vert_71

vert_71 analyzes LTR-derived microRNA expression and identifies target genes in Sebastes schlegelii, focusing on miR-1269a and its interaction with KSR2.

Key Features:

• Expression Pattern Analysis: Analyzes expression patterns of LTR-derived miR-1269a across Sebastes schlegelii tissues including muscle, liver, gonad, and brain.
• Target Gene Identification: Predicts and aggregates potential miR-1269a target genes using miRDB and TargetScan 7.1.
• Luciferase Reporter Assay Integration: Integrates luciferase reporter assay data from HINAE cells for validation of miRNA–target interactions.
• TE Association Analysis: Maps miRNAs to transposable elements using the UCSC Genome Browser and identifies derivation from the LTR retrotransposon MLT2B.
• Enhancer Activity Assessment: Assesses enhancer-like activity of miR-1269a on target genes such as KSR2 to evaluate regulatory mechanisms.

Scientific Applications:

• Genetic research in Sebastes schlegelii: Enables investigation of TE-derived miRNA roles in gene regulation in Sebastes schlegelii.
• Tissue-specific expression studies: Supports analysis of tissue-specific expression patterns of miR-1269a across muscle, liver, gonad, and brain.
• Functional validation of miRNA–target interactions: Combines computational predictions with luciferase assay data to evaluate functional interactions exemplified by miR-1269a and KSR2.
• TE–miRNA regulatory studies: Facilitates identification of miRNAs originating from transposable elements such as MLT2B to study their regulatory impact.

Methodology:

Computational methods include target prediction using miRDB and TargetScan 7.1 and transposable element mapping via the UCSC Genome Browser.