In summary, we demonstrated that 6 lncRNAs (LINC01116, KDM4A‐AS1, KMT2E‐AS1, LINC00839, UBL7‐AS1, DLX6‐AS1) related to ESCC progression could encode short peptides in ESCC by the combined analysis of WGCNA, prior ribosome‐seq data, ORF prediction, MS identification, and western blotting assay. Here, KMT2E is linked to esophageal squamous cell carcinoma.