logoC.briggsae small RNAs

miR-Intess™


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Preprocessing
Mapping
Composition
miR classification

miR expression
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cel-mir-238

cel-mir-238

Cloning frequencies
absoluteAF16
cel-mir-238 3arm627
normalizedAF16
cel-mir-238 3arm1.634
cel-mir-238 relative cloning frequencies

block1581 (miRBaseHomolog cel-mir-238) [miRBaseHomolog_cloningHIGH_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBaseHomolog cel-mir-2380.001nono0.44/0.5518/24/0.990.0
0.0
444
0
1
0
20
7
3arm
1
nd
0.23
3
6271nana
Families
Member of family miR-239a (seed UUGUACU): cel-mir-238, cbr-mir-239a, block2886_novel
block1581 hairpin
  readsmiRBase family seed
seed     ---------------------------------------------------------------------------------------------------UUGUACU--------------------------------------------------     616miR-239a
seed     ----------------------------------------------------------------------------------------------------UGUACUC-------------------------------------------------     6novel
seed     -------------------------------------------------------------------------------------------------------ACUCCGA----------------------------------------------     4novel
seed     -----------------------------------------------------------------------------------------------------GUACUCC------------------------------------------------     1novel
  lencloning frequencies
   AF16
      --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATCCAC------------------------------------     22444
      --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATCC--------------------------------------     20166
      ---------------------------------------------------------------------------------------------------TTGTACTCCGATGCCATCCAC------------------------------------     215
      ------------------------------------------------------------------------------------------------------TACTCCGATGCCATCCACA-----------------------------------     194
      --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATCCACAT----------------------------------     243
      --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATC---------------------------------------     191
      --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCAT----------------------------------------     181
      --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATCCA-------------------------------------     211
      ---------------------------------------------------------------------------------------------------TTGTACTCCGATGCCATCC--------------------------------------     191
      ----------------------------------------------------------------------------------------------------TGTACTCCGATGCCATCCAC------------------------------------     201
cbriggsae     ---TTCTTCTTATCCTCATGAATA--------------TG-ACTGTTTGGGTGTCCTTGGATGTAAAAAGCTA----TAAATCTGTTAA--G-ATTGCTTTGTACTCCGATGCCATCCACATGGTCTGACGACAAGAAGA----------------      
cremanei     ---ATTCTATTCTATTCAAAGTCAACGTGGACCACTGTGATACCATTTGGGTGGACACGGACGTAAAAAGCTATGCCCGTGGTTAGGTA--T-TTAGCTTTGTACTCCGATGCCATTCAAATGGTTGTGTGGTTTTGGATTGTGGTAAGTTTGAAT      
celegans     TACTTTTTAATATTTTCAAGAAAATGGCAATTCTCCATTG-ACTGTTTGGATGTTCTCGGACGTTCAAAGCTA------CATCCAACAAATTGGTAGCTTTGTACTCCGATGCCATTCAGATAGTTATGAGCCATGGATGTATTGTTGAGGTA---      
cbrenneri     ----------------------------------------------CTGGATGTGATCGGGTGTAAAAAGCTA--------TCCACGAA--GAATCGCTTTGTACTCCGATGCCATTCAG------------------------------------      
cjaponica     ----------------------------------------------TTGGACGTGATTGGATGTTCAAAGCCAGCGCCATATCGAAATA--TGGCAGCTTTGTACTCCGATGCCGTTCAG------------------------------------      
                                                     ***  *     **  **  ***** *               *       ****************** * **                                           
 -----   ---------------------              -- --------------------------------    ------------  - -----------------------------------------------                -----NM_001026518
 -----   ---------------------              -- --------------------------------    ------------  - -----------------------------------------------                -----NM_001090393
 -----   ---------------------              -- --------------------------------    ------------  - -----------------------------------------------                -----NM_001730
 +++++   +++++++++++++++++++++              ++ ++++++++++++++++++++++++++++++++    ++++++++++++  + +++++++++++++++++++++++++++++++++++++++++++++++                +++++NM_070558
cbriggsae        .(((((((.((.(((......              .( (((((.((((((...(((((.(((.(((((..    ..(((((....)  ) )))))))).))))))))...)))))).))))))))).)).)))))))                     1.000 -37.31
cremanei        ((((....((..(((.((((.....(((((((......(((((((((((((.((((((.(((.(((((((((((........))))  . .))))))).))))))).)))))))))))))))...)))))))..)))).)))..))...))))     0.994 -52.90
celegans     ..(((..((((((.((((......((((...((.....(( ((((((((((((...(((((.((.((((((((      ...((((....)))))))))))).)))))))...)))))))))))))).)))))))))).))))))..)))...        0.931 -48.20
cbrenneri                                                   (((((((..((((((.(((.(((((..        ((......  ))...))))).)))))))))..)))))))                                         0.999 -22.50
cjaponica                                                   .((((((..((((((.((.((((((....(((((((....)))  )))).)))))).))))))))..)))))).                                         1.000 -31.10

cbriggsaechromosome:chrIII:13410780:13410894:-1Opposite_strand|Intronic_coding|NM_001026518|Y105E8A.29 ## Opposite_strand|Intronic_non-coding|NM_001090393|Egr1 ## Same_strand|Intronic_non-coding|NM_070558|rho-1 ## {Repeats: no}
cremaneichromosome:chrUn:98387116:98387265:-1intergenic
celeganschromosome:chrIII:8867218:8867363:-1intergenic ## {MIR: cel-mir-238}
cbrennerichromosome:chrUn:17763320:17763474:-1Same_strand|Intronic_coding|NM_209159
cjaponicachromosome:chrUn:4625360:4625514:1Same_strand|Intronic_coding|NM_080787 ## Opposite_strand|Intronic_coding|NM_078517


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