BMC Genomics 2005, 6:152 http://www.biomedcentral.com/1471-2164/6/152 Table 1: List of human MHC class I and extended class I (xI) region genes used against the zebrafish whole-genome assembly. Genes with the suffix "like" are either gene fragments and/or highly similar to their human counterparts. Genes not identified by sequence similarity searches are marked as not found (NF). The official gene nomenclature for zebrafish is shown in brackets. MHC CLASS I REGION GENES xI xI xI xI xI xI xI xI xI xI I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I HUMAN name HFE HMGN4 PRSS16 POM121L2 GPX5 RFP MAS1L UBD GABBR1 MOG HLA* HCG9 PPP1R11 RPP21 GNL1 PRR3 ABCF1 PPP1R10 MRPS18B C6orf134 C6orf136 DHX16 NRM MDC1 TUBB FLOT1 IER3 DDR1 GTF2H4 VARS2L DPCR1 C6orf15 CDSN PSORS1C1 PSORS1C2 C6orf18 TCF19 POU5FI MICA HCP5 MICB accession NM_000410 NM_006353 NM_005865 NM_033482 NM_001509 NM_006510 NM_052967 NM_006398 NM_021905 NM_002433 NM_005844 NM_021959 NM_024839 NM_005275 NM_025263 NM_001090 NM_002714 NM_014046 NM_024909 NM_145029 NM_003587 NM_007243 NM_014641 NM_178014 NM_005803 NM_003897 NM_013994 NM_001517 NM_020442 NM_080870 NM_014070 NM_001264 NM_014068 NM_014069 NM_019052 NM_007109 NM_002701 NM_000247 NM_006674 NM_005931 location NF NF NF NF NF NF NF NF 15 [gabbr1] NF 19 [mhc1uea] s_1723 [mhc1ze] NF NF NF 16 [gnl1] NF 19 [zgc:85667] 19 [ppp1r10] 19 [mrps18b] 19 [c6orf134] 19 [c6orf136] NA5816 [dhx16] NA1826 [nrm] NF 20 [tubb5] 19 [flot1] NF 16 [ddr1-like] 19 [zgc:77721] 19 [vars2-like] NF NF NF NF NF NF 1 [tcf19-like] 16 [pou5f1] NF NF NF ZEBRAFISH location location location 19 [gabbr1] 19 [mhc1uaa] 19 [mhc1ufa] 1 [mhc1-like] (X3) 1 [zgc:64115] 19 [mhc1uda] 15 [dhx16] 14 [tubb2] 16 [flot1b] 22 [ier5] 4 [ddr2] 23 [tubb2] Genomic sequences encompassing the MHC are currently available for human, chimpanzee, macaque, rat, mouse, cat, pig, horse, quail, chicken, frog, teleost fish and shark [5]. While the genomic architecture of the mammalian MHC is conserved, the number of genes between species can differ greatly. In birds, for example, the minimal essential MHC in chicken consists of 19 genes [6] while gene duplications have expanded this region in quail [7] and sparrows [8]. The linkage of class I, II, and III region genes can be traced back to cartilaginous fish, which are the earliest jawed vertebrates known to have diverged from a common ancestor with humans [9]. MHC loci, however, do not always exist in a single tightly linked clus- ter as generally observed in mammals. A large scale inver- sion has separated the class IIB cluster from the MHC- linked class IIA cluster in cattle [10]. The class I and class II loci in zebrafish (Brachydanio rerio) are found on differ- ent chromosomes [11,12]. A similar organisation is Page 2 of 10 (page number not for citation purposes)