miR-Intess: classification

other hairpins

novel_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

block7530 [novel_rep_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	Satellite	0.23/0.23	22/22/1.00	0.0	0.0	1	0	1	0	16	6	5arm	1	nd	0.18	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------AGUCUUU--------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----------------------TAGTCTTT-ATCAAAATT----TTTGG-------------------------------------------------------------------------	22	1
celegans	AATTCCC--ATC----TCCCGTTAGTCTTT-ATCAAAATT----TTTGGAA--------TTTTCGCCAAAAAATGCTCCAAATTTTTTA---ATAAATACTAACAGGATTTTAAGGAGAATA
cbriggsae	-------------GAAGACTTGTAGTCTTT--CTGGAAAT----TTCGAAA------------TCGCGAAT-----TTCGGAATGTTCC---GGAAATGCTAT-------------------
cjaponica	----------------------GAGTCTTTAATTGGGGTTAAAATTTAAAA-----------------------TTTCAAAACAATTTT------AATAACAACAAAGATTA----------
cbrenneri	---------ATC----TCCTGGTAGTCTTT--------TT----CTCGAAAACT---TTTTTTTTGCGAAA-------AAAAAATTTTC---AAAAAGACTGCCAGGAGAT-----------
ppacificus	----------------------TAGTCTTT-GCTGG--TT----TATG------------TTTTCGTATGAGATTAGCAAACAAATTTTGACATGAATCGTGTAAAGTATCTA---------
cremanei	AATTCTCCTATCAAAATCCTGTCAGTCTTTCCACAAAATT----TTTGAAAAATAAACATTTTTTGAAACT-------CAAAAATTCTTGGGGAAAAGACTAGCAGGAGATG----AGAATT
	******* * * **
celegans	.(((((( ... (((.((((((.((( ((.((((.. ((((((( ((((......)))))..))))))..)))). ))))).)))))).)))......)).)))).	1.000 -24.40
cbriggsae	........(((((.((( (((((((( ((((((( (.....)) )))))))).)))) ))))).)))))	0.984 -23.80
cjaponica	.(((((((..(((..(((((((((..... .........)))))) )))..))).))))))).	1.000 -10.54
cbrenneri	((( (((((((((((((( (( ...(((((.( (((((((....))) ))))).))))) )))))))))))))))))))	0.999 -35.10
ppacificus	(((.(((( ((((( (( (((( ((.......((((((........))))))))))))))))).))))))...)))	0.899 -16.01
cremanei	(((((((..(((....(((((..(((((((((.((((((( (((((....((((.....))))....) )))))))).))).))))).))))..))))))))) ))))))	0.978 -32.30

celegans	chromosome:V:18903559:18903658:1	intergenic
cbriggsae	chromosome:chrI_random:2087620:2087683:1	Opposite_strand\|Intronic_coding\|NM_061066 ## {Repeats: MINISAT2_CB -89 261 -1 class=Satellite}
cjaponica	chromosome:chrUn:34095197:34095336:1	Same_strand\|Intronic_coding\|NM_013186 ## Same_strand\|Boundary_coding\|NM_001029376 ## Opposite_strand\|Intronic_coding\|NM_141224
cbrenneri	chromosome:chrUn:56194936:56195008:-1	intergenic
ppacificus	chromosome:chrUn:5097754:5097825:1	intergenic
cremanei	chromosome:chrUn:45892912:45893018:1	intergenic

novel_shortStem_5varHIGH_nonpairedHIGH_bulgeHIGH (1 loci)

block1069 [novel_shortStem_5varHIGH_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	0.331	no	no	0.46/0.50	22/24/1.00	1.7	2.3	3	0	1	0	4	1	5arm	1	nd	0.38	6	3	1	na	na

		reads	miRBase family seed
seed	-----UUAAGUU------------------------------------------------------------	2	novel
seed	----------UUGCGCG-------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	----GTTAAGTTGCGCGTCCAAGAGT----------------------------------------------	22	2
	---------GTTGCGCGTCCAAGAGTAAAAGTT---------------------------------------	24	1
celegans	caatGTTAAGTTGCGCGTCCAAGAGTAAAAGTTgcgaaataacaaggttttggaaggtaatgattattttga
	************************************************************************
celegans	(((.((...(((((...(((((((......((((.....))))....)))))))..)))))....)).))).	0.960 -10.40

celegans

chromosome:I:9576072:9576143:1

intergenic ## {SimpF: WRM0639cA02 1 fosmid,WRM065dH12 1 fosmid,WRM065bH01 1 fosmid,WRM0629cA06 1 fosmid,WRM0623cA08 1 fosmid,WRM0633bG11 1 fosmid,WRM0616bC07 1 fosmid}

novel_shortStem_loopOverlap (1 loci)

block5299 [novel_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	0.043	no	no	0.50/0.50	22/22/1.00	0.0	0.0	1	0	1	0	0	-1	5arm_loop	1	nd	0.23	2	1	1	na	na

		reads	miRBase family seed
seed	-AGGAUUU--------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	GAGGATTTGAGTGTAGGCGAAC------------------------------	22	1
celegans	GAGGATTTGAGTGTAGGCGAACgcaacactttcgtgatgcttaatttttctc
	****************************************************
celegans	(((((.((((((((..(((((.........))))).)))))))).)))))..	0.920 -13.40

celegans

chromosome:IV:3052192:3052243:1

intergenic ## {SimpF: WRM0636bG07 1 fosmid}

novel_shortStem_loopOverlap_randfoldOK (1 loci)

block5151 [novel_shortStem_loopOverlap_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	0.46/0.46	24/24/1.00	0.0	0.0	1	0	1	0	0	-3	3arm_loop	1	nd	0.17	2	1	1	na	na

		reads	miRBase family seed
seed	-----------------------------AUGAUUG----------------	1	novel
		len	cloning frequencies
			CE1
	----------------------------GATGATTGTTGGGTCGCCTTTTGT	24	1
celegans	agcaaatgcaggcgagaacgacgattatGATGATTGTTGGGTCGCCTTTTGT
	****************************************************
celegans	.(((((...((((((...((((((((.....))))))))..)))))))))))	0.920 -18.60

celegans

chromosome:IV:16867530:16867581:-1

intergenic ## {SimpF: WRM0621bE04 -1 fosmid}

novel_shortStem_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

block287 [novel_shortStem_loopOverlap_randfoldOK_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	0.001	no	no	0.33/0.33	24/24/1.00	0.0	0.0	1	0	1	0	0	-3	5arm_loop	1	nd	0.42	4	1	1	na	na

		reads	miRBase family seed
seed	-UUAUCAU------------------------------------	1	novel
		len	cloning frequencies
			CE1
	GTTATCATCAGCCATTATATCGAA--------------------	24	1
celegans	GTTATCATCAGCCATTATATCGAAagatgttaagctgaaaataa
	********************************************
	<<<<<<<<<<<<<<<<<<<<..................................	F26B1.5 F26B1.5 F26B1.5
celegans	.((((..(((((....(((((....)))))...)))))..))))	1.000 -13.50

celegans

chromosome:I:6309087:6309130:-1

Opposite_strand|Boundary_non-coding|F26B1.5|F26B1.5 ## F26B1.5|protein_coding|F26B1.5|F26B1.5 [Source:RefSeq_peptide;Acc:NP_001040654] ## {SimpF: WRM069bF08 -1 fosmid,WRM0617dB09 -1 fosmid,WRM0615bH10 -1 fosmid,WRM066bD04 -1 fosmid,WRM0611aC11 -1 fosmid,WRM0629aE03 -1 fosmid,WRM0627dG12 -1 fosmid}

novel_shortStem_randfoldOK (1 loci)

block4130 [novel_shortStem_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	0.003	no	no	0.50/0.50	24/24/1.00	0.0	0.0	1	0	1	0	2	29	5arm	1	nd	0.25	3	1	1	na	na

		reads	miRBase family seed
seed	---UGUGUGU---------------------------------------------------------------------------------------------------------	1	novel
		len	cloning frequencies
			CE1
	--GTGTGTGTGTGCAGTAGGCAATTG-----------------------------------------------------------------------------------------	24	1
celegans	gcGTGTGTGTGTGCAGTAGGCAATTGagaaaagtcagaaataattcaatttttcgcaatttctcgtaaaatcgattttttggttttttttgttttgccatgtttttgccacgcgt
	*******************************************************************************************************************
	<<<<<<<<<<<<<<<<<............................................................................................................	Y24D9B.1 Y24D9B.1 Y24D9B.1
celegans	(((((((.(((.(((...(((((.((((((((..((((((....((.(((((.((........)).))))).)).))))))..))))))))..))))).)))...))))))))))	0.870 -32.40

celegans

chromosome:IV:4317308:4317422:-1

Opposite_strand|Boundary_non-coding|Y24D9B.1|Y24D9B.1 ## Y24D9B.1|protein_coding|Y24D9B.1|Y24D9B.1 [Source:RefSeq_peptide;Acc:NP_500540] ## {SimpF: WRM0621dF06 -1 fosmid}

novel_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

block4789 [novel_shortStem_randfoldOK_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	0.009	no	no	0.48/0.48	21/21/1.00	0.0	0.0	2	0	1	0	1	12	3arm	1	nd	0.33	4	2	1	na	na

		reads	miRBase family seed
seed	------------------------------------------------------GUGUCCU--------------	2	novel
		len	cloning frequencies
			CE1
	-----------------------------------------------------TGTGTCCTTGGTCGAGTTTTG-	21	2
celegans	taaaatctgaaccaaaaaactttgaaagttgaagaaatccacttcacttacaaTGTGTCCTTGGTCGAGTTTTGa
	***************************************************************************
	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	LLC1.1 LLC1.1 tra-3
celegans	(((((..((.(((((...((.(((.(((.(((((.......)))))))).))).))....)))))))..))))).	1.000 -16.40

celegans

chromosome:IV:14439571:14439645:-1

Same_strand|Intronic_coding|LLC1.1|LLC1.1 ## LLC1.1|protein_coding|tra-3|tra-3 encodes an atypical calpain regulatory protease that lacks calcium-binding EF hand domains. during development, TRA-3 likely promotes female development in XX hermaphrodites by cleaving the membrane-associated TRA-2A protein to generate a TRA-2 peptide likely to have feminizing activity. in addition, TRA-3 is one of several proteases that mediate necrotic cell death during neurodegeneration. [Source: WormBase] ## {SimpF: WRM0622dH07 -1 fosmid,WRM0610aG11 -1 fosmid,[cgc5513]:LLC1 -1 RNAi,LLC1.1 -1 Expression_profile}

Page 45

miR-Intess™

block7530 [novel_rep_randfoldOK]

block1069 [novel_shortStem_5varHIGH_nonpairedHIGH_bulgeHIGH]

block5299 [novel_shortStem_loopOverlap]

block5151 [novel_shortStem_loopOverlap_randfoldOK]

block287 [novel_shortStem_loopOverlap_randfoldOK_nonpairedHIGH_bulgeHIGH]

block4130 [novel_shortStem_randfoldOK]

block4789 [novel_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH]