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. 2021 Feb 3;11:627007. doi: 10.3389/fgene.2020.627007

Figure 4.

Figure 4

Several USP18 exon 11 copies are embedded in expressed long intergenic non-coding RNA (lincRNA) genes. (A) Schematic of human chr22 (about 50 Mb) and below the chr22q11.21 region with four LCR22s. The bona fide USP18 gene resides at the boundary of LCR22A. The pseudogene USP41, located in LCR22B, contains most USP18 gene sequences, i.e., from exon 3 to exon 10, but lacks the 5’ and 3’ UTRs. The six copies of USP18 exon 11 are indicated in red. Genes and USP18 copies are shown with their genomic orientation (> for + strand, < for − strand). (B) Top, intron-exon organization of the human USP18 gene. Exons, gray boxes; introns, lines. Exon 11 is highlighted in red. Below are aligned the duplications found. Copies A1–4 contain most of USP18 intron 10 and the entire exon 11. Copies B1 and B2 contain a smaller sequence of intron 10 and exon 11. (C) Map of FAM247A-D transcripts containing USP18 exon 11 in red. The annotated exon upstream of exon 11 is represented as white box. Arrows indicate the primers (A_FW1 and A_RV1) designed across the junction and used to measure expression of FAM247A/C/D in (E). (D) Map of linc-UR-B1. The annotated exon upstream of exon 11 is represented as striped box. Arrows indicate the primers (B_FW1 and B_RV1) designed across the junction and used to measure expression of linc-UR-B1 in (F). (E) Expression of FAM247A/C/D in 20 human tissues (pool of donors for each tissue; Human Immune System MTC™ Panel, Human MTC™ Panel I, and Human MTC™ Panel II). Results shown as expression (2-ΔCt) relative to ACTB. SEM is shown for tissues present in two of the above panels. (F) Expression of linc-UR-B1 in the same samples used in (E).