Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 Page 6 of 17 Figure 2 Exon and intron boundaries for Atlantic salmon MHC class I genes from the U-, Z- and S- lineages. The exons are boxed with the sizes in bp above sequence and intron sizes below. Green exons indicate genes that do not contain typical transmembrane and cytoplasmic domains, yellow exon in ZCA indicate merged exons of a3 domain and TM and CYT. loci (ZBA, ZCA and ZDA). Figure 2 shows exon and intron boundaries for the described Atlantic salmon MHC class I genes from the U-, Z- and S-lineages. U-lineage Sasa-UDA and Sasa-UCAψ The 439J08 BAC is an allelic version of the IB region previously sequenced and represented by the BAC 8I14 [13]. Previously we identified only one MHC class I gene, the UCA pseudo locus in the IB region. A similar pseudo locus was also identified in the allelic 439J08 BAC showing 93% sequence identity towards the UCAψ in 8I14. We thus named the previously reported UCA allele UCAψ *0101, whilst the allele in 439J08 is named UCAψ *0201. The UCAψ *0201 allele contains an identi- cal internal stop codon as in UCAψ *0101 allele making this a pseudogene as well. The UCAψ *0201 allele in 439J08 shows 93% sequence identity towards the UCAψ *0101 allele in 8I14. 439J08 contains a duplicated MHC class I locus resid- ing approximately 50 kb upstream of UCAψ *0201, which we named Sasa-UDA. Dijkstra et al. [22] found a similar haplotype variation in rainbow trout. We found an EST match for this UDA locus [Genbank: GE768625], which is fully intact and expressed. The 439J08 UDA allele shows 95% sequence identity towards the UCAψ *0101 allele in 8I14. Sasa-UDA showed 90% identity towards rainbow trout UDA*0301 [Genbank: AY523671] and 89% identity to Onmy-UCA*0301 [Gen- bank: AY523661]. Only a limited polymorphism was observed in the few EST or full-length cDNAs available for UCA and UDA sequences. Further studies are needed to assess the polymorphic content for Atlantic salmon UCA and UDA loci in comparison to what Dijk- stra et al. described in rainbow trout [22]. Comparing the region between UCAψ and COLLA2, there is approx 98% identity between the 8I14 (LG3-1) and 439J08 (LG3-2) sequences, while the 439J08 sequence upstream of the UCA locus has no identity to 8I14 apart from the UDA locus. Sequence comparison shows that there is 100% identity for the other encoded proteins in 439J08 and 8I14. The partial sequence of 357C09, being an extended version of 439J08, did con- tain genes for TAPBP, DAXX, ZBTB22, KIFC1, FLOT1 and TUBB upstream of the UDA locus similar to what is found in the IA region. As the 357C09 sequence con- sists of 20 unlinked contigs the exact organization of these genes in the IB region remains unknown.