Advancements in the accuracy of long-read sequencing technologies and bioinformatic approaches have broadened the applications of RNA sequencing (RNA-seq). This review covers such developments across various aspects of genomics, transcriptomics, and proteomics, focussing on the discovery and characterisation of new genes, transcriptional isoforms, and proteins. This review also explores the different approaches to characterise transcript isoforms that transcribed from both annotated and unannotated novel genes, such as determining protein-coding potential, functional domains, and conserved regions. Finally, the long-read RNA-seq (lrRNA-seq) based approaches for analysing co-transcriptional and post-transcriptional events, such as alternative splicing, polyadenylation, and RNA modifications, are elaborated. Conflicting recommendations, limitations, and priorities for future research for such methods reported by previous studies are also addressed. Overall, this review intends to demonstrate how integrated analyses can be achieved with lrRNA-seq in various areas of molecular biology.