A: Organization of the Atlantic salmon Sasa-DAA and Sasa-DAB promoters'. 5′ of the X box a putative W box is assigned to both promoters, based on highly conserved site and the localization approximately at the same position as the W box described in mammalian species. B: Nucleotide sequence alignment of MHCIIα promoters. X, X2, Y, and W boxes are indicated. Sequences are taken from MHCIIα promoters in the accessions: zebrafish, Brachydanio rerio, Brre-DAA|L19451|; spectacled caiman, Caiman crocodiles, Cacr-DAA|AF256650|; mouse, Mus musculus, H2-Aa|Y13081| and H2-Ea|M23352|; rabbit, Oryctolagus cuniculus, RLA-DRA|M28161|; sheep, Ovis aries, OLA-DRA|Z11599|; baboon, Papio hamadryas, Paha-DRA |X59620|; gorilla, Gorilla gorilla, Gogo-DRA|X59619|; human, HLA-DPA|X03100|, HLA-DQA, [M97461], and HLA-DRA|Z84814|. C: Nucleotide sequence alignment of MHCIIβ, promoters, sequences are taken from the accessions: rainbow trout, Oncorhynchus mykiss, Onmy-DAB# |AF316426|; zebrafish, B. rerio, Brre-DAB4 |BRU08870| and Brre-DEB |BRU08874|; spectacled caiman, C. crocodiles, Cacr-DAB#|AF256652|; chicken, Gallus gallus, Gaga-DAB#|M26307|; African clawed frog, Xenopus laevis, Xela-DAB#|D50037S1|; horse, Equus caballus, ELA-DRB|AF344426|; mouse, M. musculus, H2-Ab|MMY13074| and H2-Eb|MMY13072|; human, H. sapiens, HLA-DPB|X02228|, HLA-DQB|X55425|, and HLA-DRB|HS93N13| (number sign [#] brochets indicates that the sequence is not assigned a locus in the GenBank accession. Whereas an asterisk [*] indicates that the sequence position is not within the published sequence. A question mark [?] indicates that the distance to the start codon [ATG] is not within the published sequence). (Atlantic salmon MHCIIα and MHCIIβ promoters are included in patent applications by Genomar A/S, Oslo, Norway).
In the first position downstream of the X box, but within the X2
box ( Figure 2 ), a G and an A, respectively, were found.
The Atlantic salmon MHCIIα (Sasa-DAA) and MHCIIβ (Sasa-DAB)
promoters were aligned to other MHCII promoters available in the
databases ( Figure 2 ).
The short conserved X, X2, and Y boxes were identified also in the
salmon MHCII promoters ( Figure 2 ).
The X box of Sasa-DAA promoter shares more than 50% identity in 11
of 14 positions with the other promoters in Figure 2 , B.
A putative salmon W box was identified 5′ of the X box ( Figure 2 ,
Its localization coincides approximately with the mammalian W box (
Figure 2 , B and C)..
Alignment ( Figure 2 ) of the Atlantic salmon MHCII promoters
isolated here with published MHCII promoters from other species
shows that the X, X2, and Y boxes are highly conserved between
MHCII genes of Atlantic salmon and other species.
This putative W box has not been identified in any of the other
species including rainbow trout and other fishes ( Figure 2 ).
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Isolation of the Promoters of Atlantic Salmon MHCII Genes
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