miR-Intess: classification

noncloned miRBase miRNAs

miRNAknown_randfoldOK_bulgeHIGH (1 loci)

miRNAknown_rep_lenNOK_shortStem_nonpairedHIGH (1 loci)

cel-mir-272

block3290 (miRBase cel-mir-272) [miRNAknown_rep_lenNOK_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
miRBase cel-mir-272	0.037	no	MINISATELLITE	0.50/0.50	18/18/0.00	nd	nd	0	0	0	0	0	15	3arm	1	nd	0.35	2	0	0	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------GUAGGCA----------	0	novel
		len	cloning frequencies

cel-miR-272	------------------------------------------------------TGTAGGCATGGGTGTTTG	18
celegans	caggtatgtaggcaggcgtaggcccgtaggcaagtgtaggtctgcaggcatgaaTGTAGGCATGGGTGTTTG
	************************************************************************
	++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++	Y66A7A.8 Y66A7A.8 tbx-33
celegans	((..(((.((.((..((((..(((.((((((........)))))).)))....))))..)).)).)))..))	0.830 -23.70

celegans

chromosome:III:11637858:11637929:-1

Same_strand|Intronic_coding|Y66A7A.8|Y66A7A.8 ## Y66A7A.8|protein_coding|tbx-33|Putative T-box protein 33. [Source:UniProtKB/Swiss-Prot;Acc:O45291] ## {Repeats: CEREP52 229 224 1 class=MINISATELLITE} ## {SimpF: WRM0619bA09 -1 fosmid} ## {MIR: cel-mir-272}

miRNAknown_shortStem_bulgeHIGH (1 loci)

cel-mir-256

block6551 (miRBase cel-mir-256) [miRNAknown_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
miRBase cel-mir-256	0.058	no	no	0.38/0.38	21/21/1.00	nd	nd	0	0	0	0	3	13	3arm	1	nd	0.24	4	0	0	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------GGAAUGC----------------	0	novel
		len	cloning frequencies

cel-miR-256	------------------------------------------------------------TGGAATGCATAGAAGACTGTA---	21
celegans	gagtgcagaggcttactatgagacggtcaagaggcgcctccgtcacgtggatacgtcgggTGGAATGCATAGAAGACTGTActc
	************************************************************************************
celegans	((((((((...(((.(((((......(((...((((..((((.....))))..))))...)))....)))))))).))))))))	0.800 -28.80

celegans

chromosome:V:6956037:6956120:-1

intergenic ## {SimpF: WRM061aB06 -1 fosmid,WRM0617cA05 -1 fosmid,WRM0639bB06 -1 fosmid} ## {MIR: cel-mir-256}

miRNAknown_shortStem_mirtron_randfoldOK (1 loci)

cel-mir-1018

block8179 (miRBase cel-mir-1018) [miRNAknown_shortStem_mirtron_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
miRBase cel-mir-1018	0.001	no	no	0.41/0.41	22/22/1.00	nd	nd	0	0	0	0	0	3	3arm	1	0	0.14	2	0	0	na	na

		reads	miRBase family seed
seed	---------------------------------------------------------------GAGAGAU------------------------------	0	novel
		len	cloning frequencies

cel-miR-1018	--------------------------------------------------------------AGAGAGATCAT--------TGGACTTACAG--------	22
celegans	----GTAAGTT----------------CATGATTTCTCCCATATATTTT--------TCATGAGAGAGATCAT--------TGGACTTACAG--------
cremanei	TTTTGTAGTTG----------------ATCAATTTTTTGTACGGATTTT--------TC-CGAGAGAGATATA--------GCAATGCAAAG--------
cbriggsae	---------------------------AACGAATTTTCGAA---ATTCTCACCAAAATCAAAAGATAGA------------GAGATTTGGAATATTTGGA
ppacificus	----ATGGTCTGACTCTCTCTATTTGTCATGATCTCTCGTC---ACTCTGAC-----TGACAAGAGAGATCATTGAGAAATGAGATACGAAATGAGCAT-
	* * * * * * * * * * *
	>>>>> +++++++ ++++++++++++++++++++++ ++++++++++++++++ +++++++++++ >>>>>	Y59E1B.1 Y59E1B.1 Y59E1B.1
celegans	((((((( (((((((((((.(((....... ..))).))))))))). )))))))))..	1.000 -23.80
cremanei	.((((((.((( ....(((((((...((((.... )) )).)))))))... .))))))))).	0.998 -13.80
cbriggsae	..(((((((((((( .(((((.................)) ))).))))))).)))))..	1.000 -11.13
ppacificus	(((.((......((((.((((.((((((((((((((( (....... ))))..)))))))))).)).))))))))........)).)))	0.999 -27.74

celegans	chromosome:X:1879453:1879508:1	Same_strand\|Intronic_coding\|Y59E1B.1\|Y59E1B.1 ## Y59E1B.1\|protein_coding\|Y59E1B.1\|Y59E1B.1 [Source:RefSeq_peptide;Acc:NP_508345] ## {SimpF: Y59E1B.B 1 Expression_profile,WRM066aD05 1 fosmid,WRM0616aC07 1 fosmid,WRM0632cB03 1 fosmid,WRM0624cF08 1 fosmid} ## {MIR: cel-mir-1018}
cremanei	chromosome:chrUn:5614830:5614925:-1	intergenic
cbriggsae	chromosome:chrV:11080045:11080140:-1	Same_strand\|Intronic_coding\|NM_017182 ## Opposite_strand\|Intronic_coding\|NM_001041377 ## Opposite_strand\|Boundary_non-coding\|NM_073057
ppacificus	chromosome:chrUn:57741498:57741584:-1	intergenic

miRNAknown_shortStem_randfoldOK (1 loci)

sblock32 (miRBase cel-mir-1832) [miRNAknown_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
miRBase cel-mir-1832	0.001	no	no	0.57/0.57	21/21/1.00	nd	nd	0	0	0	0	0	10	3arm	3	nd	0.15	2	0	0	na	na

		reads	miRBase family seed
seed	-------------------------------------------------------------------------GGGCGGA---------------------------------	0	novel
		len	cloning frequencies

cel-miR-1832	------------------------------------------------------------------------TGGGCGGAGCGAA--TCGATGAT------------------	21
celegans	----------------------CAGCGATTCGAACTCCG----CCCACTGCACC-TGATTGGTTGA--CAAGTGGGCGGAGCGAA--TCGATGAT------------------
cremanei	-----------------GTCTCCATCAATCAGATTTCTCGCATTCCGCCCGTTTACAATCGGTTGGGCGGGACGGGCGGAACGAGCTCCTTTGATATGGAGAC----------
cbriggsae	----------------GATTTTGAGCAATTTTGAGCCAAAACTTAGGCTCCAT--CCATTTTCAAT--AAAGTGGGCGGAGCCTATTTTGAAGTCAAGTAAACTGAAATTC--
cbrenneri	GATGCTTCTGAGAGTGGA-----AAATACTGAAATTTCCAGCCCTCACTGC---------AGCCTG--AAAGGGGGCGGAGCCAG--ATGAAGATTTCCAGACTTACAGGCTC
cjaponica	----TTCCTTCGAGTTGCATCATAAAAACATAAGTCTGCA---TTCACTGCGTGATCGTGCGCAAA--TGAGTGGGCGGAGTATCAGTTTTTGATGATGCAACTTGATTGAA-
ppacificus	---------GAGACCGTCTCTCCATTCACAATGGTCT------CTCGCTTCTC--TGACCAGCGAG--AGAGCGGGCGGAATGGA-------------GAGACGTTGGTTCTC
	* * * *******
	+++++ +++++++++++++++++ +++++++++++ +++++++++++ +++++++++++++++++ ++++++++ +++++	C18D11.4.1 C18D11.4 rsp-8
	+++++ +++++++++++++++++ +++++++++++ +++++++++++ +++++++++++++++++ ++++++++ +++++	C18D11.4.2 C18D11.4 rsp-8
celegans	((.(((((((..((((( ((((((.(((( .....)).)). ..))))))))))))))) ))).))..	1.000 -36.50
cremanei	((((((((..((((((...((((..((((((((((((.(((....)))....))))))))))))))))....))))))))))))))	1.000 -41.10
cbriggsae	((.(((.((....(((((..(((((..((((((((.. (((((((.... )))))))..)))))))))))))...)))))....)).))).))	0.859 -29.30
cbrenneri	...((((.((((..(((( ((...(((....((((.((((((..... ...... ...)))))))))).))) .......))))))..)))).))))..	0.961 -26.34
cjaponica	.((..(((((((((((((((((((((((..(((((( ((((.(((((......))))).. )))))..))))).)))..))))))).)))))))))))))..)).	0.988 -41.00
ppacificus	((((((((((((((((((....((.((( ((((((.... .....)))))) ))).))....))))))) )))))...))).)))	1.000 -43.40

celegans	chromosome:III:11829129:11829192:1	Same_strand\|Intronic_coding\|C18D11.4.1\|C18D11.4 ## C18D11.4\|protein_coding\|rsp-8\|SR Protein (splicing factor) family member (rsp-8) [Source:RefSeq_peptide;Acc:NP_499533] ## {Repeats: Ce000171 235 256 1 class=___CEMUDR1_DNA/MuDR,Ce000171 226 250 -1 class=___CEMUDR1_DNA/MuDR,Ce000171 185 206 -1 class=___CEMUDR1_DNA/MuDR,Ce000171 191 215 1 class=___CEMUDR1_DNA/MuDR} ## {SimpF: C18D11.4 1 Expression_profile} ## {MIR: cel-mir-1832}
cremanei	chromosome:chrUn:65023147:65023232:1	Opposite_strand\|Exonic_coding\|NM_067756
cbriggsae	chromosome:chrIII:10672897:10672987:1	Same_strand\|Intronic_coding\|NM_170975 ## Opposite_strand\|Intronic_coding\|NM_075402
cbrenneri	chromosome:chrUn:155643736:155643830:-1	intergenic
cjaponica	chromosome:chrUn:97024069:97024171:-1	Same_strand\|Intronic_coding\|NM_068550 ## Opposite_strand\|Intronic_coding\|NM_069102
ppacificus	chromosome:chrUn:170143661:170143741:-1	Opposite_strand\|Intronic_coding\|NM_000209

miRNAknown_shortStem_randfoldOK_nonpairedHIGH_bulgeHIGH (1 loci)

cel-mir-1834

block4331 (miRBase cel-mir-1834) [miRNAknown_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
miRBase cel-mir-1834	0.001	no	no	0.39/0.39	23/23/1.00	nd	nd	0	0	0	0	0	7	3arm	1	nd	0.36	6	0	0	na	na

		reads	miRBase family seed
seed	--------------------------------------------------------GAGAUCA-----------------------------	0	miR-80/81/82
		len	cloning frequencies

cel-miR-1834	-------------------------------------------------------AGAGATCAA-------CCATTGAGATCCAA-------	23
celegans	----TGAC------------TCGGTGTGTGATCTCTTACCGTTTTA---TGGATAAGAGATCAA-------CCATTGAGATCCAA-------
cbriggsae	--ATTGGC------------TTGTTATCTGGTCTCATAACTACTTTTCCTGGTTATGAGATCAT-------TTAATGAG-CCCAA-------
cbrenneri	---TTGAC------------CTTATGGTTGATCTCCTACCGACTAG---CGGATAAGAGATCAC---------CATGGGGTACAA-------
ppacificus	GATCTGACCGGACTCTCTCACTTTCGCATGCTCTCTCGCTGTCTCTGA-CCGACGAGAGATCATGGCGAAGTGAGAGAGTCTCGAGCGAGTT
	** * ** * * ******* * * * *
celegans	...( ((((((..((((((((((((((...) ))).)))))))))). .)))))))......	1.000 -25.90
cbriggsae	...((( (..(((..((((((((((((((.......)))))))))))))). .)))..)) ))...	1.000 -29.80
cbrenneri	.(((( (((((((.(((((((.(((((..... ))).)).)))))))) )))))))).)).	1.000 -27.70
ppacificus	((..((..(((((((((((((.((((((((.(((((((..(((...)) )...))))))).)))).))))))))))))))).))..))..))	1.000 -44.70

celegans	chromosome:IV:6660445:6660503:-1	intergenic ## {SimpF: WRM068bB04 -1 fosmid,WRM067cF04 -1 fosmid} ## {MIR: cel-mir-1834}
cbriggsae	chromosome:chrIV:157146:157244:1	Same_strand\|Intronic_coding\|NM_071218 ## Opposite_strand\|Intronic_coding\|NM_001085890
cbrenneri	chromosome:chrUn:96588142:96588240:1	intergenic
ppacificus	chromosome:chrUn:134149351:134149441:-1	intergenic

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noncloned miRBase miRNAs:

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miR-Intess™