Contents:
Table 1
Table 2
Table 3
Table 4
Supplementary Online Information

This page provides the supplementary information mentioned in C.E. Chapple and R. Guigó 2008.
It is best viewed using any STANDARDS  COMPLIANT browser such as firefox or opera (or anything but internet explorer)



Sequences used (Table 1)

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



Predictions (Table 2)


The following are gff coordinate files for each of the selenoproteins predicted in the Drosophila genomes

Species Protein
D.virilisselhselksps2
D.erectaselhselksps2
D.secheliaselhselksps2
D.simulansselhselksps2
D.mojavensisselhselksps2
D.willistoniselhselkNA
D.melanogasterselhselksps2
D.yakubaselhselksps2
D.grimshawiselhselksps2
D.persimilisselhNAsps2
D.pseudoobscuraselhselksps2
D.ananassaeselhselksps2



SECIS patterns (Table 3)

The three SECISearch (patscan) patterns used in this study were:

Standard Non-standard "Twilight"


Synteny (Table 4)

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