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Fig. 1 | Genome Biology

Fig. 1

From: Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

Fig. 1

Long-read cDNA sequencing elucidates the human pseudogene transcriptome. a Full-length consensus PacBio cDNA reads from normal tissues and cell lines were compared to Gencode annotations to generate a pseudogene transcriptome. b Most transcribed pseudogenes identified here were absent from Gencode. c The transcription start sites (TSSs) of full-length pseudogene transcripts are enriched for CAGE-seq signal (data from FANTOM5 [24]). d Open Reading Frame (ORF) lengths of potentially coding-independent pseudogene transcripts. e Fraction of parental ORF length found intact in transcribed potentially coding-independent pseudogenes. f HMGB1P1 has a novel 5′ exon and is transcribed from an upstream CAGE-confirmed TSS. g Expression of 3XHA-tagged pseudogene ORFs in HEK293T cells detected by Western blot. HMGB1P1 and AK4P3 are translated when expressed in cultured cells. h A novel isoform of retinoblastoma (RB1) is transcribed from a TSS located within the pseudogene PPP1R26P1. The pseudogene sequence adds 179 codons to the RB1 ORF

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