I can't find T cell receptors in my RNAseq expression table

Question

[Andrew]

My PI asked me to check what the level of expression of T cell receptor genes TRAC, TRBC, and TRDC in an expression table, but for some reason they don't seem to be here.

I've searched the gene names, and there is no TRAC, TRBC, or TRDC. I searched the gene descriptions for "t cell" and "receptor", and I cannot find it.

These is RNA that was reverse-transcribed and sequenced on an Illumina NextSeq 500, then mapped and quantified using the STAR aligner against the GRCh38 human reference transcriptome. I have 36,949 rows, but none of them appear to include these genes. Does anyone have any idea on why this is? I can't think of any other terms to search for, so it seems like they're not there. But if now, why not?

Thanks,

[rpolicastro]

Can you include the code you ran for STAR alignment, and give the specific annotation and assembly you used?

[ATpoint]

It should be included in both RefSeq and GENCODE. But the 36949 you mention is a strange number. Current RefSeq GTF has 61163 lines of type "gene" and GENCODE has 60649. Maybe your GTF has been filtered before. Note that these receptor components are not listed as "protein_coding" but as special biotypes, see for GENCODE right on top of the page: https://www.gencodegenes.org/pages/biotypes.html