Chapter 18, Problem 28P

Summary Introduction

To analyze:

$\text{PEG10}$ is a paternally expressed gene that has an essential role in the formation of the placenta of the mouse. In the mouse genome, the $\text{PEG10}$ gene is flanked by SGCE and $\text{PPP1R9A}$ genes. For the study of origin of $\text{PEG10}$, syntenous regions spanning the SGCE and $\text{PPP1R9A}$ loci in the genomes of several vertebrates are examined, and observed that the $\text{PEG10}$ gene is present in the genomes of placental and marsupial mammals but absent in the platypus, chicken, or fugu genomes. The green bars in the figure indicate the exons of each gene. The gray bars represent LINEs and SINEs, and the blue bars indicate long terminal repeat (LTR) elements of retrotransposons. Solid black diagonal lines link introns, and dashed black lines connect orthologous exons. Arrowheads represent the direction of transcription. A tblastn search for homologous genes shows that the most similar sequences are in belongs to a class of retrotransposons. Based on this information, propose an evolutionary scenario for the origin of the $\text{PEG10}$ gene and its origin relation to its biological function.

Introduction:

In bioinformatics, BLAST stands for “basic local alignment search tool” that finds the region of local similarity between biological sequences. This algorithm compares a DNA sequence or an amino acid sequence to the sequences that are in the databases and calculates the statistical significance of the sequence matches. There are different types of BLAST presently used according to the query sequence. One of the BLAST types, tblastn can be used to find the homologous gene sequence for the predicted sequence of $\text{PEG10}$ and can be used to find a similar sequence in a class of retrotransposons.