Transcriptderived

Transcript-derived is a term used in genomics and bioinformatics to describe genomic features, transcripts, or annotations that are inferred or established from transcript evidence rather than solely from computational prediction. In this context, a transcript-derived gene model has exon–intron structure, start and end sites, and splice variants that are supported by transcript data such as mRNA sequences, expressed sequence tags (ESTs), full-length cDNAs, or RNA-seq–based transcript assemblies.

Common sources of transcript evidence include full-length cDNAs, EST collections, and high-throughput RNA sequencing data that are aligned to the genome and assembled into transcript models. Long-read technologies, such as Iso-Seq, provide additional support for alternative splicing and complete transcript structures, contributing to transcript-derived annotations. Researchers distinguish these models from ab initio or purely computational predictions that lack direct experimental transcript evidence.

Transcript-derived annotations are central to modern gene annotation workflows in databases and pipelines such as Ensembl, RefSeq, and GENCODE. They are used to define protein-coding and noncoding transcripts, establish gene boundaries, and characterize alternative splicing events. The emphasis on transcript support helps improve accuracy and functional interpretation of gene models.

Limitations include dependence on the breadth and quality of transcript data, which may bias annotations toward tissues or conditions with extensive sequencing, while missing lowly expressed or tissue-specific transcripts. Consequently, some genuine genes or isoforms may remain transcript-poor or unresolved, highlighting the ongoing need for diverse transcriptome profiling to complement ab initio predictions.