Table 3

Unique sequences from the 20 longest ORFs that have "hits" to other insect proteins and also "hits" away from protein coding regions in the Apis genome, but are not part of the Apis protein set.

Project Identification (bom001no-)

Organism "best-hit"

Protein

Description

Potential reason for absence from A. mellifera protein set


CL2097Contig1

N. vitripennis

XP_001604128.1

similar to F-box protein 28

Stop codon

CL2223Contig1

N. vitripennis

NP_001123269.1

nucleoporin Ndc1

Unknown

CL2537Contig1

N. vitripennis

XP_001606900.1

similar to p53-like protein

Stop codon

CL2610Contig1

N. vitripennis

XP_001600663.1

similar to ENSANGP00000017887

Unknown

CL2809Contig1

N. vitripennis

XP_001604974.1

similar to GA18228-PA

Stop codon

P0115M15_F

P. humanus corporis

XP_002432715.1

nuclear pore complex protein nup98

Stop codon


Unique sequences, from the sequences with the 20 longest ORFs that have "hits" to the Apis genome at least 4'375 bases away from predicted Apis protein coding regions, with highly significant "best-hits" (BLASTX, 1e-20) to an insect protein. These "best-hit" insect proteins were "blasted" against the Apis genome (TBLASTN) and the resulting alignments scanned for potential elements hindering protein production.

Sadd et al. BMC Genomics 2010 11:110   doi:10.1186/1471-2164-11-110

Open Data