Sentence examples for mouse sequence is from inspiring English sources
To maintain consistency between mouse genome assembly and our alignment coordinates, the multi-species alignment was compressed such that the mouse sequence is ungapped.
The mouse sequence is from the February 2006 release (mm8) of the C57BL/6J mouse strain.
As can be seen, the mouse sequence is divergent immediately 5′ to the seed sequence from the human gene which might explain this discrepancy.
These measurements are consistent with the findings observed in knock-in mice samples where Ser212 (mouse sequence) is replaced with alanine to ablate the critical serine phosphorylation (Fullerton et al. 2013).
Pairwise alignments of sequence from these species with the mouse sequence were computed and the resulting alignments were summarised as "percent identity plot" or "Pipplot" (Figure S3).
The masked and annotated mouse sequence were then finally used for interspecies pairwise alignment with the sequences from the different species mentioned above using the program PipMaker [ 66].
Mouse sequence was used for continuity in the Eel Pond mRNAseq protocol and to obtain Entrez gene IDs for pathway analysis.
Despite the relatively high homology between the mouse and rat over the proximal 5'-flanking region of the HL gene (Table 1), the outcome of the genomic sequence analysis differed whether the rat or the mouse sequence was used.
To carry this out, the mouse sequence was first analysed for repetitive sequence elements using RepeatMasker and secondly, the positions of all coding sequences/exons in Jmjd6, 1110005A03Rik, and Sfrs2 were identified and annotated using the BLAST algorithm.
The masked and annotated mouse sequence was then finally used for interspecies pairwise alignment with the human, bovine, armadillo, opossum, zebrafish, chicken, western clawed frog, and puffer fish sequences using the program PipMaker [ 66].
Finding evidences of this conservation by a direct comparison of the human and mouse sequences is very difficult because most of these ancient TEs are too corrupted to be identified.
