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Vol. 12, Special Issue 11 (2023)

In-silico exploration of species-specific early gene putative promoter motif of the Indian lumpy skin disease virus vaccine strain

Author(s):
Sukanya Baruah, Romen Singh Naorem, Udipta Borthakur and Joyshikh Sonowal
Abstract:
This study focuses on the identification of conserved sequences within the early gene promoter region of the Lumpy Skin Disease Virus (LSDV) genome. These sequences are located upstream of the transcription initiation sites of specific genes. Genomic data for both LSDV and Vaccinia virus (VACV) were obtained from the NCBI nucleotide (nt) database in FASTA and GB file formats. Using the Genome Annotation Transfer Utility (GATU) online software, LSDV gene sequences were annotated by comparison with the VACV genome. These genes were categorized as "Early" or "Late" based on published poxvirus literature. Specifically, early genes of LSDV were selected to identify consensus and conserved sequences in their promoter regions. Spacer regions between these conserved sequences and the gene's start codon were analyzed. A 103nt segment upstream of the translation initiation site from 34 early genes was retrieved from the NCBI database in FASTA format. The Multiple Em for Motif Elicitation (MEME) Suite 5.5.4 online program was employed to identify conserved sequences (motifs) within the early promoter region of LSDV. The results revealed a 15nt consensus sequence (AAAAATGAAAAAAAA) at the core of the 34 numbers of early gene promoter motifs for LSDV genes. Importantly, variations in the spacer lengths between the coding region and the regulatory early promoter motif were observed among early genes, potentially influencing gene expression.
Pages: 2279-2284  |  176 Views  71 Downloads
How to cite this article:
Sukanya Baruah, Romen Singh Naorem, Udipta Borthakur and Joyshikh Sonowal. In-silico exploration of species-specific early gene putative promoter motif of the Indian lumpy skin disease virus vaccine strain. The Pharma Innovation Journal. 2023; 12(11S): 2279-2284.

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