Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 Page 5 of 17 AGPAT3 and PDXK have also been identified in zeb- rafish located on chromosome 1. AGPAT3 shows 83% identity to one Genbank EST [Genbank: ACI33566] whilst another EST clone [Genbank: DW540133] shows 93% identity suggestive of a duplicated locus elsewhere. This gene is highly conserved with the salmon sequence displaying more than 74% identity towards orthologs in mammals such as human, horse and pig. AGPAT3 is involved in the second step in the de novo phospholipid biosynthetic pathway where AGPAT3 is an acyltransfer- ase that converts lysophosphatidic acid into phosphati- dic acid [19]. PDXK phosphorylates vitamin B6, a step required for the conversion of vitamin B6 to pyridoxal- 5-phosphate, an important cofactor in intermediary metabolism [19]. We found two copies of VWA5A, which Martin et al show might function as a candidate tumor supressor gene in man and the gene is located on human chromosome 11q23-q24 [21]. Table 1 shows alternative nomenclature and matching ESTs for described genes. Other open reading frames were also identified, but they were associated with trans- poson related repetitive elements. Atlantic salmon MHC Class I genes In the IA region only one new MHC class I locus was identified (ZAA). In the IB region, a functional UDA locus was identified 50 kb upstream of the UCA pseudo locus in addition to the UGA locus and three Z-lineage Table 1 EST match to genes in the Atlantic salmon MHC IA and IB regions EST/cDNA GE768625, GE768626(a) CB498868, EG903380 GE771348, GE771349, EG819994(b) EG816925, DQ099914 EG880672 BT056476 BT072557 EG844714 GE795962(b) n.i BT046757 BT048223 n.i AY219864 n.i EG787974, DW548896(a) GE766956, DY713347 GE796418, DW540133 BT045602 DY730127, EG827413 DW576043, DW559009, DW559010, DY740683 DY713892, DW547688, DY719530(b) EG895467, DW549831, DW560133, DW560132(b) EG815474, Eg815473, DW567814, DW566896(b) DY713846, DW536069 DY734945, DY698459, GO058948 Genes in IA/IB region MHC class I MHC class I Ring finger protein 1 Ribosomal protein S18 Vacuolar protein sorting 52 VHSV induced gene MHC Class I Hypothetical Protein Activating transcription factor 6 Tenascin XB Proteasome subunit, beta type, 7 Centromere Protein A MHC Class I MHC Class I MHC Class I ATPase family, AAA domain containing 2 Zinc fingers and homeoboxes 1 Zinc fingers and homeoboxes 2 Genes in 184H23 aryl hydrocarbon receptor 2 alpha aryl hydrocarbon receptor 1 1-acylglycerol-3-phosphate O-acyltransferase 3 MHC Class I MHC Class I Pyroxidal kinase Genes in 114L13 MHC Class I von Willebrand factor A domain containing 5A BCSC-1 DY698831, DY698832, DW563762, DW538399, DW563761 v-akt murine thymoma viral oncogene homolog 2 Current abbreviation vs. older nomenclature is listed for each gene. All EST/cDNA sequences are from Genbank (n.i. denotes not identified). Additional comments: (a) Full-length sequencing of cDNA clones in-house (data not shown), (b) There is not sufficient EST/cDNA information to cover the entire open reading frame). Abbreviation UDA UGA RING1 RPS18 VSP52 VHSV ZAA Hypo ATF6 TNXB PSMB7 CENPA ZBA ZCA ZDA ATAD2 ZHX1 ZHX2 AhR2 AhR1 UHA1 UHA2 AGPAT3 PDXK VWA5A SAA AKT2 Alias RNF1 KE3 SAC2 CREBL1 XB Z CENP-A LPAAT-gamma PNK