logoC.elegans small RNAs

miR-Intess™


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Preprocessing
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Composition
miR classification

miR expression
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cel-mir-90

cel-mir-90

Cloning frequencies
absoluteCE1
cel-mir-90 3arm1111
normalizedCE1
cel-mir-90 3arm0.776
cel-mir-90 relative cloning frequencies

block3157 (miRBase cel-mir-90) [miRNAknown_cloningHIGH_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cel-mir-900.001nono0.28/0.4418/24/0.990.0
0.5
977
0
1
0
14
8
3arm
1
nd
0.13
1
11111nana
Families
Member of family miR-50/62/90 (seed GAUAUGU): cel-mir-50, cel-mir-90, cel-mir-62
block3157 hairpin
  readsmiRBase family seed
seed--------------------------------------------------------------------------------------GAUAUGU------------------------------------------------1087miR-50/62/90
seed---------------------------------------------------------------------------------------AUAUGUU-----------------------------------------------11novel
seed------------------------------------------------------------------------------------------UGUUG-UU-------------------------------------------10novel
seed----------------------------------------------------------------------------------------UAUGUUG----------------------------------------------3novel
  lencloning frequencies
   CE1
 -------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCCCC---------------------------------22524
cel-miR-90-------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCCCCT--------------------------------23453
 -------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCCC----------------------------------2177
 -------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCC-----------------------------------2019
 -------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGCCCCTT-------------------------------2410
 --------------------------------------------------------------------------------------GATATGTTG-TTTGAATGCCCC---------------------------------217
 -----------------------------------------------------------------------------------------ATGTTG-TTTGAATGCCCCT--------------------------------195
 -----------------------------------------------------------------------------------------ATGTTG-TTTGAATGCCCC---------------------------------185
 --------------------------------------------------------------------------------------GATATGTTG-TTTGAATGCCCCT--------------------------------223
 -------------------------------------------------------------------------------------TGATATGTTG-TTTGAATG-------------------------------------183
 ---------------------------------------------------------------------------------------ATATGTTG-TTTGAATGCCC----------------------------------191
 ---------------------------------------------------------------------------------------ATATGTTG-TTTGAATGCCCCT--------------------------------211
 -------------------------------------------------------------------------------------TGATATGTTG-TTTGAATGC------------------------------------191
 ---------------------------------------------------------------------------------------ATATGTTG-TTTGAATGCCCCTT-------------------------------221
 --------------------------------------------------------------------------------------GATATGTTG-TTTGAATGCCC----------------------------------201
celegans---------------------GGGCGCCA--TTTCGAGCGGCTTTCAACGACGATATCAACCGACAAC-TCACACTTTTGCGTGTTGATATGTTG-TTTGAATGCCCCTTGAATTGGATGCCA------------------ 
cbriggsaeTCTGGATTACTGTAGATCCTGCAGCACCA--TTTCAAGCGGCCTTCAACGACTATATCAACCGA-----ATCCAAATTCGCGAGTTGATATGTTGTTTTGAATGTCACTTGAGGTTTTTGCTTTTTCGGATTTTATCCTGG 
cjaponica-------------------------------------GCGGCTTTCAACGGCGCTATCAACCGA-----ACTGTGTGTCGCGTGTTGATATGTTG-TTTGAATGCCCC--------------------------------- 
cbrenneri-----------TCCTGGACTTGGGCGCCAAGTTTCGAGCGGCTTTCAACAACGATATCAACCGATTT--TCAGTAAATTGCGAGTTGATATGTTG-TTTGAATGCCCCTTGAGTTGGTTGCCCTTCTTGTT----TTAGGA 
cremanei----------TCTCCTTGTTTGGGCCTCA--CTTCGAGCGGTATTCAACGACTATCTCAACCGATATACATACCAAC---CGAGTTGATATGTTG-TTTGAATGCCCCTTGAACTCGAGGCCC--CTAGTAAACACTCAGA 
                                      ****  ******  *  * ********                ** ************ ******** * *                                  
celegans                     .(((((((  .((((((.(((.(((((((((.((((((((((.(((. ........))))).)))))))))))) .))))).))).)))))).))).)))).                  1.000 -43.20
cbriggsae...((((......((((((...((((..(  (((((((.(((.(((((((((.(((((((((((     ((....)))))...)))))))))))))..)))).))).))))))))...)))).....)))))).))))...0.804 -41.50
cjaponica                                     ..(((.((((((((((.(((((((((.     ((.....))..)).)))))))))))) )).))).)))..                                 1.000 -22.90
cbrenneri           ((((((((..(((((((((..((((((.(((.(((((((((.((((((((((((((  .....))))))...)))))))))))) )).))).))).))))))))))).)))).....)))    ).))))0.999 -48.60
cremanei          (((...((((((((((((.  .((((((.(((((((((((((.((.(((((((..............   )).))))).)))))) )).))))))).))))))...)))))))  .....)))))...)))0.961 -43.94

celeganschromosome:III:8873894:8873991:-1intergenic ## {SimpF: WRM0637aD12 -1 fosmid,WRM0622dD10 -1 fosmid} ## {MIR: cel-mir-90}
cbriggsaechromosome:chrIII:13422670:13422803:-1Opposite_strand|Intronic_coding|NM_001090393 ## Same_strand|Intronic_coding|NM_070558
cjaponicachromosome:chrUn:4612006:4612143:-1Opposite_strand|Intronic_coding|NM_080787 ## Same_strand|Intronic_coding|NM_078517 ## {SimpF: trf}
cbrennerichromosome:chrUn:17772387:17772509:1intergenic
cremaneichromosome:chrUn:78012934:78013056:-1intergenic


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