Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_multiarm_DicerNOK_Multihit_nonpairedHIGH (43 loci)

sblock7520 [novel_lenNOK_multiarm_DicerNOK_Multihit_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	0.118	no	no	0.47/0.50	18/19/0.00	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	12 1	5 15	5arm 3arm	27 27	nd nd	0.39 0.42	3 6	2	2	11	11

		reads	miRBase family seed
seed	---------------------------------------------------------UGACUGU------------	1	novel
seed	-------------UGUCACU--------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S2
	------------ATGTCACTCCTCTTTCCC----------------------------------------------	18	1	-
	--------------------------------------------------------ATGACTGTCCTCATCAAGC-	19	-	1
rat	tgctgctcttggATGTCACTCCTCTTTCCCttggtgttgcaactgctggtggagtcATGACTGTCCTCATCAAGCa
	****************************************************************************
rat	.(((......((((((((...((((..((..((((......))))..)).))))...)))).))))......))).	0.990 -20.40

rat

chromosome:3:66408169:66408244:-1

intergenic

sblock8623 [novel_lenNOK_multiarm_DicerNOK_Multihit_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	0.339	no	no	0.48/0.50	18/21/0.50	0.0 0.0	0.0 0.0	1 1	0 0	1 1	0 0	10 0	0 10	5arm 3arm	30 30	nd nd	0.39 0.45	2 6	2	2	10	8

		reads	miRBase family seed
seed	-----------------------------------------------GUUCCUG-------------	1	novel
seed	-----------GAAGACU-------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1	T2S2
	----------GGAAGACTTTGTACCCTC---------------------------------------	18	-	1
	----------------------------------------------TGTTCCTGGTGGTCTTCTTTC	21	1	-
rat	tggacattctGGAAGACTTTGTACCCTCtccttgtcgaaggttcacTGTTCCTGGTGGTCTTCTTTC
	*******************************************************************
rat	.((((...((((..(((..((.(((.((........)).))).))..))).))))..))))......	0.570 -13.00

rat

chromosome:4:150577139:150577205:-1

intergenic

novel_lenNOK_shortStem_loopOverlap_randfoldOK_bulgeHIGH (43 loci)

block79707 [novel_lenNOK_shortStem_loopOverlap_randfoldOK_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	0.001	no	no	0.47/0.47	19/19/0.00	0.0	0.0	1	0	1	0	1	-1	3arm	1	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	------------------------------GGACUUG------------	1	novel
		len	cloning frequencies
			T2S2
	-----------------------------AGGACTTGGAGTTGACAGT-	19	1
rat	actggtagctctccaagtcccagtaagtaAGGACTTGGAGTTGACAGTa
	*************************************************
rat	((((......((((((((((..........))))))))))....)))).	1.000 -20.20

rat

chromosome:10:58717432:58717480:1

intergenic

block158831 [novel_lenNOK_shortStem_loopOverlap_randfoldOK_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	0.010	no	no	0.39/0.39	18/18/0.00	0.0	0.0	1	0	1	0	0	-2	3arm_loop	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------CAAAGUA----------	1	novel
		len	cloning frequencies
			T1S2
	------------------CCAAAGTAATAATTGGCC	18	1
rat	ggcccaaattatttttctCCAAAGTAATAATTGGCC
	************************************
	----------------------------------------------	ENSRNOT00000034940 ENSRNOG00000001613 NP_001100567.1
rat	((((...((((((((.....))))))))....))))	1.000 -8.20

rat

chromosome:11:45593935:45593970:1

Opposite_strand|Intronic_coding|ENSRNOT00000034940|ENSRNOG00000001613 ## ENSRNOG00000001613|protein_coding|NP_001100567.1|zinc finger and BTB domain containing 11 [Source:RefSeq_peptide;Acc:NP_001100567]

block162017 [novel_lenNOK_shortStem_loopOverlap_randfoldOK_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	0.002	no	no	0.32/0.32	19/19/0.00	0.0	0.0	1	0	1	0	1	-3	5arm_loop	1	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	--UCGGCUU----------------------------	1	novel
		len	cloning frequencies
			T1S1
	-TTCGGCTTCCTTTTTTTTT-----------------	19	1
rat	tTTCGGCTTCCTTTTTTTTTcaagaagggaactgaga
	*************************************
rat	((((((.((((((((((....))))))))))))))))	1.000 -13.20

rat

chromosome:11:55152769:55152805:1

intergenic ## {Repeats: dust 55152780 55152788 0 class=dust}

block168206 [novel_lenNOK_shortStem_loopOverlap_randfoldOK_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	0.001	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	2	-2	3arm_loop	2	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------GGAGGUU------------	1	novel
		len	cloning frequencies
			T1S1
	----------------------TGGAGGTTTTTTTTCCCC--	18	1
rat	agggggggtggactttgttttgTGGAGGTTTTTTTTCCCCcc
	******************************************
rat	.(((((((.(((((((........)))))))....)))))))	1.000 -17.60

rat

chromosome:11:70174176:70174217:1

intergenic ## {Repeats: dust 70174204 70174211 0 class=dust}

block183142 [novel_lenNOK_shortStem_loopOverlap_randfoldOK_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	0.004	no	no	0.56/0.56	18/18/0.00	0.0	0.0	1	0	1	0	3	-2	3arm_loop	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------ACUGGAA-------------	1	novel
		len	cloning frequencies
			T3S1
	----------------------------TACTGGAAACACACCCCC---	18	1
rat	tctggaaagggtgaccaccactccagcaTACTGGAAACACACCCCCagg
	*************************************************
rat	.((((...(((((........(((((....)))))....))))))))).	0.520 -16.60

rat

chromosome:12:12045621:12045669:-1

intergenic

block196901 [novel_lenNOK_shortStem_loopOverlap_randfoldOK_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	0.009	no	no	0.33/0.33	18/18/0.00	0.0	0.0	1	0	1	0	0	-4	5arm_loop	3	nd	0.28	5	1	1	na	na

		reads	miRBase family seed
seed	-UUUUCCC---------------------------------	1	novel
		len	cloning frequencies
			T4S1
	TTTTTCCCCCTAAAAAAC-----------------------	18	1
rat	TTTTTCCCCCTAAAAAACttcagaatttggggctggagaaa
	*****************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000040724 ENSRNOG00000001002 Q63161_RAT
rat	.(((((((((((((...........)))))))..)))))).	1.000 -11.40

rat

chromosome:12:33033470:33033510:-1

Same_strand|Boundary_non-coding|ENSRNOT00000031457|ENSRNOG00000001002 ## Same_strand|Intronic_coding|ENSRNOT00000040724|ENSRNOG00000001002 ## ENSRNOG00000001002|protein_coding|Q63161_RAT|Dynein-like protein 10 (Fragment). [Source:UniProtKB/TrEMBL;Acc:Q63161]

block201136 [novel_lenNOK_shortStem_loopOverlap_randfoldOK_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	0.004	no	no	0.72/0.72	18/18/0.00	0.0	0.0	1	0	1	0	2	-3	5arm_loop	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	---AGGCGGG--------------------------------	1	novel
		len	cloning frequencies
			T2S1
	--AAGGCGGGGGAGGGGGAA----------------------	18	1
rat	gaAAGGCGGGGGAGGGGGAAgccattacctctctgccttttg
	******************************************
rat	(((((((.(((((((((....))....)))))))))))))).	1.000 -20.20

rat

chromosome:12:40385208:40385249:-1

intergenic

block277221 [novel_lenNOK_shortStem_loopOverlap_randfoldOK_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	0.008	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	4	-2	3arm_loop	1	nd	0.28	4	1	1	na	na

		reads	miRBase family seed
seed	-------------------------GAGAGUA--------------	1	novel
		len	cloning frequencies
			T4S2
	------------------------AGAGAGTATTTCCCCTGG----	18	1
rat	aaggcttagggtctactttgtaccAGAGAGTATTTCCCCTGGgctt
	**********************************************
rat	.((((((((((..((((((.......))))))....))))))))))	1.000 -16.80

rat

chromosome:13:92806903:92806948:-1

intergenic

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