Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_lenNOK_Multihit_nonpairedHIGH (807 loci)

block2083022 [novel_lenNOK_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	0.189	no	no	0.63/0.63	19/19/0.00	0.0	0.0	1	0	1	0	5	28	3arm	71	nd	0.32	3	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------------------------------------AUCCCAG----------------	1	novel
		len	cloning frequencies
			T3S1
	--------------------------------------------------------------------------------------------CATCCCAGAGCTGAACGGG-----	19	1
rat	ggcccctctggaaagctgtggcgtgatggccatggggcagcccagaacatcatccctgcatccactggtgctgccaaggctgtgggcaaggtCATCCCAGAGCTGAACGGGaagct
	********************************************************************************************************************
rat	(((...((((...((((.(((.((((((.((((((((((((((((...................)))).))))))....)))))).))...)))).))).))))...))))..)))	0.430 -44.91

rat

chromosome:7:10406631:10406746:-1

intergenic

block2083023 [novel_lenNOK_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	0.151	no	no	0.58/0.58	19/19/0.00	0.0	0.0	2	0	2	0	22	11	3arm	137	nd	0.37	3	2	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------AGGCUGU---------------------------------	2	novel
		len	cloning frequencies
			T1S2	T5S2
	----------------------------------------------------------------------------AAGGCTGTGGGCAAGGTCA----------------------	19	1	1
rat	tggcccctctggaaagctgtggcgtgatggccatggggcagcccagaacatcatccctgcatccactggtgctgccAAGGCTGTGGGCAAGGTCAtcccagagctgaacgggaagct
	*********************************************************************************************************************
rat	.(((...((((...((((.(((.((((((.((((((((((((((((...................)))).))))))....)))))).))...)))).))).))))...))))..)))	0.430 -45.11

rat

chromosome:7:10406631:10406747:-1

intergenic

block1329353 [novel_lenNOK_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	0.799	no	no	0.74/0.74	19/19/0.00	0.0	0.0	1	0	1	0	14	1	5arm	25	nd	0.37	3	1	1	na	na

		reads	miRBase family seed
seed	---------------AGAGCCG------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--------------GAGAGCCGGACGGGCACTG-------------------------------------------	19	1
rat	gcgccggggcaagtGAGAGCCGGACGGGCACTGggcgactctgtgcctcgctgaggaaaatcaactaaacatgggc
	****************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000015354 ENSRNOG00000011528 RGD1312003
	...........................................................................>>>>>>>>>>>	ENSRNOT00000015314 ENSRNOG00000024306
rat	((.(((.....(((((...((...(((((((.((....))..))))).))....))....))).)).....)))))	0.560 -21.50

rat

chromosome:2:217964225:217964300:1

Same_strand|Intronic_coding|ENSRNOT00000015354|ENSRNOG00000011528 ## ENSRNOG00000011528|protein_coding|RGD1312003|UDP-N-acetylglucosamine transferase subunit ALG14 homolog. [Source:UniProtKB/Swiss-Prot;Acc:Q6AY85]

block1402232 [novel_lenNOK_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	0.046	no	no	0.58/0.58	19/19/0.00	0.0	0.0	2	0	2	0	7	27	3arm	137	nd	0.32	3	2	2	na	na

		reads	miRBase family seed
seed	------------------------------------------------------------------------------------AGGCUGU------------------	2	novel
		len	cloning frequencies
			T1S2	T5S2
	-----------------------------------------------------------------------------------AAGGCTGTGGGCAAGGTCA-------	19	1	1
rat	ctgtgggtggcccttctggaaagctatggcatgatggctgtggggcagtccagaacatcatccctgccatcactggtgctgccAAGGCTGTGGGCAAGGTCAtcccaga
	*************************************************************************************************************
rat	(((.((((((((..(((....((((.((((((((((((...((((..((.......))..)))).))))))).......))))).))))..)))...))))))))))).	0.660 -43.61

rat

chromosome:3:116162759:116162867:-1

intergenic

novel_lenNOK_shortStem_loopOverlap (783 loci)

block5071 [novel_lenNOK_shortStem_loopOverlap]

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	0.232	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	1	-1	3arm	2	nd	0.28	2	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------GAAAACA-----------	1	novel
		len	cloning frequencies
			T2S1
	---------------------------------TGAAAACACAGGCCTTGG-	18	1
rat	tccttgggctattctggcttcctcaaatctaaaTGAAAACACAGGCCTTGGa
	****************************************************
	--------------------------------------------------------------	ENSRNOT00000061130 ENSRNOG00000005297 Adcy9
	--------------------------------------------------------------	ENSRNOT00000007042 ENSRNOG00000005297 Adcy9
rat	(((..(((((....((..(((.............)))..))..))))).)))	0.820 -9.12

rat

chromosome:10:11506726:11506777:-1

Opposite_strand|Intronic_non-coding|ENSRNOT00000061130|ENSRNOG00000005297 ## Opposite_strand|Intronic_coding|ENSRNOT00000007042|ENSRNOG00000005297 ## ENSRNOG00000005297|protein_coding|Adcy9|adenylate cyclase 9 Gene [Source:MGI (curated);Acc:Adcy9-002]

block10444 [novel_lenNOK_shortStem_loopOverlap]

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	0.026	no	no	0.61/0.61	18/18/0.00	0.0	0.0	1	0	1	0	2	-3	3arm_loop	1	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	---------------------CAGAAGG------------	1	novel
		len	cloning frequencies
			T5S2
	--------------------TCAGAAGGCTCCGCTCTC--	18	1
rat	cagggcttgggcgctttcaaTCAGAAGGCTCCGCTCTCtg
	****************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000011922 ENSRNOG00000027341 Odz2
rat	(((((..((((.((((((.....))))))))))..)))))	1.000 -16.00

rat

chromosome:10:21547125:21547164:-1

Same_strand|Boundary_non-coding|ENSRNOT00000045307|ENSRNOG00000027341 ## Same_strand|Intronic_coding|ENSRNOT00000011922|ENSRNOG00000027341 ## ENSRNOG00000027341|protein_coding|Odz2|Teneurin-2 (Ten-2) (Tenascin-M2) (Ten-m2) (Protein Odd Oz/ten-m homolog 2) (Neurestin). [Source:UniProtKB/Swiss-Prot;Acc:Q9R1K2]

block13404 [novel_lenNOK_shortStem_loopOverlap]

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	0.306	no	no	0.44/0.44	18/18/0.00	0.0	0.0	4	0	1	0	1	-1	5arm_loop	1	nd	0.28	2	4	1	na	na

		reads	miRBase family seed
seed	--CCAGUGU----------------------------------------	4	miR-199a
		len	cloning frequencies
			T4S2
	-CCCAGTGTTTTCTGAGTT------------------------------	18	4
rat	gCCCAGTGTTTTCTGAGTTgccctttattgagagtcactgtcgaaggtt
	*************************************************
rat	((((((((..((((.(((........))).)))).))))).....))).	1.000 -10.60

rat

chromosome:10:30303881:30303929:-1

intergenic

block13628 [novel_lenNOK_shortStem_loopOverlap]

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	0.072	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	1	-3	3arm_loop	1	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------AUCCAAG-----------	1	novel
		len	cloning frequencies
			T1S1
	------------------------------------AATCCAAGTCTTCCCGGA-	18	1
rat	gtctggagttgggcttggcagatgatgtgatgaagaAATCCAAGTCTTCCCGGAc
	*******************************************************
rat	((((((....((((((((.....................))))))))..))))))	0.950 -16.10

rat

chromosome:10:30914495:30914549:-1

intergenic

block15268 [novel_lenNOK_shortStem_loopOverlap]

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	0.031	no	no	0.44/0.44	18/18/0.00	0.0	0.0	1	0	1	0	2	-3	3arm_loop	1	nd	0.22	2	1	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------UCCUUGG------------	1	novel
		len	cloning frequencies
			T5S1
	---------------------------------------------------ATCCTTGGCAATACAGTC--	18	1
rat	ggttttgtgtgccaagccattcatatcccagtttcctttcacaccaataaaATCCTTGGCAATACAGTCca
	***********************************************************************
	---------------------------------------------------------------------------------	ENSRNOT00000059277 ENSRNOG00000003005 NP_001101743.1
rat	((..((((((((((((......................................))))))).))))).)).	0.970 -13.16

rat

chromosome:10:35443441:35443511:-1

Opposite_strand|Boundary_non-coding|ENSRNOT00000004050|ENSRNOG00000003005 ## Opposite_strand|Intronic_non-coding|ENSRNOT00000059277|ENSRNOG00000003005 ## ENSRNOG00000003005|protein_coding|NP_001101743.1|RasGEF domain family, member 1C [Source:RefSeq_peptide;Acc:NP_001101743]

block15970 [novel_lenNOK_shortStem_loopOverlap]

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	0.195	no	no	0.50/0.50	18/18/0.00	0.0	0.0	1	0	1	0	0	-3	3arm_loop	1	nd	0.29	3	1	1	na	na

		reads	miRBase family seed
seed	-----------------------ACUCCUG----------	1	novel
		len	cloning frequencies
			T2S1
	----------------------AACTCCTGGCTTCAACTG	18	1
rat	ccagtgcatggattaaggaattAACTCCTGGCTTCAACTG
	****************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000038838 ENSRNOG00000022555 LOC497899
rat	.((((...((((...((((......))))...))))))))	0.990 -8.00

rat

chromosome:10:36779891:36779930:-1

Same_strand|Intronic_non-coding|ENSRNOT00000038838|ENSRNOG00000022555 ## ENSRNOG00000022555|protein_coding|LOC497899|Putative uncharacterized protein LOC497899. [Source:UniProtKB/TrEMBL;Acc:Q6AXV8]

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