For mouse, opossum, chicken, zebra finch, lizard, and frog ZNF motif sequences were retrieved based on HMMER search results.
Human (Homo sapiens), mouse (Mus musculus), Western clawed frog, African clawed frog, zebrafish, and salmon OMP nucleotides sequences were acquired from DNA Data Bank of Japan (DDBJ) with the ARSA keyword search [ 63].
The new mt sequences were annotated by comparison with other reported frog mt genomes using DOGMA [ 52].
The obtained mt sequences were annotated based on sequence similarity to reported frog mt genomes.
PEDF sequences were amplified from dog, pig, chick, African clawed frog, zebrafish, fugu and medaka (Fig. 3).
Sequences were obtained from ref. [ 13] (western clawed frog, zebra fish, puffer fish, chicken) and [ 18] (human).
The western clawed frog Dpl sequence was translated from JGI4.1 scaffold_143 1604545:1605090 (Ensembl).
To investigate evolutionary conservation of the 33 novel chicken miRNAs, a search for highly similar sequences among human, mouse, rat, opossum, frog and zebrafish genomic sequences was carried out using a BLAST analysis.
OTX5 shows a similar arrangement to OTX1 and OTX2, with fish leading to frog and bird; however, no mammal sequences are represented.
The presence of AMTN exon 2b in salamander cDNA and its absence in clawed frog, for which gDNA and cDNA sequences are available, indicates that this exon has been lost either early in the anuran lineage (no AMTN sequences available in other frog lineages), or later in the lineage leading to Pipidae.
