miR-Intess: classification

other hairpins

block2122 [novel_shortStem_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	0.072	no	no	0.55/0.55	22/22/1.00	0.0	0.0	1	0	1	0	0	1	3arm	2	nd	0.24	4	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------------GAUCUUC--------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------------GGATCTTCAGAGAGCATGAGCC	22	1
celegans	ggccacaaataattcatggaggttcatctttattGGATCTTCAGAGAGCATGAGCC
	********************************************************
	.............................................<<<<<<<<<<<<<<<<<<<<<	F46F5.9 F46F5.9 F46F5.9
celegans	(((((.......(((.((((((((((.......)))))))))))))....)).)))	0.980 -14.10

celegans

chromosome:II:822482:822537:1

Opposite_strand|Boundary_non-coding|F46F5.9|F46F5.9 ## F46F5.9|protein_coding|F46F5.9|F46F5.9 [Source:RefSeq_peptide;Acc:NP_493822] ## {SimpF: WRM0622dC12 1 fosmid,WRM0626dE09 1 fosmid,WRM0627cG11 1 fosmid,F46F5.9 1 Expression_profile,WRM0638dH08 1 fosmid,WRM067dE12 1 fosmid,WRM0626dF08 1 fosmid,WRM0618cG04 1 fosmid,WRM063cA07 1 fosmid,WRM069bC02 1 fosmid}

block2322 [novel_shortStem_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	0.025	no	no	0.35/0.35	20/20/1.00	0.0	0.0	1	0	1	0	0	1	5arm	1	nd	0.25	4	1	1	na	na

		reads	miRBase family seed
seed	-UUUUAGA--------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	TTTTTAGAGTTTTCGTGTCC--------------------------------	20	1
celegans	TTTTTAGAGTTTTCGTGTCCaaatttatctggattcattaaattcgaaaaaa
	****************************************************
celegans	(((((.((((((....(((((........))))).....)))))).))))).	1.000 -10.20

celegans

chromosome:II:6078250:6078301:1

intergenic ## {SimpF: WRM0629dE02 1 fosmid,H12I13.A 1 Expression_profile,WRM0636cG08 1 fosmid,WRM0617aF06 1 fosmid,WRM0638aH12 1 fosmid,WRM0623aG07 1 fosmid,WRM066dB01 1 fosmid,WRM0613aH01 1 fosmid,WRM0636dC10 1 fosmid,WRM064bD12 1 fosmid,WRM0625bB02 1 fosmid,WRM0628bF04 1 fosmid,WRM0626dA02 1 fosmid,WRM067aH06 1 fosmid}

block8164 [novel_shortStem_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	0.217	no	no	0.30/0.30	23/23/1.00	0.0	0.0	1	0	1	0	1	15	3arm	1	nd	0.26	4	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------AUUAGAA----------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------------GATTAGAAGGTTTAGTATTGTTG-	23	1
celegans	tcggcctttcctcgattttctggaatcaaatattaattattattgatattgagggcGATTAGAAGGTTTAGTATTGTTGa
	********************************************************************************
celegans	(((((.....((.((((((((((..((.(((((((((....)))))))))...))...)))))))))).))....)))))	0.590 -15.00

celegans

chromosome:X:1668372:1668451:1

intergenic ## {SimpF: WRM066aA09 1 fosmid,WRM067dD02 1 fosmid,WRM0641aB04 1 fosmid}

block1575 [novel_shortStem_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	0.056	no	no	0.48/0.48	21/21/1.00	0.0	0.0	1	0	1	0	0	10	5arm	1	nd	0.29	4	1	1	na	na

		reads	miRBase family seed
seed	-UUCGUUA-------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	TTTCGTTAGCGTGGAGCAAGT------------------------------------------------	21	1
celegans	TTTCGTTAGCGTGGAGCAAGTactgactctggaatttagacggaacagttcttgaaacggtagaacgaa
	*********************************************************************
celegans	.(((((((.(((....((((.((((..((((.........)))).)))).))))..))).))..)))))	1.000 -18.50

celegans

chromosome:II:3303350:3303418:-1

intergenic ## {SimpF: WRM0622bD02 -1 fosmid,WRM0637bB09 -1 fosmid,WRM0639dB12 -1 fosmid,WRM0628aD03 -1 fosmid}

novel_Multihit_randfoldOK (3 loci)

block3995 [novel_Multihit_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
no	0.001	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	18	1	3arm	25	nd	0.00	0	1	1	na	na

		reads	miRBase family seed
seed	---------------------------------------------------AAAUAUA---------------------------------	1	novel
		len	cloning frequencies
			CE1
	--------------------------------------------------CAAATATAGTGACTCTGGCCGTT------------------	23	1
celegans	agtcactgttcttggtgaacggccagagtcactatatttgggccgttcacCAAATATAGTGACTCTGGCCGTTcaccaaaaatagtgactc
	*******************************************************************************************
celegans	((((((((((.((((((((((((((((((((((((((((((........)))))))))))))))))))))))))))))).)))))))))).	1.000 -71.30

celegans

chromosome:IV:448814:448904:-1

intergenic ## {Repeats: trf 19 42 0 class=trf}

block5212 [novel_Multihit_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
no	0.001	no	no	0.43/0.43	23/23/1.00	0.0	0.0	1	0	1	0	33	1	3arm	25	nd	0.00	0	1	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------AAAUAUA------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------CAAATATAGTGACTCTGGCCGTT---------------------------------	23	1
celegans	gtgcatttctgagtcactatttttggtgaacggccagagtcactatatttggtgaacggccCAAATATAGTGACTCTGGCCGTTcaccaagaacagtgactgtctcggtagacgtat
	*********************************************************************************************************************
celegans	((((.(((((((((((((.(((((((((((((((((((((((((((((((((........))))))))))))))))))))))))))))))))).))))))....)))).))).))))	0.740 -73.30

celegans

chromosome:IV:448804:448920:1

intergenic

block5429 [novel_Multihit_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
no	0.005	no	no	0.57/0.61	21/23/1.00	0.0	1.0	2	0	1	0	28	8	5arm	31	nd	0.26	3	2	1	na	na

		reads	miRBase family seed
seed	-----------------------------GUUGAGU------------------------------------------------------------------------------------	2	novel
		len	cloning frequencies
			CE1
	----------------------------TGTTGAGTGGACCAACACCCC-----------------------------------------------------------------------	21	1
	----------------------------TGTTGAGTGGACCAACACCCCGG---------------------------------------------------------------------	23	1
celegans	aggaggatacaaacaacgaccgtatcacTGTTGAGTGGACCAACACCCCGGatggagctgccaagcaattccgccgtgaatggttccaaggagacagtatggttcgtcgtaagaacctcc
	************************************************************************************************************************
	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.................................................................................	F36H12.6 F36H12.6 msp-52
celegans	.(((((......((.((((((((...((((((...(((((((.(((..((((....(((....)))...))))..)))..)))).)))....))))))))))).))).)).....)))))	0.860 -42.00

celegans

chromosome:IV:5265771:5265890:1

Same_strand|Boundary_non-coding|F36H12.6|F36H12.6 ## F36H12.6|pseudogene|msp-52|msp-52 encodes a protein that belongs to a family of proteins called the Major Sperm Proteins (MSPs) that is conserved in nematodes. this family consists of closely related, small, basic proteins that make up 15% of sperm protein. this multigene family consists of over fifty genes, including many pseudogenes. MSPs are involved in both extracellular signaling and cytoskeletal functions during reproduction-MSP antagonizes Eph/ephrin signaling, in part, by binding VAB-1 Eph receptor tyrosine kinase on oocytes and sheath cells to promote oocyte maturation and MAPK activation. MSPs assemble into fibrous networks that drive movement of the C. elegans sperm. msp genes are expressed only in late primary spermatocytes. [Source: WormBase] ## {SimpF: WRM0613dD04 1 fosmid}

novel_cloningOK_nonpairedHIGH_bulgeHIGH (3 loci)

block2733 [novel_cloningOK_nonpairedHIGH_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	0.570	no	no	0.32/0.35	19/23/0.80	0.0	1.8	5	0	1	0	16	18	5arm	1	nd	0.42	4	5	1	na	na

		reads	miRBase family seed
seed	-----------------AAAUGUG------------------------------------------------------------------------------------------------	5	novel
		len	cloning frequencies
			CE1
	----------------GAAATGTGTGAAGCTATTTGAAG---------------------------------------------------------------------------------	23	2
	----------------GAAATGTGTGAAGCTATTT-------------------------------------------------------------------------------------	19	1
	----------------GAAATGTGTGAAGCTATTTG------------------------------------------------------------------------------------	20	1
	----------------GAAATGTGTGAAGCTATTTGA-----------------------------------------------------------------------------------	21	1
celegans	gcattctctattgactGAAATGTGTGAAGCTATTTGAAGaaagttaaggaatattggaaaactaatttgcttgaggatgacgtggaaagtggaacaagtgggaggatattggagggtcgc
	************************************************************************************************************************
	<<<<<<<<<.........................................................................................................................	F26H11.5 F26H11.5 exl-1
celegans	((((((((((.((.((...((.(((....((((((.......(((.(((...(((((....)))))...)))...)))........)))))).))).))....)).)).)))))))).))	0.910 -20.36

celegans

chromosome:II:14413364:14413483:1

intergenic ## {SimpF: WRM062bF04 1 fosmid,WRM0627dC04 1 fosmid,F26H11.5 1 Expression_profile,WRM0620bB02 1 fosmid,WRM0610bH04 1 fosmid}

block3364 [novel_cloningOK_nonpairedHIGH_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	0.571	no	no	0.50/0.64	21/24/1.00	0.0 0.0	0.0 0.0	10 1	0 0	1 1	0 0	14 5	1 8	3arm 3arm	1 1	nd nd	0.41 0.50	4 5	12	1	na	na

		reads	miRBase family seed
seed	----------------------------------------------------CACCUCG----------------------------	11	novel
seed	-----------------------------------------------------------ACAACUG---------------------	1	novel
		len	cloning frequencies
			CE1
	---------------------------------------------------GCACCTCGACAACTGGCAAGGC--------------	22	10
	----------------------------------------------------------GACAACTGGCAAGGCAAAAACAGG-----	24	1
	---------------------------------------------------GCACCTCGACAACTGGCAAGG---------------	21	1
celegans	tcagcttctcaaatgctatttcagaatctgacatttgcgcttaaaattttcGCACCTCGACAACTGGCAAGGCaaaaacaggactga
	***************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<........................	F53A2.6.2 F53A2.6 ife-1
celegans	((((.((((....((((...((((....(((....((((...........))))..)))....))))...)))).....))))))))	0.530 -13.20

celegans

chromosome:III:13343435:13343521:-1

Opposite_strand|Boundary_non-coding|F53A2.6.2|F53A2.6 ## F53A2.6|protein_coding|ife-1|The ife-1 gene encodes one of five C. elegans homologs of the mRNA cap-binding protein eIF4E. it is specifically required for spermatogenesis, and is expressed in P granules. [Source: WormBase] ## {SimpF: CEOP3784 -1 Operon,WRM0629bC04 -1 fosmid,F53A2.6 -1 Expression_profile}

block5512 [novel_cloningOK_nonpairedHIGH_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	0.428	no	no	0.55/0.56	18/20/0.92	0.0	0.0	11	0	1	0	7	25	3arm	1	nd	0.35	4	12	1	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------------------------------ACGUGUG-------------------	12	novel
		len	cloning frequencies
			CE1
	-------------------------------------------------------------------------------TACGTGTGTCGAGGGTTGTG-------	20	11
	-------------------------------------------------------------------------------TACGTGTGTCGAGGGTTG---------	18	1
celegans	cgagaagatcagcgatacactggaaaaatttcgtctgtttcatgtttttgttataatgtttggaaacatttttagttgtTACGTGTGTCGAGGGTTGTGacttttt
	**********************************************************************************************************
	<<<<<<<<<<<<<<<<<<<<<<<<--------------------------------------------------------------------------------------------	T13A10.12 T13A10.12 srv-32
celegans	.(((..((((..(((((((((((...((((.....(((((((((((........)))))...)))))).....)))).))).))))))))..))))....)))...	0.500 -20.30

celegans

chromosome:IV:6281546:6281651:1

Opposite_strand|Intronic_coding|T13A10.12|T13A10.12 ## T13A10.12|protein_coding|srv-32|Serpentine Receptor, class V family member (srv-32) [Source:RefSeq_peptide;Acc:NP_500955] ## {SimpF: T13A10.12 1 Expression_profile}

Page 38

miR-Intess™

block2122 [novel_shortStem_bulgeHIGH]

block2322 [novel_shortStem_bulgeHIGH]

block8164 [novel_shortStem_bulgeHIGH]

block1575 [novel_shortStem_bulgeHIGH]

block3995 [novel_Multihit_randfoldOK]

block5212 [novel_Multihit_randfoldOK]

block5429 [novel_Multihit_randfoldOK]

block2733 [novel_cloningOK_nonpairedHIGH_bulgeHIGH]

block3364 [novel_cloningOK_nonpairedHIGH_bulgeHIGH]

block5512 [novel_cloningOK_nonpairedHIGH_bulgeHIGH]