Interestingly, this locus appears to be transcribed from a bidirectional POPDC1 promoter and, aside from the transcript encoding Popdc1, an antisense RNA (POPDC1 AS) is also generated, which has sequence overlap in antisense orientation with POPDC3.
The overall redundancy of the MGA was calculated to be less than 5.3%, thus a maximum of 138 of the 2,614 DNA fragments have a sequence overlap with another insert.
We considered host genes for these analysis only those that a) had a sequence overlapping that of the precursor miRNA either in introns, exons, or UTRs, b) were transcribed from the same strand as the miRNA, and c) were represented in the HG-U133A Affymetrix platform, which mostly includes known genes.
To confirm the phenotypes observed using the CalpA KK101294 RNAi line, we used two insertions of a second UAS RNAi construct (CalpA CG7563R1 and CalpA CG18152R2 ), from the Japanese National Institute of Genetics (NIG-Fly Stock Center), which had no sequence overlap with CalpA KK101294.
This may have been due to poor sequence overlap, i.e. the probes yielding poor correlations may have hybridized to different parts of transcripts that mapped to the same genes according to data in the Ensembl gene database.
Of the sequences missed by the Ensembl automated annotation pipeline, 20% could be considered as orthologs as they have a good structure and sequence overlap with bovine genes.
For both studies, the SNPs of each study were assigned to genes according to physical distance: a SNP was mapped to every gene whose coding sequence had an overlap with a 10 kb range around the SNP.
SNPs were mapped to genes according to their physical distance: a SNP was mapped to every gene whose coding sequence had an overlap with a 50 kb range around the SNP.
We subsequently construct the overlap graph of the dataset by creating a node to present each read, and an edge between each pair of reads if they have a sequence overlap with size no smaller than an integer k.
Similarly, of the 19,195 and 19,329 B genome gene models for Heera and Varuna, 16,748 gene models had overlapping sequences.
