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The HLA genes are amongst the most polymorphic in the human genome. Alternative splicing could add an extra layer of complexity, but has not been studied extensively. Here, we applied an RNA based approach to study the influence of allele polymorphism on alternative splicing of HLA‐C in peripheral blood. RNA was isolated from these peripheral cells, converted into cDNA and amplified specifically for 12 common HLA‐C allele groups. Through subsequent sequencing of HLA‐C, we observed alternative splicing variants of  HLA‐C*04  and  *16  that resulted in exon 5 skipping and were co‐expressed with the mature transcript. Investigation of intron 4 sequences of  HLA‐C*04  and  *16  compared with other HLA‐C alleles demonstrated no effect on predicted splice sites and branch point. To further investigate if the unique polymorphic positions in exon 5 of  HLA‐C*04  or  *16  may facilitate alternative splicing by acting on splicing regulatory elements (SRE), in‐silico splicing analysis was performed. While the  HLA‐C*04  specific SNP in exon 5 had no effect on predicted exonic SRE, the  HLA‐C*16  specific exon 5 SNP did alter exonic SRE. Our findings provide experimental and theoretical support for the concept that polymorphisms within the HLA‐C alleles influence the alternative splicing of HLA‐C.

Polymorphic differences within HLA‐C alleles contribute to alternatively spliced transcripts lacking exon 5