Full-length zebrafish wtip was identified and assembled using TBLAST searches with human and mouse WTIP C-terminus sequence (including the three LIM domains) and the PDZ binding domain to identify comparable protein sequences in the zebrafish ENSEMBL database (Sanger Center).
A mouse ε cDNA fragment starting 5'at the XbaI site located in exon 4 to the 3'end including the stop codon was cloned into a 7-kb fragment of genomic γ subunit DNA sequence including native promoter sequences.
We performed a similar analysis and found no evidence of codon usage bias among the human and mouse uORF sequences included in this study.
The phylogenic analysis confirmed that the rainbow trout zar1 sequence was orthologous to the previously characterized vertebrate ZAR1 sequences including mouse Zar1.
Human, mouse and opossum WNT4 genomic sequences including 3 kb upstream and downstream of the start codon were retrieved from the Ensembl website.
The genomes of many species have now been completely sequenced including human and mouse.
Notably, the variant Fp amino acids Y629 and V657 were conserved in mammalian Fp sequences, including orangutan, macaque, mouse, dog, rat, and bovine.
The protein sequences, including the hypothetical proteins, of mouse OBPs were retrieved from Ensembl database.
The mtDNA control region and adjacent tRNAs were amplified by PCR using the primer pair H2228 (TTA TAA GGC CAG GAC CAA AC) and L15774 (TGA ATT GGA GGA CAA CCA GT) [ 4], and resulting sequences shortened to positions 15424-16276 of Bibb et al. [ 19] to align with previously published house mouse sequences [all sequences included in 3,5,9].
Repetitive sequences, including satellite repeats at pericentric and centromeric loci, and interspersed repeat sequences, represent about 45% of the mouse genome [ 13] and are normally highly methylated.
