Prompted by the many ARS transcripts that consistently map to Qrr1d, we searched the genomic tRNA database [65] for tRNAs in this region. Interestingly, distal Chr 1 is one of many tRNA hotspots in the mouse genome and several predicted tRNAs are clustered in the non-coding regions of Qrr1 (figure 2). The majority of these tRNA sequences are in the proximal end of Qrr1, over 2 Mb away from Qrr1d. We scanned the intergenic non-coding regions in Qrr1d for tRNAs using the tRNAscan-SE software [65] and uncovered tRNAs for arginine and serine, and three pseudo-tRNA sequences between genes Igsf4b and Aim2 (175.204–175.257 Mb) in Qrr1d (dataset S3). Transfer RNAs are involved in regulating transcription of the ARS in response to cellular amino acid levels [66] and are functionally highly relevant candidates in Qrr1d. Polymorphism in the tRNA clusters (e.g., possible copy number variants, differences in tRNA species) may have significant impact on the expression of the ARS.
