Two CpG islands with a GC content of more than 80% were identified preceding and overlapping the first exons of both transcript versions of the gene.
If a motif has multiple versions in the databases, such as the DNA binding domain and full transcript versions in the high-throughput SELEX database [ 20] we only select the motif with the lowest CentriMo log adjusted p-value.
Primer sequences for amplification of an APITD1 probe were chosen with the forward primer in exon 2 (5′-AAACAGACCATTGCGGCCATT-3′) and the reverse primer in exon 5 (5′-TTCCAAGCGGCGAGGG-3′); thes, the probe was complementary to both transcript versions of APITD1.
Two mutants (mlo-6 and mlo-44) revealed evidence for aberrant Mlo transcript splicing, owing either to the presence of multiple aberrant transcript versions (mlo-6; resulting in overlapping sequence traces) or the presence of one aberrant transcript type harboring the entire Mlo intron 3 (mlo-44).
Preliminary sequence homology searches between the HDV Rz and a bank of human transcripts revealed that the ribozymes could potentially target several human transcripts (version 35.1 of the human genome).
The P. trichocarpa transcripts (version 3) and annotated gene set were downloaded from the Department of Energy Joint Genome Institute (DOE-JGI; http:://www.phytozome.net/poplar).net/poplar
We then calculated the CQs for the A. aegypti IB12 strain supercontigs (version AaegL1), contigs (version AaegL1), transcripts (version AaegL1.3), expressed sequence tag (ESTs) (Aedes-aegypti_EST-CLIPPED_2012-12.fa.gz), and BAC-ends (Aedes-aegypti-Liverpool_BAC-ENDS_2012-12.fa.gz).
To assess the quality of the de novo assembly, a similarity search against P. trichocarpa transcripts (version 3) was further conducted using BLASTN algorithm with E-value less than 1.0E-5.
