Fig. 5

Ybx3-like elements in the Nile rat genome. a Ybx3-like elements are interspersed throughout the genome. Many have been annotated as protein coding genes or pseudogenes by NCBI. Most are recognized as segmental duplications by SEDEF. b The architecture of a typical Ybx3-like gene, LOC117723436, visualized in the NCBI Genome Data Viewer. This gene has one large and one small exon. The large exon is flanked by MERVK26-int and RMER13B endogenous retroviral elements. It contains a CSD domain and is partially supported by short read RNA-seq data. c Expression of LOC117701283 in testis visualized in the UCSC genome browser. The three Iso-seq transcripts have identical CDSs, represented by thick boxes. MERV26-int is located in the 5′ UTR region, rather than outside the large exon like in most other Ybx3-like genes. d Multiple alignment of predicted Ybx3-like proteins and the canonical Ybx3, visualized by NCBI COBALT. This visualization uses the Rasmol color scheme, where amino acids with similar properties are shown in matching colors. The canonical protein is in the first row