Homology Modelling and in-silico analysis of 39bp Insertion-Deletion in
Sahiwal Cattle SERPINA14 gene: The first report
Abstract
SERPINA14 proteins are progesterone induced and are secreted during
pregnancy in large quantities by the endometrial epithelium. Serine
proteinase inhibitor being represented only in a limited group of
mammals has been associated with higher embryo survival rates,
productive life, milk production and health traits and a minisatellite
insertion has been reported in Bali cattle. The most variable exons (1
and 4) of SERPINA14 gene in Sahiwal cattle were sequenced to reveal the
39bp repeats in the coding region of the exon 4. In order to ascertain
the changes in this gene that directly affects the protein structure,
its structure was deduced using homology modelling with Bos taurus as
reference, after imputing the missing coding sequence. The comparison of
protein structure using SWISS-MODEL, I-TASSER and PHYRE2 showed that
PHYRE2 predicted the best model for the proteinswith more than 90% of
the residues lying in the most favoured regions in the Ramachandran
plot.The impact of the indel with 5 repeats was assessed to be
deleterious using PROVEANwith a score of -22.464 while indel with 4
repeats had a score of -10.676 against athreshold of -2.5 comparing with
130 sequences and 30 clusters.However, the association of the indel with
reproduction data failed to reveal any significant effect which could be
attributed to the data size. Phylogenetic study of the gene with its
relatives showed that the sequence with 5 repeats was similar to Yak and
Bison while the one with 4 repeats resembled all bovines alike.