miR-Intess: classification

other hairpins

block1726 [novel_shortStem]

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	0.448	no	no	0.45/0.45	20/20/1.00	0.0	0.0	1	0	1	0	4	10	3arm	1	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------UCAUGAG----------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------------GTCATGAGAAGCAGAGAACT----	20	1
celegans	tttcaacttcctctcgttcctcgacaattaaaatttcatcggttttctcccagcaacggattgacttGTCATGAGAAGCAGAGAACTgaaa
	*******************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-----------	F13H8.2 F13H8.2 F13H8.2
celegans	.((((.....((((.(((.(((((((..............((((...(((.......)))..))))))))..))).)))))))...)))).	0.690 -14.23

celegans

chromosome:II:6272699:6272789:-1

Opposite_strand|Boundary_coding|F13H8.2|F13H8.2 ## F13H8.2|protein_coding|F13H8.2|F13H8.2 [Source:RefSeq_peptide;Acc:NP_495256] ## {SimpF: WRM0634bD11 -1 fosmid,WRM0613aG12 -1 fosmid,WRM065aE09 -1 fosmid,WRM0625cD01 -1 fosmid,WRM0628bC05 -1 fosmid,WRM0615dG11 -1 fosmid,F13H8.2 -1 Expression_profile,WRM0638cF02 -1 fosmid,WRM0636cH12 -1 fosmid,yk272f12 -1 RNAi,WRM0626bD10 -1 fosmid,WRM064aE02 -1 fosmid,WRM0615cA09 -1 fosmid,WRM066cH09 -1 fosmid,WRM0614cA10 -1 fosmid}

block1809 [novel_shortStem]

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	0.392	no	no	0.57/0.57	21/21/1.00	0.0	0.0	1	0	1	0	1	16	3arm	1	nd	0.19	1	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------UCACGUG--------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------------TTCACGTGAGTTGCGGGTCTG-	21	1
celegans	cggttgctctcatttcatatgtgcgttttcaagaattgcatttacgtaacttaaatgttttggtgaaTTCACGTGAGTTGCGGGTCTGa
	*****************************************************************************************
celegans	(((..((((.((.(((((..(((.(((((((((....(((((((.......)))))))))))).)))).)))))))).)).))))))).	0.930 -18.10

celegans

chromosome:II:8276052:8276140:-1

intergenic ## {SimpF: WRM0634dB04 -1 fosmid,WRM0625bG03 -1 fosmid,WRM0614aF08 -1 fosmid,WRM0612dD10 -1 fosmid,WRM0624bG11 -1 fosmid,WRM0619bF12 -1 fosmid,WRM063dG12 -1 fosmid,WRM065cC06 -1 fosmid,WRM0639dG09 -1 fosmid,WRM0629cC06 -1 fosmid,WRM0631cB08 -1 fosmid,WRM067bE01 -1 fosmid,WRM0615aG04 -1 fosmid,WRM0641bG04 -1 fosmid,WRM0627cB10 -1 fosmid,WRM0621dD11 -1 fosmid,WRM0632bG11 -1 fosmid}

block2085 [novel_shortStem]

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	0.027	no	no	0.30/0.30	20/20/1.00	0.0	0.0	3	0	1	0	2	13	5arm	1	nd	0.20	2	3	1	na	na

		reads	miRBase family seed
seed	---UAGGAGU--------------------------------------------------------------------	3	novel
		len	cloning frequencies
			CE1
	--TTAGGAGTCGTCAAATTTTT--------------------------------------------------------	20	3
celegans	tgTTAGGAGTCGTCAAATTTTTtgatttttttacagcaattgtgtggaaatttcagtaattttagtacaatttctaat
	******************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	C38C6.4 C38C6.4 sre-13
celegans	.(((((((((.((.(((((..((((..((((((((.......))))))))..)))).)))))....)).)))))))))	0.990 -15.40

celegans

chromosome:II:14635643:14635720:-1

Same_strand|Intronic_coding|C38C6.4|C38C6.4 ## C38C6.4|protein_coding|sre-13|Serpentine receptor class epsilon-13 (Protein sre-13). [Source:UniProtKB/Swiss-Prot;Acc:O45300] ## {Repeats: dust 30394 30398 0 class=dust} ## {SimpF: C38C6.4 -1 Expression_profile,WRM069dE06 -1 fosmid,WRM0627aA11 -1 fosmid,WRM062cC10 -1 fosmid,WRM063bG01 -1 fosmid,WRM061cA06 -1 fosmid,WRM068cG04 -1 fosmid,WRM064aD11 -1 fosmid,WRM061cA01 -1 fosmid,WRM0628bA03 -1 fosmid,WRM0613bH08 -1 fosmid}

block2210 [novel_shortStem]

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	0.377	no	no	0.48/0.48	23/23/1.00	0.0	0.0	2	0	1	0	2	13	5arm	1	nd	0.26	3	2	1	na	na

		reads	miRBase family seed
seed	---CUUGUGA------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	--GCTTGTGACATTTGACGCCTTTG---------------------------------------------------------------	23	2
celegans	caGCTTGTGACATTTGACGCCTTTGaaaagctgctttgtcctcaaagcatgataggttccgggttgaaaaaaatgttttcagtcggct
	****************************************************************************************
celegans	.((((((.(((((((...((((..(((....(((((((....))))))).......))).))))......)))))))..))...))))	0.600 -18.80

celegans

chromosome:II:3373793:3373880:1

intergenic ## {SimpF: WRM0636cD03 1 fosmid,WRM0610dH04 1 fosmid,WRM069bC03 1 fosmid,WRM0613aE01 1 fosmid,WRM0631bH09 1 fosmid}

block3094 [novel_shortStem]

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	0.611	no	no	0.57/0.57	23/23/1.00	0.0	0.0	1	0	1	0	4	15	5arm	1	nd	0.30	3	1	1	na	na

		reads	miRBase family seed
seed	-----GGUGAUU-----------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----GGGTGATTGCGGCCAATCTGAGT--------------------------------------------------------------------------------------	23	1
celegans	atccGGGTGATTGCGGCCAATCTGAGTcacgtcgttctcaacttctgcaattgttgcggcgacatcttctgtgacctgaatgctgccaatttaaatcaagaaaaatgcaagga
	*****************************************************************************************************************
	---------------------------------------------------------------------------------------------------------------------------	C18H2.1 C18H2.1 C18H2.1
celegans	.(((..(((((((((((...((...(((((((((.((.((((..........)))).)))))).......)))))..))..))))).))))...............))..)))	0.640 -24.27

celegans

chromosome:III:7670379:7670491:-1

Opposite_strand|Intronic_coding|C18H2.1|C18H2.1 ## C18H2.1|protein_coding|C18H2.1|C18H2.1 [Source:RefSeq_peptide;Acc:NP_498674] ## {SimpF: WRM0612dH07 -1 fosmid,WRM0623dA11 -1 fosmid,WRM064aE12 -1 fosmid,WRM061cG07 -1 fosmid,WRM0633bE08 -1 fosmid,WRM0613dD12 -1 fosmid,WRM0622cC10 -1 fosmid,WRM067aF03 -1 fosmid,WRM0633cH11 -1 fosmid,WRM0613bE05 -1 fosmid}

block3123 [novel_shortStem]

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	0.390	no	no	0.38/0.38	21/21/1.00	0.0	0.0	2	0	1	0	3	5	3arm	1	nd	0.24	3	2	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------AGAAUUU----------------	2	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------GAGAATTTGAGATGCTAATGG---	21	2
celegans	cttgtagtactcgtaaggtgggatttgttccatatacgacattgatggaGAGAATTTGAGATGCTAATGGagg
	*************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<....................................	C02F5.5 C02F5.5 C02F5.5
celegans	(((.(((((((((........(((((.((((((...........)))))).))))))))).)))))...))).	0.720 -13.60

celegans

chromosome:III:8236101:8236173:-1

intergenic ## {SimpF: WRM0610bE09 -1 fosmid,C02F5.5 -1 Expression_profile,WRM0628dD12 -1 fosmid,WRM064cD03 -1 fosmid,WRM0619cF04 -1 fosmid,WRM0620aC12 -1 fosmid,WRM0633aA03 -1 fosmid,WRM0633aE10 -1 fosmid}

block3185 [novel_shortStem]

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	0.093	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	3	0	3arm	1	nd	0.19	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------CCAAACA----------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------GCCAAACAATGAGGTCGAACT---	21	1
celegans	ttctgttcgtttttagtgataagtttgagcgaaaatGCCAAACAATGAGGTCGAACTgaa
	************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<----------	F55H2.4 F55H2.4 lrg-1
celegans	.((.(((((.(((((.......(((((.((......)))))))..))))).))))).)).	0.710 -12.90

celegans

chromosome:III:9504752:9504811:-1

Opposite_strand|Boundary_non-coding|F55H2.4|F55H2.4 ## F55H2.4|pseudogene|lrg-1|lrg-1 encodes a truncated paralog of let-99, a protein with a DEP domain (Domain found in Dishevelled, Egl-10, and Pleckstrin). lrg-1(RNAi) animals have no obvious phenotype. since the nucleotide similarity of lrg-1 to let-99 extends beyond the lrg-1 CDS, and since lrg-1 has no obvious function in RNAi assays, this gene may be decaying towards pseudogene status. [Source: WormBase] ## {SimpF: WRM0637cA05 -1 fosmid,WRM0616bE10 -1 fosmid,WRM0611cG01 -1 fosmid,WRM0618aH06 -1 fosmid}

block4206 [novel_shortStem]

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	0.676	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	2	13	5arm	2	nd	0.24	2	1	1	na	na

		reads	miRBase family seed
seed	---AAAUAUG----------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--GAAATATGATGAGCCCGTTGG---------------------------------------------------------	21	1
celegans	cgGAAATATGATGAGCCCGTTGGactatctgcatgtcactttgctgctcattggcccgaaggcgatcgaagtattgttcc
	********************************************************************************
celegans	.((((((((..((((((..((((.(((...(((.((......)))))....))).)))).)))..)))..)))))..)))	0.670 -17.60

celegans

chromosome:IV:5217566:5217645:-1

intergenic ## {SimpF: WRM0616bF04 -1 fosmid,WRM0632cH10 -1 fosmid,WRM067dF01 -1 fosmid,yk578d4 -1 RNAi}

block4310 [novel_shortStem]

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	0.309	no	no	0.59/0.59	22/22/1.00	0.0	0.0	1	0	1	0	4	0	5arm	1	nd	0.27	2	1	1	na	na

		reads	miRBase family seed
seed	-----AGCUGAG---------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----GAGCTGAGGTAGAAGAAGCCGG-------------------------------------	22	1
celegans	tcttGAGCTGAGGTAGAAGAAGCCGGcattctggttgtatctgtaaatataacagtgtttaga
	***************************************************************
celegans	(((...((((..(((..(((((((((....))))))...))).....)))..))))....)))	0.840 -12.20

celegans

chromosome:IV:6353974:6354036:-1

intergenic

block4327 [novel_shortStem]

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	0.330	no	no	0.50/0.50	20/20/1.00	0.0	0.0	1	0	1	0	4	16	3arm	1	nd	0.20	2	1	1	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------UAUCCAU----------------	1	novel
		len	cloning frequencies
			CE1
	------------------------------------------------------------------GTATCCATCGTCTGCCATTC----	20	1
celegans	tggaggaaccatcgtgggcatcggtgatgcaagaggaggcaccgaatagacgggaccaattacttcGTATCCATCGTCTGCCATTCtttt
	******************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...........	F38A5.8 F38A5.8 F38A5.8
celegans	.(((((((........((((.((((((((((((((..((..(((......)))..))..)).))).))))).))))..)))).)))))))	0.510 -24.60

celegans

chromosome:IV:6599860:6599949:-1

Opposite_strand|Boundary_non-coding|F38A5.8|F38A5.8 ## F38A5.8|protein_coding|F38A5.8|F38A5.8 [Source:RefSeq_peptide;Acc:NP_501014] ## {SimpF: F38A5.8 -1 Expression_profile,WRM0626bB10 -1 fosmid,WRM0640dC01 -1 fosmid,WRM0618cA01 -1 fosmid}

Page 16

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Page 45

miR-Intess™

block1726 [novel_shortStem]

block1809 [novel_shortStem]

block2085 [novel_shortStem]

block2210 [novel_shortStem]

block3094 [novel_shortStem]

block3123 [novel_shortStem]

block3185 [novel_shortStem]

block4206 [novel_shortStem]

block4310 [novel_shortStem]

block4327 [novel_shortStem]