Fig. 5
Sequence of the crow (C. cornix cornix) gene coding for TNFα (b) and organization of orthologous genes in the RJF (b). In (a), the crow sequence was extracted between positions 44,354 to 46,058 from the MVNZ01000346.1 contig [22], a sequence that was present in the original version of the C. cornix cornix genome model, but which was later split into several contigs in the second version. Above the DNA sequence is the translation into amino acids in all three frames of the plus strand. The crow TNFα sequence is shown in yellow. This sequence contained frame shifts in exons that resulted from errors in the assembly of the PacBio and Illumina reads. The start and stop codons are shown in bold and blue. Statistically significant blocks in direct and inverted repeats were identified with MEME at http://meme-suite.org/tools/meme and are indicated in black or dark grey boxes (depending on their orientation), green and blue boxes respectively. Motifs matching with the consensus of G4 structures (G3 + N1-12G3 + N1-12G3 + N1-12G3) are indicated in red. In (b) sequence features of the RJF gene are summarized, these were deduced from the alignment of PacBio reads (Additional file 5). The start and end positions of the PacBio read alignments for the four exons are indicated. Motifs in parentheses indicate tandem repeats, these are the only components of introns and the 5′ and 3′ regions. n, n’, n”, n”‘, n”“ and n”“‘describe different numbers of tandem repetition between motifs