#418 NTR: disabled reading frame

[Stacia Engel]

NTR: disabled_reading_frame

parent: is_a reading_frame (SO:0000717)

PMID: 11866506

definition: reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons).

synonym: dORF
synonym: disabled ORF

[Karen Eilbeck]

There has been a term for a long time, (looks like it was made by Rama) blocked reading frame. I believe this to be a synonym of disabled reading frame given the definitions. I added frameshift to the existing term as another kind of disruption.
SO:0000718
If this is in error let me know

[Stacia Engel]

Hi Karen,
that is indeed an error to merge these two terms. blocked_reading_frame needs to stay as is. the disabled_reading_frame is further degraded, further along the sad path of mutation toward becoming a pseudogene, but not there yet.

please reinstate the previous definition for BRF, and add disabled_reading_frame as a new term. they are specifically supposed to be different beasts.

thank you.

[Karen Eilbeck]

SO:0002048

On Feb 9, 2015, at 4:01 PM, Stacia Engel wrote:

dORF

Karen Eilbeck
Associate Professor
Department of Biomedical Informatics, University of Utah

[Karen Eilbeck]

OK. Sorry for making it worse
--K

On Feb 9, 2015, at 4:01 PM, Stacia Engel wrote:

Hi Karen,
that is indeed an error to merge these two terms. blocked_reading_frame needs to stay as is. the disabled_reading_frame is further degraded, further along the sad path of mutation toward becoming a pseudogene, but not there yet.

please reinstate the previous definition for BRF, and add disabled_reading_frame as a new term. they are specifically supposed to be different beasts.

thank you.

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[term-tracker:#418]http://sourceforge.net/p/song/term-tracker/418 NTR: disabled reading frame

Status: closed
Group:
Created: Mon Oct 20, 2014 06:52 PM UTC by Stacia Engel
Last Updated: Mon Feb 09, 2015 10:55 PM UTC
Owner: nobody

NTR: disabled_reading_frame

parent: is_a reading_frame (SO:0000717)

PMID: 11866506

definition: reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons).

synonym: dORF
synonym: disabled ORF

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Karen Eilbeck
Associate Professor
Department of Biomedical Informatics, University of Utah