TranscriptDB

TranscriptDB catalogs conserved transcripts and phylogenies for 317 annotated eukaryotic species to enable the study of transcript conservation and evolution within gene families.

Key Features:

• Conserved Transcript Catalog: Provides extensive catalogs of conserved transcripts sourced from Ensembl database version 111.
• Phylogenetic Reconstruction: Offers phylogenies for conserved transcripts across 317 annotated eukaryotic species.
• Web Server Analysis: Enables users to retrieve information on transcript evolution using their own data as input.
• REST API: Supports programmatic data retrieval.
• Bulk Data Access: Provides a data directory for bulk downloads.

Scientific Applications:

• Transcript Homology Determination: Identifies conserved transcripts from homologous genes that have retained similar exon composition to determine transcript homology relationships.
• Transcript Function Study: Supports investigation of transcript functions through analysis of conserved transcript features.
• Transcript Phylogeny Reconstruction: Facilitates reconstruction of transcript phylogenies for evolutionary analysis.
• Gene and Transcript Evolution Exploration: Enables exploration of evolutionary patterns in genes and transcripts across eukaryotic species.
• Alternative Splicing Evolution Research: Supports study of alternative splicing mechanism evolution across different eukaryotic species.

Methodology:

Conserved transcripts are identified from homologous genes that have retained similar exon composition; data is sourced from Ensembl database version 111.