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Open Access Research

Ancient genomic architecture for mammalian olfactory receptor clusters

Ronny Aloni, Tsviya Olender and Doron Lancet*

Author Affiliations

Department of Molecular Genetics and the Crown Human Genome Center, The Weizmann Institute of Science, Rehovot 76100, Israel

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Genome Biology 2006, 7:R88  doi:10.1186/gb-2006-7-10-r88

Published: 1 October 2006

Additional files

Additional data file 1:

Shown is a table listing the complete collection of the 251 CLICs defined in the study, each with the number of genes from each species, and the corresponding cluster names.

Format: XLS Size: 132KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional data file 2:

Shown is a table of genomic coordinates of non-OR genes shown in Figure 3.

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This file can be viewed with: Microsoft Excel Viewer

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Additional data file 3:

The number of OR clusters with at least two genes decreases as we increase the maximal intergenic distance allowed between consecutive genes in the same cluster. This dependency is shown for different species.

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Additional data file 4:

A suggested ancestral configuration is shown at the top row. Genes are presented as parallelograms colored by subfamily affiliation. Inferred chromosomal rearrangements relative to the ancestor are specified for each species: circle = insertion, X = deletion, arrow = inversion, broken line with number of genes = tandem duplication.

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Additional data file 5:

The figure shows schematic alignment of human-chicken genomic regions. Genes shared by human and chicken are shown as filled triangles, and others as empty triangles. Blue = ORs, red = β-globins, purple = taste receptors, green = ephrin receptors. Cluster names are as in Table 3. (a) Partial conservation of a human class I OR cluster containing β-globin genes (HBB@). Only a sample of the 103 human ORs is shown. The filled triangles were arbitrarily chosen to demonstrate that the 12 chicken ORs were aligned to 12 different locations in this human cluster. (b) Conservation of one human OR gene (OR10AC1P) from CLIC #16 in chicken alongside with partial conservation of syntenic bitter taste (TAS2R39, TAS2R40, TAS2R62P, TAS2R60, TAS2R41) and ephrin receptors (EPHB6, EPHA1).

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Additional data file 6:

For each chicken OR that appears in the chicken human-alignment net, including those that were not assigned a genomic location, the corresponding chain length was recorded. These are sorted from the longest (667026 bp) to the shortest (130 bp), with about 50% longer than 1000 bp.

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Additional data file 7:

The human versus mouse (red) comparison has provided 651 gene pairs with a mean identity value of 75%, compared with 63% for the 693 human-opossum pairs (blue).

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Additional data file 8:

Shown is a table of the genomic coordinates and cluster assignment for all OR genes used in this study.

Format: XLS Size: 703KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 9:

Shown are DNA sequences in FASTA format of the opossum ORs used in this study with their genomic coordinates in the Opossum October 2004 assembly (monDom1).

Format: ADDI Size: 1.5MB Download file

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Additional data file 10:

Shown are protein sequences in FASTA format of the opossum ORs used in this study with their genomic coordinates in the Opossum October 2004 assembly (monDom1).

Format: TXT Size: 606KB Download file

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Additional data file 11:

Shown are DNA sequences in FASTA format of the dog ORs used in this study with their genomic coordinates in the Dog July 2004 assembly.

Format: TXT Size: 1.1MB Download file

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Additional data file 12:

Shown are protein sequences in FASTA format of the dog ORs used in this study with their genomic coordinates in the Dog July 2004 assembly.

Format: TXT Size: 422KB Download file

Open Data