Alleles With Aberrant Splice Sites
Release 2.14.0 was the first to address the problem of representing alleles with aberrant splice sites. We have previously not marked the exon borders for aberrantly spliced alleles. In the current release the cDNA and protein sequences for the some alleles have been modified to reflect these changes. The following table lists the alleles for which we have currently identified aberrant splice sites.
| Allele | Description |
|---|---|
| A*01:11N | Point mutation near the end of exon 3, cDNA597G>T, results in a 24 bp reduction to the length of exon 3 due to premature start of intron 3. |
| A*03:01:01:02N | Point mutation at the start of intron 4, gDNA1846G>A, extends the exon by 65 bps. |
| A*29:01:01:02N | Point mutation at the start of intron 4, gDNA1846G>T, extends the exon by 62 bps. |
| B*07:44N | Point mutation near the end of exon 4, cDNA852T>G, results in a 43 bp reduction to the length of exon 4 due to premature start of intron 4. |
| B*15:01:01:02N | Deletion at the end of intron 1, gDNA175-184, causes incorporation of intron 1 into coding sequence. |
| B*44:02:01:02S | Point mutation at the end of intron 4, gDNA1934A>G, means the splice site for exon 5 is not recognised and consequently exon 5 is spliced out of the CDS. |
| B*56:01:01:05S | Point mutation at the end of intron 4, gDNA1934A>G, means the splice site for exon 5 is not recognised and consequently exon 5 is spliced out of the CDS. |
| C*03:03:01:32 | Point mutation at the end of intron 5, gDNA2538G>A, results in 18bp extension of exon 6. |
| C*03:23N | Point mutation in Exon 3, 406G>A, causes activation of cryptic splice site and the deletion of 64bp from the CDS. |
| C*07:02:01:17 | Point mutation at the start of intron 3, g710T>A, causes incorrect splicing and the deletion of 110bp from the CDS. |
| C*15:02:01:08N | Point mutation at the end of intron 2, gDNA431A>T, means the splice site for exon 3 is not recognised and consequently part of exon 3 is spliced out of the CDS. |
| DRB4*01:03:01:02N | Point mutation at the end of intron 1, gDNA9656G>A, means the splice site for exon 2 is not recognised and consequently part of exon 2 is spliced out of the CDS. |
| DRB4*01:03:01:13N | Point mutation at the end of intron 1, gDNA9656G>A, means the splice site for exon 2 is not recognised and consequently part of exon 2 is spliced out of the CDS. |
| DRB4*01:14N | Point mutation at the end of intron 1, gDNA9656G>A, means the splice site for exon 2 is not recognised and consequently part of exon 2 is spliced out of the CDS. |
In the database the alleles listed above have been modified to better reflect these changes, which include:
- As the alignment tool is an aid to visually representing these sequences it will show the aberrant sequences in full. Any sequence which is spliced into or out of the CDS will be highlighted to aid identification of these regions.
- All remaining CDS sequences and files will only contain the correct CDS sequence with the impact of the splice variation taken into account. This includes the fasta, msf and pir sequence files and also the hla.dat and hla.xml files.