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. Author manuscript; available in PMC: 2016 Sep 1.
Published in final edited form as: FEBS J. 2015 Jul 16;282(18):3556–3578. doi: 10.1111/febs.13358

Figure 4. Comparison of the transcriptome structure of novel rat transcript across mouse and human.

Figure 4

The top box (Rat) is the genomic region, chr12:40,902,059–40,918,309, in the RGSC 5.0/rn5 version of the rat genome. In the rat, the novel transcript is transcribed from the negative strand. The numerical values of the coordinates have been reversed, 40,918,309 bp to 40,902,059 bp, so that the direction of transcription (left to right in the graphic) is consistent across species. In this box, the transcript structure of three transcripts derived from the transcriptome reconstruction using the polyA+-selected RNA is shown as the first series of tracks in black (e.g., GENE_07345.ISO_1). GENE_07346 is the hub gene for the co-expression module (Figure 3). The second series (grey) in this box is the exon organization of GENE_07345 deduced from the PCR product sequence. The third series of tracks within this box indicate the genomic regions in the rat that are orthologous to the A930024E05Rik gene in mouse. The labels on the right are the relevant mouse RefSeq ncRNA ID. The final series of tracks in this box indicates the genomic region in the rat that is orthologous to LOC101928346 in humans. The label on the left is the relevant human RefSeq ncRNA ID. The second box (Mouse) is the genomic region, chr5:122,988,841-123,005,091, in the GRCm38/mm10 version of the mouse genome. The track within this box contains the A930024E05Rik gene as annotated in mouse. Regions that were identified as orthologous to the rat are colored with the same colors used in the Regions Orthologous to Mouse A930024E05Rik in the Rat box above. The third box (Human) is the genomic region, chr12:121579996-121596246, in the GRCh38/hg38 version of the human genome. The track within this box is the LOC101928346 lincRNA annotated in human with the relevant human RefSeq ncRNA IDs on the left. Regions that were identified as orthologous in the rat are colored with the same colors as in the Regions Orthologous to Human LOC101928346 in the Rat box above. It should be noted that the GENE_07346 and orthologous regions in the other two species are located between the Kdm2b and the Orai1 gene sequences. This figure was generated using the UCSC Genome Browser (http://genome.ucsc.edu).