Repeated product tag in a genbank file
0
0
Entering edit mode
4.9 years ago

While I was parsing all annotation records from the Pongo abelii (Sumatran orangutan) genome I realized that there are some annotations repeated, same location, strand, even note tag, but different (in some cases) product tag, here's an example from a log:

Species: PONAB | 42202927:42211982(+) | Product: zinc finger protein 155 isoform X1 | Note: By Gnomon.
Species: PONAB | 42202927:42211982(+) | Product: zinc finger protein 155 isoform X1 | Note: By Gnomon.
Species: PONAB | 42202927:42211982(+) | Product: zinc finger protein 155 isoform X1 | Note: By Gnomon.
Species: PONAB | 42202927:42211982(+) | Product: zinc finger protein 155 isoform X1 | Note: By Gnomon.
Species: PONAB | 42204537:42211982(+) | Product: zinc finger protein 155 isoform X2 | Note: By Gnomon.

What does this mean? Are they redundant? Should I remove repeated annotations or not?

Best regards, Marcos

genome annotation sequence genbank gbff • 806 views
ADD COMMENT
1
Entering edit mode

Duplicated features does happen from time to time, and they can often be ignored safely depending on what you're doing. It may be an artifact of a reannotation process or similar.

Its worth noting that one of those entries has a different coordinate, so may be something subtly different (since those are isoforms, it may be the same entity but with a legitimately subtly different start site).

ADD REPLY
0
Entering edit mode

This may be a glitch from Gnomon (NCBI's eukaryotic gene prediction tool). Let NCBI know by emailing the help desk.

ADD REPLY

Login before adding your answer.

Traffic: 2539 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6