Figure 2

Evolutionary constraint of AK043754. (a) The genomic region of mouse chromosome 6 (chr6) encompassing the lncRNA locus AK043754 (1.7 kb) is depicted. Note the locations of flanking protein-coding genes: Grin2B (glutamate receptor, ionotropic, NMDA2B (N-methyl-D-aspartic acid)) and Emp1 (epithelial membrane protein 1). Also shown are the positions of mouse-chicken ECRs (evolutionarily conserved regions at least 100 bp in size with 70% sequence identity between the mouse and chicken genomes); ECRs within protein-coding regions are shown in blue. (b) A more detailed representation of AK043754 (single exon highlighted in orange) and its immediate flanking regions, including the 3' end of Grin2B. Below the gene structures are the positions of H3K4me1 chromatin marks (green) detected in mouse embryonic stem cells (obtained from UCSC Genome Browser), EvoFold predictions of RNA secondary structures (grey), a SinicView conservation plot [68] based on a 21-vertebrate multispecies sequence alignment (using Threaded Blockset Aligner) generated with mouse as the reference sequence, and Gmaj [66] views of alignments between mouse and the indicated species' sequences (note the detected homology with the orthologous lizard and chicken, but not frog, sequences). (c) Conservation and relative sizes of AK043754 orthologs in various species. The TSSs (arrows) and transcript lengths are depicted in each case. Note the conserved position of a polyA signal (red) and increased sequence conservation (relative to the mouse sequence) towards the 3' end. ECR, evolutionarily conserved region.