'stem_loop' children 'stem' and 'loop' - giving the ability to differentiate between the stem and loop regions.

[RichardJActon]

I've been doing some work looking at tRNA genes and it would be useful to be able to create more detailed GFF3 files with a full description of the stem-loop substructure.

A further child of stems might be non-complimentary regions to indicate regions in a stem that are not exact palindromes of it partner.

[keilbeck]

First off, sorry we are so late getting back to you on this.

I think you are asking for parts of stem_loop

stem_loop
part stem
kind of non_complimentary_stem
part loop

@davidwsant could you help figure out the definitions of these terms? The parts must also be child terms of a different root node probably RNA_sequence_secondary_structure

--K

[keilbeck]

stem_loop
--part stem
----kind of non_complimentary_stem
--part loop

[davidwsant]

Hi Richard,

I apologize that this has again taken a delay. I thought I had created the terms, but I had not. The terms have now been created. Please let me know if you have any changes to the names or definitions of the terms created. The SO Browser should be updated within about the next 24 hours.

Thanks,

Dave

id: SO:0002253
name: stem_loop_region
def: "A portion of a stem loop secondary structure in RNA."
is_a: SO:0000122 ! RNA_sequence_secondary_structure
relationship: part_of SO:0000313 ! stem_loop

id: SO:0002254
name: loop
def: "The loop portion of a stem loop, which is not folded back upon itself. "
is_a: SO:0002253 ! stem_loop_region

id: SO:0002255
name: stem
def: "The portion of a stem loop where the RNA is folded back upon itself. "
is_a: SO:0002253 ! stem_loop_region

id: SO:0002256
name: non_complimentary_stem
def: "A region of a stem in a stem loop structure where the sequences are non-complimentary."
is_a: SO:0002255 ! stem