Fig. 5

A conserved translated ORF at the 5′ end of the JPX lncRNA has evolved from an upstream ORF (uORF) in the USPL gene. a Ribosome protected fragment (RPF) and RNA-seq coverage across the JPX locus in human. Ribo-seq and RNA-seq data from HEK293 cells (RPL10A pulldown for Ribo-seq) [28] and MDA-MB-231 [29]. The codons in the ORF are color-coded above the tracks as in the UCSC genome browser: a green square indicates an AUG codon and a red box indicates a stop codon. b Same as in a for the mouse locus. Ribo-seq and RNA-seq data from mouse embryonic stem cells (mESCs) and mouse embryoid bodies (mEBs) [27]. c Sequence alignment between the uORFs in USP12 and USPL and the ORF in JPX lncRNAs from different species. Sequences were obtained from the UCSC whole genome alignments and from manual inspection of transcripts in syntenic regions, aligned using CLUSTALW, and the alignment was manually refined. The TISU element region is in yellow and the beginning of the annotated coding sequences of the USP genes is in blue. d Same as a and b but for the human and mouse USP12 5′ UTR