Small RNA from different tissues of two rat strains.

miR-Intess™

miR classification

Alignments

other hairpins

novel_cloningOK_shortStem_nonpairedHIGH (7 loci)

block712819 [novel_cloningOK_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	0.769	no	no	0.50/0.52	20/24/1.00	0.0	0.0	10	0	2	0	2	6	3arm	1	nd	0.33	2	12	2	na	na

		reads	miRBase family seed
seed	-----------------------------------------------UCACGCC------------------	11	novel
seed	-------------------------------------------ACAUUCA----------------------	1	miR-181a/181b/181c/181d
		len	cloning frequencies
			T4S2	T5S1
	----------------------------------------------TTCACGCCATGGTACTTGGAGACT--	24	-	10
	------------------------------------------CACATTCACGCCATGGTACT----------	20	1	-
	----------------------------------------------TTCACGCCATGGTACTTGGAGAC---	23	-	1
rat	ctgggattctgtcatttcagggtgttttgttcatgcagccgacacaTTCACGCCATGGTACTTGGAGACTag
	************************************************************************
rat	((((..(((.((....(((.(((((..(((((........)).)))...))))).))).))..)))..))))	0.860 -14.70

rat

chromosome:18:63560691:63560762:-1

intergenic

block1973460 [novel_cloningOK_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	0.094	no	no	0.42/0.50	19/24/0.87	0.0	0.0	19	0	7	0	1	8	3arm	1	nd	0.35	3	30	7	na	na

		reads	miRBase family seed
seed	-------------------------------------------------CGGACUG----------------	26	novel
seed	------------------------------------------------------UGGUUUC-----------	2	miR-29b
seed	----------------------------------------------CAUCGGA-------------------	1	novel
seed	---------------------------------------UGGGAGU--------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T4S2	T5S1
	------------------------------------------------TCGGACTGGTTTCTTGTCTTCCT-	23	1	1	1	1	-	1	19
	-----------------------------------------------------CTGGTTTCTTGTCTTCCTA	19	-	-	-	-	-	-	2
	------------------------------------------------TCGGACTGGTTTCTTGTCTT----	20	-	-	-	-	1	-	-
	---------------------------------------------TCATCGGACTGGTTTCTTG--------	19	1	-	-	-	-	-	-
	--------------------------------------TTGGGAGTCATCGGACTGGTTTCT----------	24	-	-	-	-	-	-	1
	------------------------------------------------TCGGACTGGTTTCTTGTCT-----	19	-	-	-	-	-	-	1
rat	aggaacaatcaaattcgctggactcattttgtctccccttgggagtcaTCGGACTGGTTTCTTGTCTTCCTa
	************************************************************************
rat	(((((....(((....(((((..((....((.(((((...))))).))...)))))))...)))..))))).	0.960 -16.90

rat

chromosome:6:122575518:122575589:-1

intergenic

block2188814 [novel_cloningOK_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	0.088	no	no	0.38/0.45	19/24/0.92	0.0	0.3	7	0	2	0	4	9	5arm	10	nd	0.36	2	12	2	na	na

		reads	miRBase family seed
seed	-----UUCAGGA----------------------------------------------------------------	8	novel
seed	-------CAGGAAG--------------------------------------------------------------	2	novel
seed	------UCAGGAA---------------------------------------------------------------	2	novel
		len	cloning frequencies
			T1S1	T5S1
	----TTTCAGGAAGATGCAAAGTCTG--------------------------------------------------	22	-	5
	----TTTCAGGAAGATGCAAAGTCT---------------------------------------------------	21	-	2
	-----TTCAGGAAGATGCAAAGTCT---------------------------------------------------	20	-	1
	------TCAGGAAGATGCAAAGTCT---------------------------------------------------	19	1	-
	------TCAGGAAGATGCAAAGTCTGCA------------------------------------------------	22	-	1
	-----TTCAGGAAGATGCAAAGTCTG--------------------------------------------------	21	-	1
	----TTTCAGGAAGATGCAAAGTCTGCA------------------------------------------------	24	-	1
rat	gcctTTTCAGGAAGATGCAAAGTCTGcattgaggttcaggtcacctctgtctatttctcatcaacctctgactggc
	****************************************************************************
rat	(((.((..(((..((((..((((..(((..(((((.......))))))))..))))..))))..)))..))..)))	0.810 -19.20

rat

chromosome:7:17179399:17179474:1

intergenic

block2551080 [novel_cloningOK_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	0.703	no	no	0.17/0.23	19/23/0.97	0.0	0.5	21	0	4	0	3	9	5arm	2	nd	0.32	2	30	4	na	na

		reads	miRBase family seed
seed	----GGAUUAA-------------------------------------------------------------------	29	novel
seed	---------AACGAUU--------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T2S2	T5S1
	---AGGATTAACGATTTTATTAAAC-----------------------------------------------------	22	2	1	2	10
	---AGGATTAACGATTTTATTAAACT----------------------------------------------------	23	1	-	-	11
	---AGGATTAACGATTTTATTA--------------------------------------------------------	19	-	-	-	1
	--------TAACGATTTTATTAAACTTTTTG-----------------------------------------------	23	-	-	-	1
	---AGGATTAACGATTTTATTAAA------------------------------------------------------	21	-	-	1	-
rat	aggAGGATTAACGATTTTATTAAACTttttgtcccatacaactcagggatttgtagagtacaacttgggaacttttta
	******************************************************************************
rat	((((((.((..(((((.((((..((.....(((((..........)))))..))..)))).)).)))..)))))))).	0.620 -10.90

rat

chromosome:9:105242538:105242615:-1

intergenic

block1109120 [novel_cloningOK_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	0.470	no	no	0.35/0.40	18/23/0.91	0.0	0.0	13	0	2	0	0	20	5arm	1	nd	0.33	3	22	2	na	na

		reads	miRBase family seed
seed	-GGGCAUC------------------------------------------------------------------------------------	21	novel
seed	--GGCAUCU-----------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			T1S2	T5S1
	AGGGCATCTGTAAAGAATAGT-----------------------------------------------------------------------	21	1	13
	AGGGCATCTGTAAAGAATAG------------------------------------------------------------------------	20	-	3
	AGGGCATCTGTAAAGAAT--------------------------------------------------------------------------	18	-	2
	AGGGCATCTGTAAAGAATAGTT----------------------------------------------------------------------	22	1	-
	-GGGCATCTGTAAAGAATAGT-----------------------------------------------------------------------	20	-	1
	AGGGCATCTGTAAAGAATAGTTT---------------------------------------------------------------------	23	-	1
rat	AGGGCATCTGTAAAGAATAGTttagcacaacagcccccggccataattaggagctgtggtactgtgtcagtgggagggttcgatgtgccttc
	********************************************************************************************
	------------------------------------------------------------------------------------------------------	ENSRNOT00000035355 ENSRNOG00000023712 Stox1_predicted
rat	(((((((..((...((((..((..((...((((..((((((...........)))).))..))))....))..))..)))).))))))))).	0.810 -23.90

rat

chromosome:20:29928289:29928380:1

Opposite_strand|Intronic_non-coding|ENSRNOT00000035355|ENSRNOG00000023712 ## Opposite_strand|Boundary_non-coding|ENSRNOT00000057578|ENSRNOG00000023712 ## ENSRNOG00000023712|protein_coding|Stox1_predicted|

block1696342 [novel_cloningOK_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	0.104	no	no	0.55/0.61	18/23/0.79	0.0	0.3	7	0	4	0	4	3	3arm	1	nd	0.36	3	14	4	na	na

		reads	miRBase family seed
seed	----------------------------------------CAGCAGA------------------	11	novel
seed	-----------------------------------------AGCAGAG-----------------	2	novel
seed	--------------------------------------AUCAGCA--------------------	1	novel
		len	cloning frequencies
			T1S1	T1S2	T4S2	T5S1
	---------------------------------------TCAGCAGAGCCTACAGGACACA----	22	-	1	-	5
	---------------------------------------TCAGCAGAGCCTACAGGACAC-----	21	-	-	1	2
	---------------------------------------TCAGCAGAGCCTACAGGAC-------	19	1	-	-	1
	-------------------------------------CATCAGCAGAGCCTACAGGACAC-----	23	-	-	-	1
	----------------------------------------CAGCAGAGCCTACAGGACACA----	21	-	-	-	1
	----------------------------------------CAGCAGAGCCTACAGGAC-------	18	-	-	-	1
rat	ggcatttctctcgtggttccagctccactgggaaaaccaTCAGCAGAGCCTACAGGACACAtgtc
	*****************************************************************
rat	(((((...((..(((((((..(((....(((.....)))..))).))))).))..))...)))))	0.480 -17.80

rat

chromosome:4:164268015:164268079:1

intergenic

novel_lenNOK_cloningHIGH_loopOverlap_bulgeHIGH (7 loci)

block262824 [novel_lenNOK_cloningHIGH_loopOverlap_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	0.245	no	no	0.32/0.33	18/19/0.00	0.0	0.0	46	0	10	0	16	-3	5arm_loop	1	nd	0.28	4	59	10	na	na

		reads	miRBase family seed
seed	-----------------UACAGUA--------------------------------------------------------	51	novel
seed	------------------ACAGUAC-------------------------------------------------------	8	miR-101a/101b
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------TTACAGTACTGTGATACT----------------------------------------------	18	10	9	3	5	1	5	1	1	9	5
	-----------------TACAGTACTGTGATACTT---------------------------------------------	18	2	-	2	-	-	-	-	-	-	1
	-----------------TACAGTACTGTGATACTTT--------------------------------------------	19	-	-	1	2	-	-	-	-	-	-
	----------------TTACAGTACTGTGATACTT---------------------------------------------	19	1	-	-	-	-	-	-	-	1	-
rat	agtacagcacaaacttTTACAGTACTGTGATACTttgaattctagtatttcattttttcctaagtaaaagtagtttacta
	********************************************************************************
rat	((((.(((....(((((((((((((((.(((.......))).)))))))..............)))))))).))))))).	0.730 -10.63

rat

chromosome:13:58588245:58588324:-1

intergenic

block408327 [novel_lenNOK_cloningHIGH_loopOverlap_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	0.124	no	no	0.47/0.50	18/19/0.00	0.0	0.0	64	0	10	0	22	-3	5arm_loop	1	nd	0.28	4	96	10	na	na

		reads	miRBase family seed
seed	-----------------------GGCUGAG--------------------------------------------------------	96	novel
		len	cloning frequencies
			T1S1	T1S2	T2S1	T2S2	T3S1	T3S2	T4S1	T4S2	T5S1	T5S2
	----------------------TGGCTGAGACCCTAACTT----------------------------------------------	18	24	25	4	2	5	5	3	15	6	6
	----------------------TGGCTGAGACCCTAACTTT---------------------------------------------	19	-	1	-	-	-	-	-	-	-	-
rat	taggtgttagctcaaataagaaTGGCTGAGACCCTAACTTtcatacattgggtgttgctggccttctcgtttatgtttttgttcct
	**************************************************************************************
rat	.(((....(((..(((..((((.(((((.((((((((..........))))).)))..)))))))))..)))..)))......)))	1.000 -20.10

rat

chromosome:14:72277268:72277353:1

intergenic

block449695 [novel_lenNOK_cloningHIGH_loopOverlap_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	0.633	no	no	0.44/0.47	18/19/0.00	0.0	0.0	95	0	2	0	35	-4	5arm_loop_3arm	1	nd	0.28	4	96	2	na	na

		reads	miRBase family seed
seed	------------------------------------AAGGCAA---------------------------------------------------	96	novel
		len	cloning frequencies
			T4S1	T4S2
	-----------------------------------TAAGGCAATTTCCCTGCA-----------------------------------------	18	47	48
	-----------------------------------TAAGGCAATTTCCCTGCAG----------------------------------------	19	-	1
rat	tgtttgaaaactttctccaaacctggttgcttgtcTAAGGCAATTTCCCTGCAgggatgttgagccttccacgccggtgcctttgtgacagacg
	**********************************************************************************************
rat	.(((((...((.........(((.(((.....((..((((((((.((((....)))).)))..)))))..))))))))......))..))))).	0.500 -22.06

rat

chromosome:15:52831001:52831094:-1

intergenic

block607510 [novel_lenNOK_cloningHIGH_loopOverlap_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	0.075	no	no	0.50/0.53	18/19/0.00	0.0	0.0	69	0	4	0	11	-1	3arm_loop	1	nd	0.26	4	84	4	na	na

		reads	miRBase family seed
seed	-----------------------------------------------CCUCACA----------------------	84	novel
		len	cloning frequencies
			T1S1	T2S1	T2S2	T5S2
	----------------------------------------------ACCTCACACTGTGCTTGTG-----------	19	1	28	41	1
	----------------------------------------------ACCTCACACTGTGCTTGT------------	18	-	5	8	-
rat	agagtttttctaatataatacttgaggctttatttcttttctttatACCTCACACTGTGCTTGTGtcttcctctct
	****************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	ENSRNOT00000019389 ENSRNOG00000014460 Hivep1
rat	((((........(((((((((.(((((....................)))))....))).))))))......))))	0.910 -9.19

rat

chromosome:17:28452207:28452282:-1

Same_strand|Intronic_coding|ENSRNOT00000019389|ENSRNOG00000014460 ## ENSRNOG00000014460|protein_coding|Hivep1|human immunodeficiency virus type I enhancer binding protein 1 Gene [Source:MGI Symbol;Acc:MGI:96100]

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