The TAIR 10 assembly represents the Arabidopsis thaliana Col-0 genome. The TAIR 10 is a high-quality assembly but even the best assembly probably has some deficiencies. Has the Arabidopsis community found any errors?
The SEC10 locus may have a collapsed tandem gene duplication.
Here is one published claim of a TAIR 10 sequence problem. "Re-sequencing and manual assembly of the Arabidopsis thaliana SEC10 (At5g12370) locus revealed that this locus, comprising a single gene in the reference genome assembly, indeed contains two paralogous genes in tandem, SEC10a and SEC10b, and that a sequence segment of 7 kb in length is missing from the reference genome sequence."
Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus. PLoS One. 2014 Apr 11;9(4):e94077. doi: 10.1371/journal.pone.0094077. eCollection 2014. Vukašinović, Cvrčková, Eliáš, Cole, Fowler, Žárský, Synek. http://www.ncbi.nlm.nih.gov/pubmed/24728280