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BIOINF 11-022: Evolution of the let-7 microRNA Family

Jana Hertel, Sebastian Bartschat, Axel Wintsche, Christian Otto, The Students of the Bioinformatics Computer Lab 2011, Peter F Stadler



Extended Cluster Summary

Extendend tables summarizing the deuterostomian let-7 associated cluster can be downloaded here. Therein, miRBase names were noted when this microRNA is already annotated.
  • Extended summary of clusters A-D [pdf]
  • Extended summary of clusters E-L [pdf]


Genomic Location

  • GFF file containing all collected let-7 associated microRNAs among Deuterostomia [gff]
  • Genome versions we used during our analysis [list]
    Please note that the sequences ssc-C-mir-125 and ggo-D-mir-100 are solely experimentally derived and hence won't appear in the gff file.
  • GFF file containing all mirbase-derived let-7 associated microRNAs among Protostomia and Cnidaria [gff]
  • Genome versions of protostomes we used during out analysis [list]


MicroRNA family Alignments

Alignments of let-7, mir-100, and mir-125 families in Stockholm format can be downloaded here.

Deuterostomia:
Cluster A   A-mir-100.stk   A-let-7.stk   A-mir-125.stk 
Cluster A(Tel)   A-Tel-let-7.stk   A-Tel-mir-125.stk 
Cluster C   C-mir-100.stk   C-let-7.stk   C-mir-125.stk 
Cluster D   D-mir-100.stk   D-let-7.stk   D-mir-125.stk 
Cluster E   E-let-7-1.stk   E-let-7-2.stk   E-let-7-3.stk 
Cluster F   F-let-7-1.stk   F-let-7-2.stk 
Cluster G   G-let-7-1.stk   G-let-7-2.stk 
Cluster H   H-let-7-1.stk   H-let-7-2.stk 
Cluster I   I-let-7.stk 
Cluster J   J-let-7.stk 
Cluster K   K-let-7.stk 
Cluster L   L-let-7.stk 
Protostomia:
mixed Cluster   mir-100.stk   let-7.stk   mir-125.stk 
lin-4  lin4.stk 


Covariance Models

(Sub)family-wide covariance models were used for structure and sequence-based homology searches for the deuterosome microRNAs of the let-7, mir-100, and mir-125 families.

Cluster A   A-mir-100.cm   A-let-7.cm   A-mir-125.cm 
Cluster A(Tel)   A-Tel-let-7.cm   A-Tel-mir-125.cm 
Cluster C   C-mir-100.cm   C-let-7.cm   C-mir-125.cm 
Cluster D   D-mir-100.cm   D-let-7.cm   D-mir-125.cm 
Cluster E   E-let-7-1.cm   E-let-7-2.cm   E-let-7-3.cm 
Cluster F   F-let-7-1.cm   F-let-7-2.cm 
Cluster G   G-let-7-1.cm   G-let-7-2.cm 
Cluster H   H-let-7-1.cm   H-let-7-2.cm 
Cluster I   I-let-7.cm 
Cluster J   J-let-7.cm 
Cluster K   K-let-7.cm 
Cluster L   L-let-7.cm