modeling miRNAs in gff3

[Nicole Washington]

hi folks,

so, i don't think i've seen much documentation out there for how to  
model miRNAs (and their genes) in gff3 format.  so i wanted to start a  
discussion.

let's say i have at least a miRNA sequence, and know where it maps.

would i annotate it like:

IV Embryo miRNA_gene 5280064 5280086 . - . ID=mir-2217;Name=mir-2217
IV Embryo miRNA 5280064 5280086 . - . Parent=mir-2217


now, that's if i only know the miRNA sequence, and nothing about the  
primary transcript from which it was derived.

let's say now that i do have that information, and i wanted to  
annotate it all.  let's take this one for an example:
http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?acc=MI0000006

i imagine it might look something like:

II Embryo miRNA_gene 11535524 11539620 . + . ID=cel-mir-35
II Embryo pre_miRNA 11535524 11539620 . + . ID=cel-mir-35_mRNA
II Embryo miRNA_stem 11535524 11537572 . + . Parent=cel-mir-35_mRNA
II Embryo miRNA_loop 11537573 11537578 . . . Parent=cel-mir-35_mRNA
II Embryo miRNA_stem 11537578 11539620 . + . Parent=cel-mir-35_mRNA
II Embryo miRNA 11537585 11537707 . + . Parent=cel-mir-35_mRNA

a couple things that aren't clear to me would be:
1.  how to model that one side effectively becomes the opposite strand  
in the pre-miRNA?  do we need to introduce match features between the  
stems?
2.  if the miRNA should be the child of the miRNA_stem, or of the  
pre_miRNA, or of the miRNA_gene itself?

nicole



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