[Arabidopsis] pseudogene or not

[Jxy]

Hi collegues,
 
I recently cloned some genes of Brassica napus by RT-PCR/RACE through mining ESTs in GenBank. The primers were designed based on ESTs. After sequencing more than 2 clones for each gene,  I found, for quite a few genes, obviously, alleles exist. The most common is nucleotide substitution, next indel(insertion/deletion). An interesting phenomenon I found is for those alleles with a a long insertion compared to the other allele, the insertion is not 3-folds, i.e. the insertion leads to premature stop codon in the insertion or immedialtely after the insertion. The means that the translated amino acid sequence of one allele is normal (compared to At homolog), while the other is much shorter (premature stop codon). 
 
My question is why the insertion is not 3-folds and they are, for example 79bp, 100bp, etc? Are the alleles bearing the 79bp, 100bp insertion pseudogenes? BTW, I used high-fidelity polymerase when cloning those genes and, sequenced the clones from two ends with the same sequence, which excludes sequencing errors. Although RTase is error-prone, I have no way to predict this.
 
>From Wikipedia, I know that:
Pseudogenes are defunct relatives of known genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell. 
 
Therefore, a pseudogene may be transcribed, but not translated into a functional protein as a results of "extra" premature stop codon. 
 
Could someone provide any explanation? 
 
Thanks.
 
 
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