logoC.elegans small RNAs


miR classification

Alignments

other hairpins

novel_loopOverlap_nonpairedHIGH (11 loci)

block3240 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.231nono0.48/0.4821/21/1.000.0
0.0
1
0
1
0
18
-3
3arm_loop
1
7
0.33
3
11nana
  readsmiRBase family seed
seed     ------------------------------------GUGUCUC-------------------------------     1novel
  lencloning frequencies
   CE1
      -----------------------------------AGTGTCTCAATCGAGTTTCCG------------------     211
celegans     agcctaagaatgatccaacgagaaaagcggtgaccAGTGTCTCAATCGAGTTTCCGtcggggatctctgatcct      
      **************************************************************************      
 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>++++++++++++++++++++++++++++++++++++++++++++++++++Y39A1A.2 Y39A1A.2 Y39A1A.2
celegans     ......(((..(((((.(((.((((..(((((((....)))...))))..)))))))...))))))))......     0.950 -18.80

celeganschromosome:III:10602627:10602700:-1Same_strand|Intronic_coding|Y39A1A.2|Y39A1A.2 ## Y39A1A.2|protein_coding|Y39A1A.2|Y39A1A.2 [Source:RefSeq_peptide;Acc:NP_499336] ## {SimpF: Y39A1A.2 -1 Expression_profile}


block3306 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.309nono0.50/0.5022/22/1.000.0
0.0
1
0
1
0
37
-3
3arm_loop
1
nd
0.32
3
11nana
  readsmiRBase family seed
seed     ---------------------------------------------------------UUUGUGG---------------------------------------------------     1novel
  lencloning frequencies
   CE1
      --------------------------------------------------------GTTTGTGGCATCGTTCGAGTAG-------------------------------------     221
celegans     gtggtggtggtggtggtggtggtctagcagttgtgtcgttgagctgccacgccgacGTTTGTGGCATCGTTCGAGTAGagatagtctaacaccgaaaaaaaacaccaaattagcg      
      *******************************************************************************************************************      
 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.....................................................Y79H2A.11 Y79H2A.11 zyg-8
celegans     ((..(((((.......(((((...(((...((((.((.(((((((((((((........)))))))..))))))...)).)))).))).)))))........))))).....)).     0.690 -33.26

celeganschromosome:III:12061572:12061686:-1Opposite_strand|Boundary_non-coding|Y79H2A.11|Y79H2A.11 ## Y79H2A.11|protein_coding|zyg-8|The zyg-8 gene encodes a protein with a doublecortin-like domain and a protein kinase domain. mutations of zyg-8 impair mitosis at the one-cell embryonic stage, which is normally asymmetrical, but which fails to show proper asymmetry in zyg-8 mutant embryos. [Source: WormBase]


block3394 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.771nono0.45/0.4522/22/1.000.0
0.0
2
0
1
0
15
-1
5arm_loop
1
nd
0.41
3
21nana
  readsmiRBase family seed
seed----------------AUGGACA------------------------------------------------------------2novel
  lencloning frequencies
   CE1
 ---------------CATGGACATAAGAGCAAAGCGT----------------------------------------------222
celegansgccagctgggaccccCATGGACATAAGAGCAAAGCGTacaattcctgttgatcctcgtgatccggattccaaatcagcttagc 
 *********************************************************************************** 
celegans((.((((((((..((...((((((..(((...((((.........))))....)))))).)))))..)))....)))))..))0.440 -15.40

celeganschromosome:III:178782:178864:1intergenic ## {SimpF: WRM068dG09 1 fosmid,WRM0621dC05 1 fosmid}


block4249 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.036nono0.40/0.4020/20/1.000.0
0.0
3
0
1
0
21
-4
3arm_loop
1
nd
0.35
3
31nana
  readsmiRBase family seed
seed-------------------------------------------------------------UAUGCGU---------------------------------3novel
  lencloning frequencies
   CE1
 ------------------------------------------------------------TTATGCGTCCCTAAAAACTG---------------------203
celegansgtgatctataattttctgtttcaatatgtttgtttaatgggatgctattcagtgtttcagTTATGCGTCCCTAAAAACTGatattcaaagatggaattaca 
 ***************************************************************************************************** 
celegans(((((.........(((((((....(((((.((((...(((((((...................)))))))...)))).)))))....)))))))))))).0.990 -21.71

celeganschromosome:IV:5426030:5426130:-1intergenic


block5529 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.159nono0.45/0.4520/20/1.000.0
0.0
1
0
1
0
42
-2
3arm_loop
3
nd
0.35
3
11nana
  readsmiRBase family seed
seed---------------------------------------------------------AGAAGAA------------------------------------------------------1novel
  lencloning frequencies
   CE1
 --------------------------------------------------------AAGAAGAACAGCTTGTCACG------------------------------------------201
celeganstgatatgattaatagaacagatgattaaaacgggaaatccacaggatgggttttacAAGAAGAACAGCTTGTCACGgaggtacccatttgcatcatcgtgaagtgattgggctgtcaa 
 ********************************************************************************************************************** 
celegans(((((((((((.....((.((((((..(((.(((...((((((((.((..((((....))))..)).)))))...)))....))).)))..))))))))....))))))...))))).0.950 -26.30

celeganschromosome:IV:6539139:6539256:1intergenic ## {SimpF: WRM0628aE01 1 fosmid,WRM0631dD07 1 fosmid,WRM0615cA12 1 fosmid,WRM0624aF05 1 fosmid,WRM0625dB01 1 fosmid,WRM0613dD06 1 fosmid}


block6769 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.019nono0.50/0.5022/22/1.000.0
0.0
1
0
1
0
6
-2
5arm_loop
1
nd
0.36
3
11nana
  readsmiRBase family seed
seed-------AUUCUCU------------------------------------------------1novel
  lencloning frequencies
   CE1
 ------GATTCTCTCGTGTTCAGCTGTC----------------------------------221
celeganscaaattGATTCTCTCGTGTTCAGCTGTCatcatcagaggaatcgagcaaagatctagtttga 
 ************************************************************** 
celegans(((((((..(((((((.((((..(((.......)))..))))))))...)))..))))))).1.000 -17.10

celeganschromosome:V:13931632:13931693:-1intergenic ## {SimpF: WRM0620cE11 -1 fosmid,WRM0634aF11 -1 fosmid,WRM0628bE12 -1 fosmid,WRM0635bB01 -1 fosmid,WRM0622dC05 -1 fosmid}


block7375 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.160nono0.36/0.3622/22/1.000.0
0.0
2
0
1
0
17
-1
5arm_loop
1
nd
0.36
3
21nana
  readsmiRBase family seed
seed     ------------------CAUGAGG------------------------------------------------------------------     2novel
  lencloning frequencies
   CE1
      -----------------TCATGAGGAACCAACTGAAATT----------------------------------------------------     222
celegans     tccgtcgcggctggtttTCATGAGGAACCAACTGAAATTaattttatttattttaaggttaagtgtggaaatttggcttggcttaccggaa      
      *******************************************************************************************      
 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-------------------------------------------------------<<<<<<<<<<C15H11.4 C15H11.4 dhs-22
celegans     ((((..((((((((((((((((...((((...((((((...........)))))).))))...)))))))))).))))..))....)))).     0.670 -19.90

celeganschromosome:V:14420343:14420433:1Opposite_strand|Boundary_coding|C15H11.4|C15H11.4 ## C15H11.4|protein_coding|dhs-22|dhs-22 encodes a short-chain dehydrogenase predicted to be mitochondrial. [Source: WormBase] ## {SimpF: WRM0614dC12 1 fosmid,WRM0615aB07 1 fosmid,WRM0630cB06 1 fosmid,CEOP5416 -1 Operon,WRM0612dC05 1 fosmid,WRM0617aH02 1 fosmid,yk176b4 1 RNAi,WRM0623cD09 1 fosmid,WRM0617cF09 1 fosmid}


block7564 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.284nono0.45/0.4522/22/1.000.0
0.0
1
0
1
0
14
-1
3arm
1
nd
0.32
3
11nana
  readsmiRBase family seed
seed     -----------------------------------------------------------------UGUUGGU----------------------------     1novel
  lencloning frequencies
   CE1
      ----------------------------------------------------------------GTGTTGGTGGGGTGTTAAATAG--------------     221
celegans     attcgtcgaaaaagtgtgcgttttcatcatataaatagaaaaaaagaaagagagagagtaatatGTGTTGGTGGGGTGTTAAATAGcacaagatacgaat      
      ****************************************************************************************************      
 ........................................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<Y113G7B.23 Y113G7B.23 psa-1
celegans     ((((((........(((((.((..((((.(((.((((............................)))).))).))))..))...)))))....))))))     0.650 -13.19

celeganschromosome:V:20234565:20234664:1Opposite_strand|Boundary_non-coding|Y113G7B.23|Y113G7B.23 ## Y113G7B.23|protein_coding|psa-1|psa-1 encodes an ortholog of SWI3, a component of the SWI/SNF complex that is conserved from yeast to mammals and that is involved in chromatin remodeling. psa-1 is probably required during mitosis of the T cells for asymmetric cell division, and in addition, is required for embryonic and larval development, as well as normal levels of fertility. psa-1 exhibits strong genetic interactions with lin-35/Rb, as psa-1 larval lethality and sterility at 20 degrees C are greatly enhanced in lin-35.psa-1 double mutants. [Source: WormBase] ## {SimpF: CEOP5508 -1 Operon}


block8040 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.228nono0.38/0.3821/21/1.000.0
0.0
1
0
1
0
35
-2
5arm_loop
2
nd
0.48
3
11nana
  readsmiRBase family seed
seed------------------------------------UACGAGU---------------------------------------------------------------------1novel
  lencloning frequencies
   CE1
 -----------------------------------ATACGAGTTGCAGTTGTTGTT--------------------------------------------------------211
celegansttgttatcatatcgcttgtacttcttcttttctttATACGAGTTGCAGTTGTTGTTagttgatgacgaaacgagtgtgagtaggcgagtagaagccagggggggggagcagg 
 **************************************************************************************************************** 
celegans(((((.((...((.((((..(((((.(((.(((((((((..(((...((..(((.....)))..))..)))..))))))..))).))).))))).)))).)).)).))))).0.440 -29.20

celeganschromosome:X:16002920:16003031:-1intergenic ## {SimpF: WRM0616bB09 -1 fosmid,WRM0619bA05 -1 fosmid}


block8041 [novel_loopOverlap_nonpairedHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.454nono0.38/0.3821/21/1.000.0
0.0
1
0
1
0
38
-2
5arm_loop
2
nd
0.48
3
11nana
  readsmiRBase family seed
seed---------------------------------------UACGAGU------------------------------------------------------------------------1novel
  lencloning frequencies
   CE1
 --------------------------------------ATACGAGTTGCAGTTGTTGTT-----------------------------------------------------------211
celegansgattttttatcatatcgcttgtacttctttttttctttATACGAGTTGCAGTTGTTGTTagttgatgacgagacgagtgtgagtagacgagtagaagccagcggggggagcaggggtt 
 ********************************************************************************************************************** 
celegans(((..((..((...(((((....(((((.(((.(((((((((..(((...((..(((.....)))..))..)))..))))))..))).))).)))))..)))))...))..))..)))0.980 -27.60

celeganschromosome:X:16003516:16003633:-1intergenic ## {SimpF: WRM0616bB09 -1 fosmid,WRM0619bA05 -1 fosmid}


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