rat	ggaagagaagtgacattttgaaatggtagatgagggaaaaaaagagatgagtctcttggtcTGCCTCCAGGTCTCCCAACTCTCTtcca
	*****************************************************************************************
rat	(((((((.(((............(((.((((((((......((((((....))))))......))))...)))).))))))))))))).	0.460 -28.60

rat

chromosome:10:9444210:9444298:-1

intergenic

block7265 [novel_shortStem_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	0.59/0.59	22/22/1.00	0.0	0.0	1	0	1	0	2	5	3arm	1	nd	0.18	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------CCUCCUG----------------	1	novel
		len	cloning frequencies
			T4S1
	--------------------------------------------TCCTCCTGTTCCTGCCTCTGTC--	22	1
rat	gggcacttaaggtagggaaattctgaggaccagttttctattctTCCTCCTGTTCCTGCCTCTGTCtc
	********************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000026139 ENSRNOG00000019174 NP_001099243.1
rat	(((((....(((((((((......(((((..(((.....)))..)))))...))))))))).))))).	1.000 -21.60

rat

chromosome:10:14995613:14995680:-1

Same_strand|Intronic_coding|ENSRNOT00000026139|ENSRNOG00000019174 ## ENSRNOG00000019174|protein_coding|NP_001099243.1|CTF18, chromosome transmission fidelity factor 18 homolog [Source:RefSeq_peptide;Acc:NP_001099243]

block7641 [novel_shortStem_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	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	3	30	3arm	1	nd	0.25	3	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------------------------GAAGCAC---------------	1	novel
		len	cloning frequencies
			T5S2
	------------------------------------------------------------------------------------------AGAAGCACTCCTGTGATCAG---	20	1
rat	gcctagtcatgtggtctttgacagtcagccctcagtggctcctgggttacctctgaacctggggattttaggagcctttcggggggaactAGAAGCACTCCTGTGATCAGgta
	*****************************************************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000038962 ENSRNOG00000028241 ITFG3_RAT
rat	((((.(((((..(((((((...(((...(((((...((((((((((...((((.......))))..)))))))))).....))))).))).)))).)))...))))).)))).	0.990 -44.20

rat

chromosome:10:15487119:15487231:-1

Same_strand|Intronic_coding|ENSRNOT00000038962|ENSRNOG00000028241 ## ENSRNOG00000028241|protein_coding|ITFG3_RAT|Protein ITFG3. [Source:UniProtKB/Swiss-Prot;Acc:Q5M7W6]

block9582 [novel_shortStem_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	0.40/0.40	20/20/1.00	0.0	0.0	1	0	1	0	3	11	5arm	1	nd	0.20	2	1	1	na	na

		reads	miRBase family seed
seed	----ACCAUCU----------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	---AACCATCTCCTTAAGTGACA----------------------------------------------------	20	1
rat	gcaAACCATCTCCTTAAGTGACAacctctgactacttacttggtgaggtttgtccctgaggaggaagtcctgtgc
	***************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000009524 ENSRNOG00000006932 Q3MIE5_RAT
rat	(((.((..(((((((.((.(((((((((..((((......)))))))))).))).)))))))))..))....)))	1.000 -24.30

rat

chromosome:10:19370489:19370563:-1

Same_strand|Intronic_coding|ENSRNOT00000009524|ENSRNOG00000006932 ## Same_strand|Boundary_non-coding|ENSRNOT00000059810|ENSRNOG00000006932 ## ENSRNOG00000006932|protein_coding|Q3MIE5_RAT|Dock2 protein. [Source:UniProtKB/TrEMBL;Acc:Q3MIE5]

block26100 [novel_shortStem_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	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	4	15	5arm	1	nd	0.30	2	1	1	na	na

		reads	miRBase family seed
seed	-----UGAUGAG----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S1
	----CTGATGAGAGCTAAGGGTGT----------------------------------------------------------	20	1
rat	gaggCTGATGAGAGCTAAGGGTGTtggaggctagtgtctgcaaaggcaaaaagactctacaagctcgtagctcccatgacct
	**********************************************************************************
rat	.(((...(((.((((((.((((..(((((.((..(((((....)))))...)).)))))...)))).)))))).)))..)))	1.000 -29.60

rat

chromosome:10:57746384:57746465:-1

intergenic

block26478 [novel_shortStem_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	0.70/0.70	20/20/1.00	0.0	0.0	1	0	1	0	1	6	3arm	1	nd	0.20	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------GGGGUGG-------------	1	novel
		len	cloning frequencies
			T2S1
	------------------------------------------------TGGGGTGGGGGGTGGGAGTT-	20	1
rat	ggcccctgcccccactccaactttcaatgagagaaaaagacagagggaTGGGGTGGGGGGTGGGAGTTg
	*********************************************************************
	-------------------------------------------------------------------------------	ENSRNOT00000010358 ENSRNOG00000007869 RGD1308212
rat	((((((..(((((((((((.(((((.................))))).)))))))))))..))).))).	1.000 -33.53

rat

chromosome:10:58635680:58635748:-1

Opposite_strand|Intronic_coding|ENSRNOT00000010358|ENSRNOG00000007869 ## ENSRNOG00000007869|protein_coding|RGD1308212|WSC domain-containing protein 1. [Source:UniProtKB/Swiss-Prot;Acc:Q505J3]

block27672 [novel_shortStem_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	0.70/0.70	20/20/1.00	0.0	0.0	1	0	1	0	0	4	5arm	1	nd	0.15	2	1	1	na	na

		reads	miRBase family seed
seed	-GGGGUGG---------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	TGGGGTGGGGGTGGACTTGG---------------------------------------	20	1
rat	TGGGGTGGGGGTGGACTTGGatgcaaatgttttgggtagcactcttgttatgccaccct
	***********************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000042954 ENSRNOG00000002652 NP_001100489.1
rat	.((((((((((((.(((..((.((....))))..)))..)))))........)))))))	1.000 -21.60

rat

chromosome:10:61756369:61756427:-1

Same_strand|Intronic_coding|ENSRNOT00000042954|ENSRNOG00000002652 ## ENSRNOG00000002652|protein_coding|NP_001100489.1|GTPase activating RANGAP domain-like 4 [Source:RefSeq_peptide;Acc:NP_001100489]

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