We previously reported alternatively spliced expression of these Helitrons in inbred B73 (Barbaglia et al. 2012).
Since the noncanonical AS events in the plant stress-responsive genes in the majority of experiments have been identified using RT-PCR and subsequent sequencing of the amplified RT-PCR products (e.g., [ 11, 24, 56, 58, 59]), there is likelihood that at least some of the reported alternatively spliced transcripts were artifacts of reverse transcription.
The CTIP2 gene (both mouse and human) contains 4 exons and the majority of the CTIP2 open reading frame is encoded by exon 4. Kominami's group has reported two alternatively spliced transcript variants, which encode distinct isoforms called CTIP2 long (containing exon1, 2,3 and 4) and CTIP2 short (lacking exons 2 and 3), [15].
Since a predominant expression of arginase over that of iNOS was reported in alternatively activated MØ [4] and a change in the L-Arg metabolism has been proposed to be an important component of wound healing [5], M2 MØ have been classified as reparative cells.
In addition to HXK1, further potential glucose sensors have been reported, which alternatively or additionally might be involved in glucose induced stromule formation [ 27].
In previous publications it has been reported that alternatively polyadenylated transcripts of the same gene can oscillate in counter-phase to one another [ 42].
In our previous work, we reported an alternatively spliced, nonfunctional CDH1 transcript that lacks the final 83 base pairs of exon 8 (1054 del83) of the gene.
Currently, only the Δ11 Brca1 splice variant has been confirmed to be present in mouse [ 48, 49], but no comprehensive search results have been reported for alternatively spliced Brca1 transcripts.
Recently, it has been reported that alternatively spliced RNA isoforms of some clock genes are degraded through the nonsense-mediated decay (NMD) pathway [ 28- 33], unlike the productive alternative splicing of CCA1 gene.
Previous studies reported that alternatively spliced exons tend to have higher nonsynonymous substitution rates (dn) and nonsynonymous-synonymous substitution rates (dn/ds) than constitutively spliced ones, indicating faster protein-level evolution in the former [ 40- 47].
At least three MMP-28 transcripts of 2.6, 2.0, and 1.2 kb have been reported representing alternatively spliced forms, differentially expressed in human tissues [ 60] and isoforms which encode proteins of 520 and 393 amino acids with predicted respective masses of 58.9 and 44.5 kDa.
