logoC.elegans small RNAs


miR classification

Alignments

other hairpins

novel_nonpairedHIGH_bulgeHIGH (27 loci)

block4273 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.219nono0.20/0.2020/20/1.000.0
0.0
1
0
1
0
8
0
3arm
1
nd
0.35
4
11nana
  readsmiRBase family seed
seed     -----------------------------------------UAUCUCA--------------------     1novel
  lencloning frequencies
   CE1
      ----------------------------------------TTATCTCATAATTTTCTGAT--------     201
celegans     agatagtttttaaattgttatgatatgaaattagtttcgaTTATCTCATAATTTTCTGATacgctatt      
      ********************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C39H7.9 C39H7.9 srsx-16
celegans     .((((((..(((....(((((((.((((............)))).)))))))....)))...))))))     1.000 -8.90

celeganschromosome:IV:5617094:5617161:-1Same_strand|Intronic_coding|C39H7.9|C39H7.9 ## C39H7.9|protein_coding|srsx-16|Serpentine Receptor, class SX family member (srsx-16) [Source:RefSeq_peptide;Acc:NP_001023055] ## {SimpF: WRM0627bB10 -1 fosmid,WRM068bC07 -1 fosmid}


block4790 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.297nono0.25/0.2520/20/1.000.0
0.0
1
0
1
0
27
10
3arm
1
nd
0.40
4
11nana
  readsmiRBase family seed
seed-----------------------------------------------------------------------UAAUUCC---------------------------------------1novel
  lencloning frequencies
   CE1
 ----------------------------------------------------------------------TTAATTCCTTCTGAAATAAC---------------------------201
celeganscttacactttaaaaatttgaaattactgtttcacaaaagtggtaaattttctggaaattttcacatctaaTTAATTCCTTCTGAAATAACaaggctaattttgaatgtaatttgtga 
 ********************************************************************************************************************* 
celegans.(((((..(((...(((..((((((((((((((...(((..((.((((...((((.....)).))...)))).))..))).)))))).....)).))))))..))).)))..)))))0.510 -16.70

celeganschromosome:IV:14444301:14444417:-1intergenic ## {SimpF: WRM0622dH07 -1 fosmid,WRM0610aG11 -1 fosmid}


block4856 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.268nono0.35/0.3520/20/1.000.0
0.0
1
0
1
0
16
2
5arm
1
nd
0.45
4
11nana
  readsmiRBase family seed
seed     -----------------GUUAUUG----------------------------------------------------------------     1novel
  lencloning frequencies
   CE1
      ----------------TGTTATTGTTTCCAGCTTTG----------------------------------------------------     201
celegans     catattttttttacaaTGTTATTGTTTCCAGCTTTGacttaccgcatattgttgttgctcaaatggcaccattgacaaaattgtgtgt      
      ****************************************************************************************      
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24a.1 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.3 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24h Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.8 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.10 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24a.4 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.5 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.1 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24a.3 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.6 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.2 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24e.2 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24e.1 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24g Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.9 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.4 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24a.2 Y57G11C.24 eps-8
 -----------------------------------------------<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y57G11C.24d.7 Y57G11C.24 eps-8
celegans     (((((..((((..(((((....((((...(((..((((............))))..))).....)))).)))))..))))..))))).     0.420 -12.90

celeganschromosome:IV:14894932:14895019:-1Opposite_strand|Intronic_coding|Y57G11C.24e.1|Y57G11C.24 ## Y57G11C.24|protein_coding|eps-8|eps-8 is predicted to encode five protein isoforms with similarity to mouse epidermal growth factor receptor kinase substrate that affects embryonic viability, growth, locomotion, osmoregulation, and larval viability. interacts with GEX-3 in yeast two-hybrid assays. [Source: WormBase] ## {SimpF: [cgc5194]:gei-19 -1 RNAi,WRM061bG05 -1 fosmid,WRM0617dG08 -1 fosmid,yk393c10 -1 RNAi,WRM066cF03 -1 fosmid}


block5041 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.837nono0.33/0.3321/21/1.000.0
0.0
1
0
1
0
24
0
3arm
1
nd
0.33
4
11nana
  readsmiRBase family seed
seed--------------------------------------------------------------UUGACAG-------------------------------------1novel
  lencloning frequencies
   CE1
 -------------------------------------------------------------TTTGACAGTTGCTAGGTTTTT------------------------211
celegansttttccaagtttgtcatgtttcaacattaggatattattgcaagttatttcactctaccgtTTTGACAGTTGCTAGGTTTTTgaaaatttcggaccaattttgaaa 
 ********************************************************************************************************** 
celegans.((((.(((((.(((...((((((..((((......((((((((.................)))).))))..))))....))))))......))).))))).))))0.670 -12.63

celeganschromosome:IV:16047258:16047363:-1intergenic ## {SimpF: WRM0627aG02 -1 fosmid}


block5089 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.721nono0.55/0.5520/20/1.000.0
0.0
1
0
1
0
8
16
3arm
1
nd
0.40
4
11nana
  readsmiRBase family seed
seed     -----------------------------------------------------------------UUGCACC--------------------     1novel
  lencloning frequencies
   CE1
      ----------------------------------------------------------------GTTGCACCACGAGATGTGTG--------     201
celegans     tggaaccggggcgttcgctgggacctggacgacgggaagcggagcagcttcttcttccttctttGTTGCACCACGAGATGTGTGaaggttct      
      ********************************************************************************************      
 ------------------------------------------------------------------------------------------------------K03D3.13 K03D3.13 rac-3
celegans     .((((((...(((((((.(((......(((((.((((((.((((....)))).))))))...)))))...)))))).)))).....))))))     0.410 -26.70

celeganschromosome:IV:16317575:16317666:-1Opposite_strand|Intronic_non-coding|K03D3.13|K03D3.13 ## K03D3.13|pseudogene|rac-3| ## {SimpF: WRM0633dF01 -1 fosmid,WRM0639bB12 -1 fosmid,WRM0621bE04 -1 fosmid,WRM0641bC05 -1 fosmid,K03D3.6 -1 Expression_profile}


block5111 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.216nono0.30/0.3020/20/1.000.0
0.0
1
0
1
0
16
20
5arm
1
nd
0.40
4
11nana
  readsmiRBase family seed
seed-----------------UCUUCAU---------------------------------------------------------------------------------------1novel
  lencloning frequencies
   CE1
 ----------------TTCTTCATTGTTTTCGTTTG---------------------------------------------------------------------------201
celeganstttgagttttcaataaTTCTTCATTGTTTTCGTTTGaataaaacttttttttaaacattagttttttaagttttcgaaatagcgattagcatagaataacaaaaatacaaa 
 *************************************************************************************************************** 
celegans.(((.(((((.....(((((....((((.(((((.....(((((((......((((....))))...)))))))......)))))..)))).)))))....))))).))).0.920 -15.90

celeganschromosome:IV:16534793:16534903:-1intergenic ## {SimpF: WRM0621bE04 -1 fosmid}


block5113 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.423nono0.25/0.2520/20/1.000.0
0.0
1
0
1
0
7
32
5arm
1
nd
0.45
4
11nana
  readsmiRBase family seed
seed--------AUUAUCG---------------------------------------------------------------------------------------------------------1novel
  lencloning frequencies
   CE1
 -------TATTATCGTCGAAATGTTAT---------------------------------------------------------------------------------------------201
celeganstccatatTATTATCGTCGAAATGTTATaaatttgagaggaaaaggaaaatcagtttttagtctaaacaaatatgaaaaatgattcactgccagcaaagcttgtttgagattttaattggg 
 ************************************************************************************************************************ 
celegans.(((.((((..(((.(((((..((......((((...((...((...(((((.((((((.............)))))).)))))..)).))..))))))...))))))))..))))))).0.850 -19.22

celeganschromosome:IV:16566054:16566173:-1intergenic ## {SimpF: WRM0630bE09 -1 fosmid,WRM0621bE04 -1 fosmid}


block5126 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.109nono0.32/0.3321/22/1.000.5
0.0
2
0
1
0
31
7
5arm
1
nd
0.33
4
21nana
  readsmiRBase family seed
seed--------------------------------UUUUUUC---------------------------------------------------------------------------------1novel
seed---------------------------------UUUUUCU--------------------------------------------------------------------------------1novel
  lencloning frequencies
   CE1
 --------------------------------TTTTTTCTGCAGCAAAGAATC-------------------------------------------------------------------211
 -------------------------------TTTTTTTCTGCAGCAAAGAATC-------------------------------------------------------------------221
celegansgagaaaatacatggggtttagtaatttttcgTTTTTTTCTGCAGCAAAGAATCacaagaatcatgttttttattttttgtgaaaattcgaaattttttactgtttctaaatagcattcta 
 ************************************************************************************************************************ 
celegans.((((........(((..((((((..(((((...(((((....(((((((((...(((((......)))))))))))))))))))..)))))....))))))..)))........)))).0.720 -21.69

celeganschromosome:IV:16661263:16661382:-1intergenic ## {Repeats: dust 64625 64632 0 class=dust} ## {SimpF: WRM0621bE04 -1 fosmid}


block5594 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.082nono0.27/0.2722/22/1.000.0
0.0
1
0
1
0
13
30
3arm
1
nd
0.36
4
11nana
  readsmiRBase family seed
seed     ------------------------------------------------------------------------------------AAUCGAA---------------------------     1novel
  lencloning frequencies
   CE1
      -----------------------------------------------------------------------------------GAATCGAATTTGAATATGAATG-------------     221
celegans     cttttttcgttttaaattcttcattgtttcgaggcattgaatcttcatcctctgatggctgcattcttttttctttaatcctcGAATCGAATTTGAATATGAATGatgaaaatatggg      
      **********************************************************************************************************************      
 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<...........................................................B0218.5 B0218.5 B0218.5
celegans     ((.(((((((((((.((((....(((.(((((((.((((((...(((((....)))))...............))))))))))))).)))....)))).)))..))))))))...)).     0.920 -22.57

celeganschromosome:IV:8156365:8156482:1intergenic ## {SimpF: WRM0634bC01 1 fosmid,WRM0631cA04 1 fosmid,WRM0634dG03 1 fosmid,WRM0621dE12 1 fosmid,WRM0617cF03 1 fosmid,WRM0614bA01 1 fosmid,WRM0632aA07 1 fosmid,WRM0638cH10 1 fosmid,WRM068dG01 1 fosmid,WRM064cD07 1 fosmid,WRM0632bC05 1 fosmid}


block6391 [novel_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.053nono0.59/0.5922/22/1.000.0
0.0
1
0
1
0
16
18
5arm
1
nd
0.41
4
11nana
  readsmiRBase family seed
seed-----------------UGAUUUG---------------------------------------------------------------------------------------1novel
  lencloning frequencies
   CE1
 ----------------GTGATTTGCTGGGTGCGCAGGT-------------------------------------------------------------------------221
celegansgaatgagactaccgccGTGATTTGCTGGGTGCGCAGGTagccggcgcgctcccaacaattgttgggtagaatgtgcgctctaacgcacttttcgaaggcgtcactggttcc 
 *************************************************************************************************************** 
celegans((((.((.....((((....((((..(((((((....(((..(((((((.((((((....))))))......)))))))))).)))))))..))))))))...)).)))).0.640 -42.00

celeganschromosome:V:2639525:2639635:-1intergenic ## {SimpF: WRM0617bC11 -1 fosmid}


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