Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

candidate novel loci of miRBase miRNAs

miRBaseNonMapped_randfoldOK (16 loci)

rno-mir-423-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-423-as 5arm	0	0	0	0	0	1	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-423-as 5arm	0	0	0	0	0	0.000	0	0	0	0

rno-mir-423-as relative cloning frequencies

block30674 (Antisense miRBase rno-mir-423-as) [miRBaseNonMapped_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
miRBaseAS rno-mir-423-as	0.001	no	no	0.70/0.70	20/20/1.00	0.0	0.0	1	0	1	0	31	4	5arm	1	nd	0.20	3	1	1	na	na

Families
Member of family novel115 (seed GAGGGGC): rno-mir-423, block3014842_cand

block30674 hairpin

		reads	miRBase family seed
seed	------------------------------------------------GAGGGGC-----------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T3S2
	-----------------------------------------------TGAGGGGCCTCAGACCGAGC-----------------------------------------------------------------------------------------	20	1
rat	----------------AGAAACTCAAGCGCGGGTTAGGAAGCAAGACTGAGGGGCCTCAGACCGAGCTTTTGGAAAATAGAAAAGTCTCGCTCTCTGCCCCTCAGCCTAACTTCCTTTATTTCCTCACAAGTTTCT--------------------
human	GAGCATCCAAGCGGGGAGAAACTCAAGCGCGGGTTAGGAAGCAAGACTGAGGGGCCTCAGACCGAGCTTTTGGAAAATAGAAAAGTCTCGCTCTCTGCCCCTCAGCCTAACTTCCTTTATTTCCTCACAAGTTTCTCCCTCAAACTTCGGGCTT--
mouse	--GCATCCAACCGGG-AGAAACTCAAGCGCGGGGTAGGAAGCAAGACTGAGGGGCCTCAGACCGAGCTTTTGGAAAATAGAAAAGTCTCGCTCTCTGCCCCTCAGCCTAACTTCCTTTATTTCCTCACAAGTTTCT----CAAACTTCGGGCTTGC
	*************** ****************************************************************************************************
	----- ------------------------------------------------------------------------------------------------------------------------ -----	ENSRNOT00000030749 ENSRNOG00000022502 RGD1309863
	..... ..........<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<................ .....	ENSRNOT00000053660 ENSRNOG00000035537 rno-mir-423
rat	(((((((.......(((..((((((..((.(((((((((...(((.(((((((((.........))))).)))).)))..))))))))).))..)))))).....))).....)))))))	0.980 -45.40
human	((((..(((((.(((((((((((.......(((..((((((..((.(((((((((...(((.(((((((((.........))))).)))).)))..))))))))).))..)))))).....))).....)))))))))))....))).))))))	0.981 -61.10
mouse	(((.....((((( (((((((.......((((.((((((..((.(((((((((...(((.(((((((((.........))))).)))).)))..))))))))).))..))))))......))))...))))))) ).....))))...)))	0.939 -55.30

rat	chromosome:10:67078707:67078826:-1	Opposite_strand\|Intronic_coding\|ENSRNOT00000030749\|ENSRNOG00000022502 ## Opposite_strand\|Exonic_non-coding\|ENSRNOT00000053660\|ENSRNOG00000035537 ## ENSRNOG00000035537\|miRNA\|rno-mir-423\|rno-mir-423 [Source:miRBase;Acc:MI0006145] ## ENSRNOG00000022502\|protein_coding\|RGD1309863\|Coiled-coil domain-containing protein 55. [Source:UniProtKB/Swiss-Prot;Acc:Q4FZU3] ## {ASMIR: rno-mir-423-as}
human	chromosome:17:25468189:25468342:-1	Opposite_strand\|Intronic_coding\|ENST00000247026\|ENSG00000126653\|protein_coding\|Coiled-coil domain-containing protein 55 [Source:UniProtKB/Swiss-Prot;Acc:Q9H0G5] ## Opposite_strand\|Boundary_non-coding\|ENST00000362201\|ENSG00000199071\|miRNA\|hsa-mir-423 [Source:miRBase;Acc:MI0001445] ## {ASMIR: hsa-mir-423-as}
mouse	chromosome:11:76891546:76891694:1	Opposite_strand\|Intronic_coding\|ENSMUST00000102494\|ENSMUSG00000037958\|protein_coding\|coiled-coil domain containing 55 Gene [Source:MGI (curated);Acc:Ccdc55-001] ## Opposite_strand\|Boundary_non-coding\|ENSMUST00000083584\|ENSMUSG00000065518\|miRNA\|mmu-mir-423 [Source:miRBase;Acc:MI0004637] ## {ASMIR: mmu-mir-423-as}

rno-mir-10a-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-10a-as 3arm	0	0	0	0	0	0	0	0	0	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-10a-as 3arm	0	0	0	0	0	0	0	0	0	0.000

rno-mir-10a-as relative cloning frequencies

block39129 (Antisense miRBase rno-mir-10a-as) [miRBaseNonMapped_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
miRBaseAS rno-mir-10a-as	0.009	no	no	0.45/0.45	22/22/1.00	0.0	0.0	1	0	1	0	28	0	3arm	1	nd	0.18	2	1	1	na	na

Families
Member of family miR-10a (seed AAAUUCG): rno-mir-10a, rno-mir-10a

block39129 hairpin

		reads	miRBase family seed
seed	------------------------------------------------------------------------------ACAAAUU-----------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	-----------------------------------------------------------------------------CACAAATTCGGATCTACAGGGT---------------------------------------------	22	1
rat	------------GAGCGGAGTGTTTATGTCAACTACATATTCCCCTAGATACGAATTTGTGACCACAAAATTCCTTACACAAATTCGGATCTACAGGGTATATACAGAAGACAGACAGGTCTTCTTG-----------------
human	CTGGAAAAATAAGAGCGGAGTGTTTATGTCAACTACATATTCCCCTAGATACGAATTTGTGACCACAAAATTCCTTACACAAATTCGGATCTACAGGGTATATACAGAAGACAGACAGATCTTCTTGGCCCAGAAATTTTCCAG
mouse	------------------------------------ATATTCCCCTAGATACGAATTTGTGACCACAAAATTCCTTACACAAATTCGGATCTACAGGGTATAT-----------------------------------------
	*******************************************************************
	....< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...... .....	ENSRNOT00000053658 ENSRNOG00000035535 rno-mir-10a
rat	(((.(((.((((..((((..((..((((.(((.(((((.((((((((((................)))))))))).)))))..))).))))..))..))))))))..))).))).	0.890 -31.49
human	((((((((......((.(((.((((.((((..((..((((.(((.(((((.((((((((((................)))))))))).)))))..))).))))..))..))))...))))...))).)).......))))))))	0.852 -40.41
mouse	((((.(((.(((((.((((((((((................)))))))))).)))))..))).))))	1.000 -20.39

rat	chromosome:10:85049308:85049422:-1	Opposite_strand\|Exonic_non-coding\|ENSRNOT00000053658\|ENSRNOG00000035535 ## ENSRNOG00000035535\|miRNA\|rno-mir-10a\|rno-mir-10a [Source:miRBase;Acc:MI0000841] ## {ASMIR: rno-mir-10a-as}
human	chromosome:17:44012188:44012331:1	Opposite_strand\|Boundary_non-coding\|ENST00000385043\|ENSG00000207777\|miRNA\|hsa-mir-10a [Source:miRBase;Acc:MI0000266] ## {ASMIR: hsa-mir-10a-as}
mouse	chromosome:11:96178497:96178563:-1	Opposite_strand\|Exonic_non-coding\|ENSMUST00000083585\|ENSMUSG00000065519\|miRNA\|mmu-mir-10a [Source:miRBase;Acc:MI0000685] ## {ASMIR: mmu-mir-10a-as}

rno-mir-125b-2-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-125b-2-as 3arm	0	0	0	0	0	0	0	0	0	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-125b-2-as 3arm	0	0	0	0	0	0	0	0	0	0.000

rno-mir-125b-2-as relative cloning frequencies

block112259 (Antisense miRBase rno-mir-125b-2-as) [miRBaseNonMapped_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
miRBaseAS rno-mir-125b-2-as	0.001	no	no	0.52/0.52	23/23/1.00	0.0	0.0	2	0	1	0	24	3	3arm	2	nd	0.13	2	2	1	na	na

block112259 hairpin

		reads	miRBase family seed
seed	------------------------------------------------------------CACAAGU---------------------------------------	2	novel
		len	cloning frequencies
			T5S2
	-----------------------------------------------------------TCACAAGTTAGGGTCTCAGGGAC------------------------	23	2
rat	CTGCTGGTACCTCTCCGCCTAGGTCCCAAGAGCCTGACTTGTGATGTTACTAAAATACCTCACAAGTTAGGGTCTCAGGGACTAGGAAAAGTCTGGTTTGATGCAG
human	-----------------CCTAGGTCCCAAGAGCCTGACTTGTGATGTTACTAAAATACCTCACAAGTTAGGGTCTCAGGGACTAGG--------------------
mouse	-----------------------TCCCAAGAACCTGACTTGTGATGTTACTAAAATACCTCACAAGTTAGGGTCTCAGGGA-------------------------
	****** ***********************************************
	..............<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<..............	ENSRNOT00000053649 ENSRNOG00000035526 rno-mir-125b-2
rat	((((....(((.((...((((.(((((.(((.((((((((((((.((.........)).)))))))))))).)))..)))))))))...))...))).....))))	1.000 -46.10
human	((((.(((((.(((.((((((((((((.((.........)).)))))))))))).)))..)))))))))	1.000 -36.00
mouse	((((.(((.((((((((((((.((.........)).)))))))))))).)))..))))	1.000 -26.20

rat	chromosome:11:16443657:16443762:-1	Opposite_strand\|Exonic_non-coding\|ENSRNOT00000053649\|ENSRNOG00000035526 ## ENSRNOG00000035526\|miRNA\|rno-mir-125b-2\|rno-mir-125b-2 [Source:miRBase;Acc:MI0000897] ## {ASMIR: rno-mir-125b-2-as}
human	chromosome:21:16884439:16884507:-1	Opposite_strand\|Boundary_non-coding\|ENST00000400176\|ENSG00000215386\|protein_coding\|Putative uncharacterized protein C21orf34 (Chromosome 21 open reading frame 34, isoform CRA_a) [Source:UniProtKB/TrEMBL;Acc:A6NJD3] ## Opposite_strand\|Intronic_non-coding\|ENST00000400178\|ENSG00000215386\|protein_coding\|Putative uncharacterized protein C21orf34 (Chromosome 21 open reading frame 34, isoform CRA_a) [Source:UniProtKB/TrEMBL;Acc:A6NJD3] ## Opposite_strand\|Exonic_non-coding\|ENST00000385128\|ENSG00000207863\|miRNA\|hsa-mir-125b-2 [Source:miRBase;Acc:MI0000470] ## {ASMIR: hsa-mir-125b-2-as}
mouse	chromosome:16:77646479:77646624:-1	Opposite_strand\|Boundary_non-coding\|ENSMUST00000083538\|ENSMUSG00000065472\|miRNA\|mmu-mir-125b-2 [Source:miRBase;Acc:MI0000152] ## {ASMIR: mmu-mir-125b-2-as}

rno-mir-29c-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-29c-as 5arm	0	0	0	0	0	0	0	0	0	2
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-29c-as 5arm	0	0	0	0	0	0	0	0	0	0.000

rno-mir-29c-as relative cloning frequencies

block284880 (Antisense miRBase rno-mir-29c-as) [miRBaseNonMapped_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
miRBaseAS rno-mir-29c-as	0.003	no	no	0.40/0.40	20/20/1.00	0.0	0.0	2	0	1	0	26	2	5arm	1	nd	0.20	3	2	1	na	na

block284880 hairpin

		reads	miRBase family seed
seed	---------------------------CCGAUUU-------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			T5S2
	--------------------------ACCGATTTCAAATGGTGCTA-------------------------------------------------------------	20	2
rat	GCTGGTGCTTTTCCCCCTACATCATAACCGATTTCAAATGGTGCTAGACAAAAACAGACTCTGAACACCAGGAGAAATCGGTCAGCCTGTGTAAGAGATGGACCAGT
human	--------------------------ACCGATTTCAAATGGTGCTAGACAAAAACAGACTCTGAACACCAGGAGAAATCGGT-------------------------
mouse	--------------------------ACCGATTTCAAATGGTGCTAGACAAAAACAGACTCTGAACACCAGGAGAAATCGGT-------------------------
	********************************************************
	................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.............	ENSRNOT00000053632 ENSRNOG00000035509 rno-mir-29c
rat	((((((.((((((....(((((....(((((((((...(((((.((((...........))))..)))))...)))))))))......))))).)))).))))))))	1.000 -31.30
human	(((((((((...(((((.((((...........))))..)))))...)))))))))	1.000 -19.20
mouse	(((((((((...(((((.((((...........))))..)))))...)))))))))	1.000 -19.20

rat	chromosome:13:110968040:110968146:-1	Opposite_strand\|Exonic_non-coding\|ENSRNOT00000053632\|ENSRNOG00000035509 ## ENSRNOG00000035509\|miRNA\|rno-mir-29c\|rno-mir-29c [Source:miRBase;Acc:MI0000865] ## {ASMIR: rno-mir-29c-as}
human	chromosome:1:206041789:206041935:1	Opposite_strand\|Boundary_non-coding\|ENST00000385231\|ENSG00000207966\|miRNA\|hsa-mir-29c [Source:miRBase;Acc:MI0000735] ## {ASMIR: hsa-mir-29c-as}
mouse	chromosome:1:196863713:196863859:-1	Opposite_strand\|Boundary_non-coding\|ENSMUST00000083614\|ENSMUSG00000065548\|miRNA\|mmu-mir-29c [Source:miRBase;Acc:MI0000577] ## {ASMIR: mmu-mir-29c-as}

rno-mir-205-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-205-as 5arm	1	0	0	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-205-as 5arm	0.000	0	0	0	0	0	0	0	0	0

rno-mir-205-as relative cloning frequencies

block331596 (Antisense miRBase rno-mir-205-as) [miRBaseNonMapped_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
miRBaseAS rno-mir-205-as	0.001	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	32	0	5arm	1	nd	0.24	3	1	1	na	na

block331596 hairpin

		reads	miRBase family seed
seed	---------------------------------CUUCACU------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1
	--------------------------------GCTTCACTCCACTGAAATCTG-----------------------------------------------------------------	21	1
rat	CAGTCCACCGCTGGCAGCTCCATGCCTCCTGAGCTTCACTCCACTGAAATCTGGTT-GGCATAAGACAGACTCCGGTGGAATGAAGGACAGGAGGA-CCCATGGATTGTCTGGGGCTG
human	------------------TCCATGCCTCCTGAACTTCACTCCACTGAAATCTGGTTGGGTATGAGACAGACTCCGGTGGAATGAAGGACAAGAGAAGCACATGGA-------------
mouse	------------GGCAGCTCCATGCCTCCTGAGCTTCACTCCACTGAAATCTGGTT-GGCATAAGACAGACTCCGGTGGAATGAAGGACAAGAGGA-CCCATGGATTGTC--------
	************ ******************* *********************** * * * ******
	................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< <<<<<<<<<<<<<<<<<<<<<<<<..	ENSRNOT00000053643 ENSRNOG00000035520 rno-mir-205
rat	((((((......(((((.(((((((((((((..(((((.(((((((...((((... .........))))...))))))).)))))..))))))). ..)))))))))))..))))))	1.000 -54.20
human	((((((.(((.((..(((((.(((((((...((((.............))))...))))))).)))))..)).))).....))))))	0.987 -31.32
mouse	(((((.((((((((((.((..(((((.(((((((...((((... .........))))...))))))).)))))..)).)))). ..)))))))))))	1.000 -38.70

rat	chromosome:13:109352360:109352475:1	Opposite_strand\|Exonic_non-coding\|ENSRNOT00000053643\|ENSRNOG00000035520 ## ENSRNOG00000035520\|miRNA\|rno-mir-205\|rno-mir-205 [Source:miRBase;Acc:MI0000947] ## {ASMIR: rno-mir-205-as}
human	chromosome:1:207672117:207672203:-1	Opposite_strand\|Exonic_non-coding\|ENST00000384891\|ENSG00000207623\|miRNA\|hsa-mir-205 [Source:miRBase;Acc:MI0000285] ## {ASMIR: hsa-mir-205-as}
mouse	chromosome:1:195333644:195333739:1	Opposite_strand\|Boundary_non-coding\|ENSMUST00000083599\|ENSMUSG00000065533\|miRNA\|mmu-mir-205 [Source:miRBase;Acc:MI0000248] ## {ASMIR: mmu-mir-205-as}

rno-mir-217-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-217-as 3arm	0	0	0	0	0	0	0	0	0	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-217-as 3arm	0	0	0	0	0	0	0	0	0	0.000

rno-mir-217-as relative cloning frequencies

block377413 (Antisense miRBase rno-mir-217-as) [miRBaseNonMapped_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
miRBaseAS rno-mir-217-as	0.002	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	19	5	3arm	1	nd	0.09	1	1	1	na	na

block377413 hairpin

		reads	miRBase family seed
seed	----------------------------------------------------------------UCCAGUC---------------------------------	1	novel
		len	cloning frequencies
			T5S2
	---------------------------------------------------------------ATCCAGTCAGTTCCTGATGCAG-------------------	22	1
rat	GTTTGCTGGTGGCTGTTTAGATGCTGAAGGCAATGCATTAGGAACTGATGGTGACTGAGTCTTATCCAGTCAGTTCCTGATGCAGTATCTGCGACATCAAAACT
mouse	-----------------------CTGAAGGCAATGCATTAGGAACTGATGGGGATTAAGTCTTATCCAGTCAGTTCCTGATGCAG-------------------
	************************** * ****************************
	..................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	ENSRNOT00000053641 ENSRNOG00000035518 rno-mir-217
rat	((((..(((((..(((..((((((.........((((((((((((((((((.(((...)))....))).)))))))))))))))))))))))).))))))))).	0.530 -39.20
mouse	..........((((((((((((((((..((((........)))).)))))))))))))))).	0.962 -31.30

rat	chromosome:14:109673494:109673597:-1	Opposite_strand\|Exonic_non-coding\|ENSRNOT00000053641\|ENSRNOG00000035518 ## ENSRNOG00000035518\|miRNA\|rno-mir-217\|rno-mir-217 [Source:miRBase;Acc:MI0000956] ## {ASMIR: rno-mir-217-as}
mouse	chromosome:11:28663724:28663867:-1	Opposite_strand\|Boundary_non-coding\|ENSMUST00000083481\|ENSMUSG00000065415\|miRNA\|mmu-mir-217 [Source:miRBase;Acc:MI0000731] ## {ASMIR: mmu-mir-217-as}

rno-let-7d-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-let-7d-as 3arm	0	2	0	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-let-7d-as 3arm	0	0.000	0	0	0	0	0	0	0	0

rno-let-7d-as relative cloning frequencies

block604561 (Antisense miRBase rno-let-7d-as) [miRBaseNonMapped_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
miRBaseAS rno-let-7d-as	0.001	no	no	0.43/0.43	21/21/1.00	0.0	0.0	2	0	1	0	13	8	3arm	1	nd	0.19	1	2	1	na	na

block604561 hairpin

		reads	miRBase family seed
seed	-----------------------------------------------------------------------------ACUAUGC----------------------------------------------	2	novel
		len	cloning frequencies
			T1S2
	----------------------------------------------------------------------------AACTATGCAACCTACTACCTC---------------------------------	21	2
rat	---------------GGCCCTAAGAAAGGCAGCAGGTCGTATAGTTAACTCCTTGTGGGCAAAATCTCTGCCCTAAAACTATGCAACCTACTACCTCTTCCTAGGAGCCC--------------------
human	ATCGGTGAATAATAAGGCCCTAAGAAAGGCAGCAGGTCGTATAGTTACCTCCTTGTGGGCAAAATCCCTGCCCTAAAACTATGCAACCTACTACCTCTTCCTAGGAACCCATTTTTTTTTTCTTGCTGGT
mouse	-------------------------AAGGCAGCAGGTCGTATAGTTAACTCCTTGTGGGCAAAATCTCTGCCCTAAAACTATGCAACCTACTACCTC---------------------------------
	******************** ************** ****************************
	...<< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< <....	ENSRNOT00000053717 ENSRNOG00000035594 rno-let-7d
rat	(((((((.((((((.((.((((.((((((((......(((.(((((.......)))))))))))))))).)))).)).))).))).)))).))).	0.500 -37.40
human	(((((((((.((.((((.((((.((((((.((.((((.((((((((......(((.(((((.......)))))))))))))))).)))).)).))).))).))))...)).))...)).)))..))))))	0.905 -35.30
mouse	.(((.((.((((.((((((((......(((.(((((.......)))))))))))))))).)))).)).))).	0.502 -24.30

rat	chromosome:17:22121895:22121989:-1	Opposite_strand\|Exonic_non-coding\|ENSRNOT00000053717\|ENSRNOG00000035594 ## ENSRNOG00000035594\|miRNA\|rno-let-7d\|rno-let-7d [Source:miRBase;Acc:MI0000601] ## {ASMIR: rno-let-7d-as}
human	chromosome:9:95980912:95981041:-1	Opposite_strand\|Boundary_non-coding\|ENST00000362263\|ENSG00000199133\|miRNA\|hsa-let-7d [Source:miRBase;Acc:MI0000065] ## {Repeats: dust 0 class=dust} ## {ASMIR: hsa-let-7d-as}
mouse	chromosome:13:48631366:48631500:1	Opposite_strand\|Boundary_non-coding\|ENSMUST00000083519\|ENSMUSG00000065453\|miRNA\|mmu-let-7d [Source:miRBase;Acc:MI0000405] ## {ASMIR: mmu-let-7d-as}

rno-mir-133a-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-133a-as 5arm	0	1	0	0	0	0	0	0	1	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-133a-as 5arm	0	0.000	0	0	0	0	0	0	0.000	0

rno-mir-133a-as relative cloning frequencies

block724672 (Antisense miRBase rno-mir-133a-as) [miRBaseNonMapped_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
miRBaseAS rno-mir-133a-as	0.002	no	no	0.55/0.57	21/22/1.00	0.5	0.0	2	0	2	0	32	3	5arm	1	nd	0.10	1	2	2	na	na

block724672 hairpin

		reads	miRBase family seed
seed	------------------------------------CAGCUGG-------------------------------------------------------------------------------------------------	1	novel
seed	-------------------------------------AGCUGGU------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1
	-----------------------------------ACAGCTGGTTGAAGGGGACCAA-----------------------------------------------------------------------------------	22	1	-
	------------------------------------CAGCTGGTTGAAGGGGACCAA-----------------------------------------------------------------------------------	21	-	1
rat	---GCTGGCTGTCCTGTGGCAATCAATGCATAGCTACAGCTGGTTGAAGGGGACCAAATCCATTGAAGAGGCGATTTGGTTCCATTTTACCAGCTTTAGCAAAGCATTGC--CGCTGCTGGTT-----------------
human	AACGTTGGTTGTCCCGTAGTAATCAATGCATAGCTACAGCTGGTTGAAGGGGACCAAATCCATTGAAGAGGCGATTTGGTTCCATTTTACCAGCTCTAGCAAAGCATTGTAGTGCTGCTAGTTTGGAATCCAAAACAGTT
mouse	-ACACTGGCTGTCCATGTGTAATCAATGCATAGCTACAGCTGGTTGAAGGGGACCAAATCCATTGAAGAGGCGATTTGGTTCCATTTTACCAGCTTTAGCAAAGCATTGC--CGCTGCTGGTGT----------------
	* *** * ************************************************************************* ********* **
	+++++ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++ +++++	ENSRNOT00000018025 ENSRNOG00000013281 NP_001100875.1
	..... ...................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<. ........... .....	ENSRNOT00000053774 ENSRNOG00000035651 rno-mir-133a
rat	((..((......((((((....((((...((((.(((((((.(((.(((((((((((............))))))))))).))).))))))).))))...))))))) ))).))..)).	1.000 -52.00
human	(((.((((...(((.((((((..((((((...((((.(((((((.(((.(((((((((((............))))))))))).))).))))))).))))...))))))...))))))......)))..))))....)))	0.953 -55.30
mouse	((((..((.......(((....((((((...((((.(((((((.(((.(((((((((((............))))))))))).))).))))))).))))...)))))). ))).))..))))	0.889 -50.80

rat	chromosome:18:2189197:2189314:1	Opposite_strand\|Exonic_non-coding\|ENSRNOT00000053774\|ENSRNOG00000035651 ## Same_strand\|Intronic_coding\|ENSRNOT00000018025\|ENSRNOG00000013281 ## ENSRNOG00000013281\|protein_coding\|NP_001100875.1\|mindbomb homolog 1 [Source:RefSeq_peptide;Acc:NP_001100875] ## ENSRNOG00000035651\|miRNA\|rno-mir-133a\|rno-mir-133a [Source:miRBase;Acc:MI0000906] ## {ASMIR: rno-mir-133a-as}
human	chromosome:18:17659635:17659774:1	Same_strand\|Intronic_coding\|ENST00000261537\|ENSG00000101752\|protein_coding\|E3 ubiquitin-protein ligase MIB1 (EC 6.3.2.-)(Mind bomb homolog 1)(DAPK-interacting protein 1)(DIP-1)(Zinc finger ZZ type with ankyrin repeat domain protein 2) [Source:UniProtKB/Swiss-Prot;Acc:Q86YT6] ## Opposite_strand\|Boundary_non-coding\|ENST00000385052\|ENSG00000207786\|miRNA\|hsa-mir-133a-1 [Source:miRBase;Acc:MI0000450] ## {ASMIR: hsa-mir-133a-1-as}
mouse	chromosome:18:10782876:10782996:1	Same_strand\|Intronic_coding\|ENSMUST00000052838\|ENSMUSG00000024294\|protein_coding\|mindbomb homolog 1 (Drosophila) Gene [Source:MGI (curated);Acc:Mib1-001] ## Opposite_strand\|Boundary_non-coding\|ENSMUST00000083465\|ENSMUSG00000065399\|miRNA\|mmu-mir-133a-1 [Source:miRBase;Acc:MI0000159] ## {ASMIR: mmu-mir-133a-1-as}

rno-mir-210-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-210-as 5arm	0	0	1	0	0	0	0	0	0	0
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-210-as 5arm	0	0	0.000	0	0	0	0	0	0	0

rno-mir-210-as relative cloning frequencies

block1027589 (Antisense miRBase rno-mir-210-as) [miRBaseNonMapped_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
miRBaseAS rno-mir-210-as	0.001	no	no	0.64/0.64	22/22/1.00	0.0	0.0	1	0	1	0	29	5	5arm	1	nd	0.09	1	1	1	na	na

block1027589 hairpin

		reads	miRBase family seed
seed	------------------------------CAGCCGC---------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T2S1
	-----------------------------TCAGCCGCTGTCACACGCACAG-------------------------------------------------------------------	22	1
rat	GCCAGGGGTTCGCGCTGCCCAGGGACAGATCAGCCGCTGTCACACGCACAGTGGGTCCGGAGCAACGCAGTGTGCTGTGGGCAGTGGCTGTCCTGAGCCTGGAGGGACTGCCCCGGTG
human	-----------------------------TCAGCCGCTGTCACACGCACAGTGGGTCTGGGGCAGCGCAGTGTGCGGTGGGCAGGGGCTGC---------------------------
mouse	-----------------------------TCAGCCGCTGTCACACGCACAGTGGGTCCGGAGCAACGCAGTGTGCGGTGGGCAGTGGCTGT---------------------------
	************************** * ****** **** ***
	...........<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.......	ENSRNOT00000053739 ENSRNOG00000035616 rno-mir-210
rat	(((.(((((.....((..(((((..(((..(((((((((((.((((((((.((.((........)).)).))))).))))))))))))))..)))..)))))..))...)))))))).	1.000 -65.60
human	.(((((.(((((...((((((.((.((........)).)).))))))...))))).))))).	1.000 -35.00
mouse	.(((((((((((...((((((.((.((........)).)).))))))...))))))))))).	1.000 -37.10

rat	chromosome:1:201415650:201415767:1	Opposite_strand\|Exonic_non-coding\|ENSRNOT00000053739\|ENSRNOG00000035616 ## ENSRNOG00000035616\|miRNA\|rno-mir-210\|rno-mir-210 [Source:miRBase;Acc:MI0000950] ## {ASMIR: rno-mir-210-as}
human	chromosome:11:558063:558220:1	Opposite_strand\|Boundary_non-coding\|ENST00000362168\|ENSG00000199038\|miRNA\|hsa-mir-210 [Source:miRBase;Acc:MI0000286] ## {SimpF: oe = 0.88 0 CpG} ## {ASMIR: hsa-mir-210-as}
mouse	chromosome:7:148407257:148407414:1	Opposite_strand\|Boundary_non-coding\|ENSMUST00000083617\|ENSMUSG00000065551\|miRNA\|mmu-mir-210 [Source:miRBase;Acc:MI0000695] ## {ASMIR: mmu-mir-210-as}

rno-mir-483-as

Cloning frequencies
absolute	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-483-as 5arm	0	0	0	0	0	0	0	0	0	1
normalized	T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
rno-mir-483-as 5arm	0	0	0	0	0	0	0	0	0	0.000

rno-mir-483-as relative cloning frequencies

block1028409 (Antisense miRBase rno-mir-483-as) [miRBaseNonMapped_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
miRBaseAS rno-mir-483-as	0.001	no	no	0.61/0.61	23/23/1.00	0.0	0.0	1	0	1	0	28	1	5arm	1	nd	0.17	2	1	1	na	na

block1028409 hairpin

		reads	miRBase family seed
seed	-----------------------------CAAGACG-------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T5S2
	----------------------------ACAAGACGGGAGGGGAGGAGTGA----------------------------------------------------------------	23	1
rat	ACAGGAAGGGAAGATAGGGCAGGAGAGAACAAGACGGGAGGGGAGGAGTGAGGCACCCAAAAACCACTCCCTTCTCTTCTCCCGTCTTCCCCCTCTCCCCCACGGTCCGAGGCTG
mouse	-----------AGATAGGGCAGGAGAGAACAAGACGGGAGGGGAGGAGTGAGGCACCCAAAAACCACTCCCTTCTCTTCTCCCGTCTTCCCCCTCTCC-----------------
	***************************************************************************************
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000027602 ENSRNOG00000020369 Igf2
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000050760 ENSRNOG00000020369 Igf2
	-----------------------------------------------------------------------------------------------------------------------------	ENSRNOT00000052058 ENSRNOG00000020369 Igf2
	...........................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.........................	ENSRNOT00000054369 ENSRNOG00000036246 rno-mir-483
rat	.(((....(((.....(((..((((((...((((((((((..((((((.(((..............))).))))))..))))))))))....)))))))))....)))....)))	0.920 -52.44
mouse	..........((((((...((((((((((..((((((.(((..............))).))))))..))))))))))....))))))	1.000 -43.24

rat	chromosome:1:202910587:202910701:1	Opposite_strand\|Intronic_coding\|ENSRNOT00000050760\|ENSRNOG00000020369 ## Opposite_strand\|Exonic_non-coding\|ENSRNOT00000054369\|ENSRNOG00000036246 ## ENSRNOG00000020369\|protein_coding\|Igf2\|Insulin-like growth factor II precursor (IGF-II) (Multiplication- stimulating polypeptide) (Multiplication-stimulating activity) (MSA). [Source:UniProtKB/Swiss-Prot;Acc:P01346] ## ENSRNOG00000036246\|miRNA\|rno-mir-483\|rno-mir-483 [Source:miRBase;Acc:MI0003485] ## {ASMIR: rno-mir-483-as}
mouse	chromosome:7:149840818:149840904:1	Opposite_strand\|Intronic_coding\|ENSMUST00000121128\|ENSMUSG00000048583\|protein_coding\|insulin-like growth factor 2 Gene [Source:MGI (curated);Acc:Igf2-004] ## Opposite_strand\|Boundary_non-coding\|ENSMUST00000093631\|ENSMUSG00000070140\|miRNA\|mmu-mir-483 [Source:miRBase;Acc:MI0003484] ## {ASMIR: mmu-mir-483-as}

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candidate novel loci of miRBase miRNAs:

Page 1

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