Biological evidence includes transcript overlap (spliced or un-spliced), peptide hit, protein homolog alignment overlap, or InterPro domain presence.
Provided their biological authenticity, what is the nature of overlapping splice site choice?
While young gene overlaps can arise from new splice variants, ancient overlaps can disappear due to the loss of the overlapping splice variant.
In previous versions of Artemis, it could prove difficult to build and annotate overlapping splice forms from a single gene.
This clearly shows that overlapping splice variant of gene encoding ITFG3 is lineage specific and arose recently after divergence of primates.
For BRCA1 and BRCA2 expression analysis, probes and primers were designed so that they overlapped splice junction, thereby avoiding the potential amplification of genomic DNA.
To exclude the possibility that the overlapping splice variant was missed in annotations in non primate genomes we investigated alignments of human and other genomes in two genomic browsers, Ensemble and UCSC browser.
The central outcome of our study points to a splicing dichotomy between human alternative 5'ss and 3'ss exons in that they were markedly biased toward overlapping splice sites, with A5Es biased for E = 4 nucleotides (tandem donors, A5EΔ4), in contrast to A3Es biased for E = 3 nucleotides (tandem acceptors, A3EΔ3).
Of genes that overlapped spliced transcript alignments, we identified genes that were narrowly expressed and genes that were broadly expressed on the basis of overlap to the four single-tissue libraries (brain [combined Illumina forager and nurse brain libraries] and 454 libraries of mixed antennae, ovary and testes).
For at least three regions (4q13.1, 6p21.2 and 11p12 (shown in Figure 1D, Additional file 1C and Figure 1B respectively)), our CNV mapping data in fact identify two distinct clusters of CNVs at the same locus, all overlapping spliced ESTs and thus with a possible regulatory role.
