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IPD - The Immuno Polymorphism Database provides specialist databases for the study of polymorphism in genes of the immune system.
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EBI Databases Nucleotide Databases IMGT/HLA

IMGT/HLA Database

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*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.

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 out of the CDS, as in A*01:11N and B*44:02:01:02S, will be highlighted to aid identification of these regions. For A*03:01:01:02N and A*29:01:01:02N the genomic sequence alignments contain a highlighted region which is normally part of the intron but due to the aberrant splicing is now part of the CDS.
     
  • All remaining CDS sequences and files will only contain the sequence of the spliced exons. They will not contain any of the aberrant sequence, so for A*01:11N the exon 3 sequence will be 24 bps shorter than normal and the B*44:02:01:02S sequence will not contain the sequence corresponding to exon 5. For A*03:01:01:02N and A*29:01:01:02N, the CDS sequences will appear longer than the A*01:01:01:01 reference sequence.
     

Information

For more information about the database, IMGT/HLA queries (including website) or to subscribe to the IMGT/HLA mailing list please contact IMGT/HLA Support.

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