Map of mouse and human orthologous OR clusters. Thick, black lines indicate finished or ordered sequence, encompassing mouse BAC 22b5, two mouse M50-phage contigs, three mouse B5-phage contigs, human Q25 cosmid, human Q27 cosmid, and human PAC 610i20. Thin, gray lines represent unfinished draft sequence (italicized BAC names, estimated sizes, and number of contigs indicated). OR genes are represented by green (ORF) and red (pseudogene) flags, with the orientation of the gene indicated by the flags. Non-OR genes are represented by gray arrows (accession numbers for highest blastx homologies are indicated in brackets below name). These include: mouse and human novel RNI-like genes, mouse cyclophilin-A processed pseudogene (Cyp) and HP1 chromobox-containing genes, two human zinc-finger genes (ZNF214, ZNF215), human L21 ribosomal, cadherin FIB1 (Cad), lysosomal pepstatin-insensitive protease (LPIP), TATA-binding factor II-30 (TAFII30), and integrin-linked kinase-1 (ILK) genes. Gene-linked CpG islands (CpG/GpC ≥ 0.75) are indicated by blue signs. Putative orthologous relationships are indicated by gray lines connecting genes from both clusters.

Phylogenetic tree of OR genes identified at the mouse and human orthologous locations. All 26 OR genes identified from both mouse (red) and human (blue) OR clusters (plus one mouse T1-like gDNA fragment) are represented in a paup (Sinauer Associates, Sunderland, MA) parsimony tree. Zonal expression patterns in the mouse main olfactory epithelium (1 = dorsalmost to 4 = ventralmost zones) are indicated by bracketed red numbers beneath gene names. Percent identities for the seven pairs of putative mouse–human orthologs are indicated (square brackets). The four major clades in the tree are rooted by black circles (MI, P, T, and B). Average pairwise identities between OR genes from different major clades are 54%. Percent identities within the MI clade range between 74% (M51–M51L) and 60% (M50–I7), within the P clade range between 95% (P3–P4) and 74% (P2–P4), within the T clade range between 92% (hT1–hT1L) and 80% (T2–T4), and within the B clade range between 98% (B5–B6) and 65% (B2–B7).

pipmaker and analysis of the 5′ UTRs and promoter regions of mouse OR genes. Gene structures for 12 mouse OR genes are plotted as determined by 5′ RACE-PCR. Coding sequences are shown as thick arrows, upstream exons are shown as thin lines, and introns are shown as bent lines. The B6 and M51 genes are alternatively spliced as shown. Relative positions to translation start sites are shown in kilobases (kb). The positions of putative promoters (excluding those found within repeats) between 3 kb upstream and 1 kb downstream of transcription start sites as predicted by three algorithms (N = NNPP, G = TSSG, W = TSSW) are indicated. Only NNPP scores >0.90 (0.33% false-positive rate) and TSSG/TSSW LDF scores >4.0 are shown. The sequence of each gene was compared with all other mouse and human OR genes at the P2 loci. Detected sequence homology (>50% identity) is plotted according to position along the test gene and level of sequence similarity. Dark-gray-shaded boxes surround regions of homology detected between the mouse OR gene and its human ortholog. Light-gray-shaded boxes indicate paralogy detected between P3 and P4 and among B4, B5, and B6. A region at the putative promoter of B1 has high sequence identity to an inverted sequence upstream of P4 (hatched rectangles). All other plots in noncoding regions represent sequence similarity of the test sequence to itself at some other position.