Frameshift in TRBV21-1*01 leader sequence?


#1

Hi All,

I have encountered a problem with the TRBV21-1*01 sequence from IMGT (http://www.imgt.org/genedb/fasta?outputFormat=fastaNConstructs&selectGenes=TRBV21-1&selectSpecies=Homo%20sapiens). If one translates the sequence starting with the ATG, there are multiple STOP condons. If you align them via V-Quest, it get’s obvious that the alignment is not in frame with the ATG.

Any thoughts on what is going on here?

Many thanks
Tim


#2

It’s listed as a pseudogene…


#3

I totally agree that this appears to be a pseudogene. It is denoted as a pseudogene by IMGT. There is no ATG codon in the expected place and the sequence itself is somewhat unusual (note two cysteins in FR3). Expression of the gene has been suggested (e.g. https://doi.org/10.1179/102453311X12902908411634, https://doi.org/10.1016/j.trim.2007.05.011, https://doi.org/10.1016/j.canep.2010.06.010) but it appears that at least these studies did not really sequence the PCR products but relied on the specificity of the primers used for amplification.