confident homolog loci of miRBase miRNAs
miRBaseHomolog_cloningHIGH_randfoldOK (2 loci)
cel-mir-238
| absolute | AF16 |
| cel-mir-238 3arm | 627 |
| normalized | AF16 |
| cel-mir-238 3arm | 1.634 |
block1581 (miRBaseHomolog cel-mir-238) [miRBaseHomolog_cloningHIGH_randfoldOK]
| 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 |
| miRBaseHomolog cel-mir-238 | 0.001 | no | no | 0.44/0.55 | 18/24/0.99 | 0.0 | 0.0 | 444 | 0 | 1 | 0 | 20 | 7 | 3arm | 1 | nd | 0.23 | 3 | 627 | 1 | na | na |
| Member of family miR-239a (seed UUGUACU): cel-mir-238, cbr-mir-239a, block2886_novel |
| reads | miRBase family seed | ||
| seed | ---------------------------------------------------------------------------------------------------UUGUACU-------------------------------------------------- | 616 | miR-239a |
| seed | ----------------------------------------------------------------------------------------------------UGUACUC------------------------------------------------- | 6 | novel |
| seed | -------------------------------------------------------------------------------------------------------ACUCCGA---------------------------------------------- | 4 | novel |
| seed | -----------------------------------------------------------------------------------------------------GUACUCC------------------------------------------------ | 1 | novel |
| len | cloning frequencies | ||
| AF16 | |||
| --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATCCAC------------------------------------ | 22 | 444 | |
| --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATCC-------------------------------------- | 20 | 166 | |
| ---------------------------------------------------------------------------------------------------TTGTACTCCGATGCCATCCAC------------------------------------ | 21 | 5 | |
| ------------------------------------------------------------------------------------------------------TACTCCGATGCCATCCACA----------------------------------- | 19 | 4 | |
| --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATCCACAT---------------------------------- | 24 | 3 | |
| --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATC--------------------------------------- | 19 | 1 | |
| --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCAT---------------------------------------- | 18 | 1 | |
| --------------------------------------------------------------------------------------------------TTTGTACTCCGATGCCATCCA------------------------------------- | 21 | 1 | |
| ---------------------------------------------------------------------------------------------------TTGTACTCCGATGCCATCC-------------------------------------- | 19 | 1 | |
| ----------------------------------------------------------------------------------------------------TGTACTCCGATGCCATCCAC------------------------------------ | 20 | 1 | |
| 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 |
| cbriggsae | chromosome:chrIII:13410780:13410894:-1 | Opposite_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} |
| cremanei | chromosome:chrUn:98387116:98387265:-1 | intergenic |
| celegans | chromosome:chrIII:8867218:8867363:-1 | intergenic ## {MIR: cel-mir-238} |
| cbrenneri | chromosome:chrUn:17763320:17763474:-1 | Same_strand|Intronic_coding|NM_209159 |
| cjaponica | chromosome:chrUn:4625360:4625514:1 | Same_strand|Intronic_coding|NM_080787 ## Opposite_strand|Intronic_coding|NM_078517 |
miRBaseHomolog_cloningOK_multiarm_DicerOK_randfoldOK (1 loci)
cel-mir-54
| absolute | AF16 |
| cel-mir-54 5arm | 5 |
| cel-mir-54 3arm | 5 |
| normalized | AF16 |
| cel-mir-54 5arm | 0.013 |
| cel-mir-54 3arm | 0.013 |
sblock75 (miRBaseHomolog cel-mir-54) [miRBaseHomolog_cloningOK_multiarm_DicerOK_randfoldOK]
| 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 |
| miRBaseHomolog cel-mir-54 | 0.001 | no | no | 0.40/0.45 | 20/23/1.00 | 0.0 0.0 | 0.0 0.0 | 5 4 | 0 0 | 1 1 | 0 0 | 25 31 | 4 6 | 5arm 3arm | 1 1 | nd nd | 0.23 0.22 | 3 3 | 10 | 1 | 1 | 2 |
| Located in cluster 10: cel-mir-56, cbr-mir-55, block4662_novel, cel-mir-54, block4665_novel, block4666_novel |
| Member of family miR-51/52/55 (seed ACCCGUA): cel-mir-56, cel-mir-54, cbr-mir-55, cbr-mir-52, cbr-mir-51, block4665_novel, block4666_novel |
| reads | miRBase family seed | ||
| seed | ----------------------------------GGGAUAU------------------------------------------------------------------------------------------------ | 5 | novel |
| seed | ---------------------------------------------------------------------------------ACCCGUA------------------------------------------------- | 5 | miR-51/52/55 |
| len | cloning frequencies | ||
| AF16 | |||
| ---------------------------------TGGGATATGA-GCAAACGTGTAC--------------------------------------------------------------------------------- | 22 | 5 | |
| --------------------------------------------------------------------------------TACCCGTATTC-TCAT-ATCTGAGC-------------------------------- | 23 | 4 | |
| --------------------------------------------------------------------------------TACCCGTATTC-TCAT-ATCTG----------------------------------- | 20 | 1 | |
| cbriggsae | CAGGA--------CGTCTAAGCCGATCCTTGGCTGGGATATGA-GCAAACGTGTACACGATACTTATTC-------CCTGTACCCGTATTC-TCAT-ATCTGAGCCAAGGATCGTCGCAAAAGGCGGTGCTTCCTG- | ||
| celegans | CTGGA--ATTGGTAATGTGAGTCGCGCTCTGACTAGGATATGA-GACGACGAGAACAT--TGCTTTTTTAAAAGA-CTTGTACCCGTAATCTTCATAATCCGAGTCAGGGCTAGCTGACCATAAACATGCCTTCCAG | ||
| ppacificus | CTACATCATGCTCACTCTGAGGGGAGTTGCCACTAGGCAGCAATGCTAACGAGTGTGT--TGATCTTTCGTATCATCTCATACCCGTAAGC--CATTCTGTCGAGCGGCTCTCTCCATTCCGAGTGAGGATCCCTAG | ||
| * * * * ** * ** ** * * *** * * * ** * ******** * *** * * * * * | |||
| ---------- ------------------------------ ------------------------- --------------- ---- --------------------------------------- ----- | NM_026450 | ||
| ---------- ------------------------------ ------------------------- --------------- ---- --------------------------------------- ----- | NM_001011629 | ||
| ++++++++++ ++++++++++++++++++++++++++++++ +++++++++++++++++++++++++ +++++++++++++++ ++++ +++++++++++++++++++++++++++++++++++++++ +++++ | NM_064155 | ||
| ++++++++++ ++++++++++++++++++++++++++++++ +++++++++++++++++++++++++ +++++++++++++++ ++++ +++++++++++++++++++++++++++++++++++++++ +++++ | NM_001101467 | ||
| ---------- ------------------------------ ------------------------- --------------- ---- --------------------------------------- ----- | NM_205032 | ||
| cbriggsae | ((((( (((((..((((((((((((((.(((((((( (...(((.(((((.((.......)) ..))))).)))...) )))) )))).))))))))))))..))...))))).....))))) | 0.760 -55.50 | |
| celegans | ((((( (..((((.((((.((((((((((((((.(((((((( ((..(((...(((. ..((((....)))). ..)))...)))..))).)))).))).)))))))))..)).)))))))....)))))))))) | 1.000 -47.20 | |
| ppacificus | .......((.(((((((.((((((((..(((.((.(((((.((((((.(((.(((((. ((((.......))))...))))).))).))) .)))))))).)).))).))))))..)).))))))).))...... | 0.999 -51.90 |
| cbriggsae | chromosome:chrX:16837257:16837374:-1 | Opposite_strand|Intronic_non-coding|NM_026450|Zfp169 ## Same_strand|Intronic_non-coding|NM_064155|Y17G7B.3 ## {Repeats: no} |
| celegans | chromosome:chrX:13144899:13145029:-1 | intergenic ## {MIR: cel-mir-54} |
| ppacificus | chromosome:chrUn:139887477:139887609:1 | Same_strand|Intronic_coding|NM_023879 ## Opposite_strand|Intronic_coding|NM_100443 |
| Back to summary page | confident homolog loci of miRBase miRNAs: | Page 1 | Page 2 |
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