This page provides the supplementary information mentioned in C.E. Chapple and R. Guigó 2008.
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The following are the query sequences used for our genomic searches:
D.melanogaster protein | Other known eukaryotic selenoproteins |
Efsec | Multifasta file |
SBP2 | |
SPS2 | |
SLA/LP | |
secp43 | |
SelK | |
SelH | |
pstk |
The following are gff coordinate files for each of the selenoproteins predicted in the Drosophila genomes
The three SECISearch (patscan) patterns used in this study were:
Standard | Non-standard | "Twilight" |
For each selenoprotein and each gene coding for a factor involved in selenoprotein synthesis we have extracted the region including both upstream and downstream flanking genes from Lior Pachter's whole genome alignments of the 12 Drosophila species.
The files provided are an image (png) of the alignment as well as the alignments themselves in FASTA format. Finally we provide a jalview features file which shows the position of the START and STOP codons of each gene as well as the selenocysteine codon TGA if present. You will find three genes delineated (START-STOP) in each file, the one in the middle is the gene of interest in each case.
Factor | Alignment (text) | Features file | Image |
Efsec | alignment | features | image |
SBP2 | alignment | features | image |
SPS1 | alignment | features | image |
SPS2 | alignment | features | image |
SLA/LP | alignment | features | image |
secp43 | alignment | features | image |
SelK | alignment | features | image |
SelH | alignment | features | image |
pstk | alignment | features | image |
tRNASec | alignment | features | image |