Using expressed sequence tag (EST) analyses of cDNA libraries, orthologs of cortexin 3 with highly conserved sequences have been identified in mouse, rat, cow, dog, zebrafish, chicken, chimpanzee, Rhesus monkey and frog ([ 5]; cf. GenBank).
In this report, the proposed comparative genomics SSR discovery (CG-SSR) web service comprises eleven representative vertebrate species (human, chimpanzee, orangutan, mouse, rat, opossum, rhesus, cow, dog, zebrafish, and medaka) for constructing the fundamental SSR database.
The ATG13 gene has been annotated as an autophagy factor required for autophagosome formation and it is conserved in human, chimpanzee, mouse, dog, cow, rat, chicken and zebrafish.
We first collected previously published T2R gene sequences from human, mouse, dog, opossum, chicken, frog and zebrafish genomes as query sequences.
This score (between 0 and 1) is calculated for each nucleotide in the genome as a measure for evolutionarily constraint and was derived by comparing the rat genome to 8 other species: mouse, dog, cow, opossum, chicken, frog, zebrafish and human.
Orthologs of human ST pre-miRNAs were identified in seven other species (mouse, dog, opossum, platypus, chicken, frog and zebrafish).
(i) Infer the phylogenetic tree from the multiple alignment of vertebrate homologous TPI1 protein sequences (human, mouse, dog, cow, chicken, xenopus, fugu, and zebrafish), which is consistent with the known vertebrate phylogeny.
Opioid peptide precursor genes were identified in the genome databases for human, mouse, dog, grey short-tailed opossum, chicken, western clawed frog, zebrafish, medaka and stickleback, accession numbers for all sequences are available in Table S1.
Although teleost genomes may contain large number of 3R-WGD-derived duplicate genes as suggested above, it is reported that teleost and tetrapod genomes have similar number of protein-coding genes in general (mammals: 22,000 on average in human, mouse, dog, and cow; teleosts: 23,000 on average in Tetraodon, stickleback, medaka, and zebrafish) [ 41].
We were able to identify the complete protein sequence in mouse, dog (643 amino-acids, >78% PSI), chimpanzee (99% PSI), frog (38.7% PSI) and zebrafish (23.5% PSI), and partial sequences in chicken (>32% PSI).
