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Old 09-21-2014, 04:12 PM   #1
arkilis
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Location: Australia

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Default Transcript id naming in Ensembl?

I am quite curious on the naming pattern on the Transcript ID on Ensembl. i.e.

http://www.ensembl.org/Homo_sapiens/...54893-27722058


Transcript ids:


BDNF-015
BDNF-016
BDNF-202

There is no BDNF-019? What Ensembl does the naming like this?

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Old 10-07-2014, 06:24 AM   #2
Emily_Ensembl
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Numbers that begin with 0 are transcripts that have been identified by Havana manual annotation, whereas numbers that begin with 2 have only been identified by Ensembl automatic annotation. There's more information on gene annotation here:
http://www.ensembl.org/info/genome/g...nnotation.html

On top of this, numbers are assigned to transcripts when we identify them. Sometimes, a transcript will be identified, then later found to be false, so we will lose that transcript model. This means that we might start with transcripts 001, 002 and 003, but if 002 is found to be false, we'll just have 001 and 003. A new transcript that is identified will then be 004. We don't want to call it 002 and think it's the same as the false transcript.
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Old 10-07-2014, 02:51 PM   #3
arkilis
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Smile

Quote:
Originally Posted by Emily_Ensembl View Post
Numbers that begin with 0 are transcripts that have been identified by Havana manual annotation, whereas numbers that begin with 2 have only been identified by Ensembl automatic annotation. There's more information on gene annotation here:
http://www.ensembl.org/info/genome/g...nnotation.html

On top of this, numbers are assigned to transcripts when we identify them. Sometimes, a transcript will be identified, then later found to be false, so we will lose that transcript model. This means that we might start with transcripts 001, 002 and 003, but if 002 is found to be false, we'll just have 001 and 003. A new transcript that is identified will then be 004. We don't want to call it 002 and think it's the same as the false transcript.

That explained a lot. Thanks for your reply!
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