January 25, 2002 © Mitrick A. Johns Dept. of Biological Sciences, Northern Illinois University
Genes in these families have predicted peptides that match at least one other peptide in the famliy with a BLAST e-value of better than 10-180. Predicted genes come from the TIGR 08-10-2001 release (XML file). The predicted functions for these gene families are a concensus derived from the TIGR functional predictions for each of the genes.
Peptide and DNA sequences were aligned using the GCG (Wisconsin Package) "BestFit", "FrameAlign", and "PileUp" tools, with final adjustments made by hand. The aligned sequences can be seen for each family under the "Aligned DNA and peptide sequences" link.
Exon regions often contain short gaps that are not indicated here. Similarly, introns are often of different lengths, which are not indicated here. These drawings show the relative start and end positions of the coding sequences of the genes and the relative lengths of the aligned exons and introns.
The Arabidopsis ESTs (Expressed Sequence Tags) from the August 2001 release containing 117,000 ESTs were each used as queries in a BLASTN search using the TIGR predicted genes as a database. The 5000 full length cDNAs from Ceres deposited with TIGR in March 2001 were also used. The gene with the best BLAST score was assumed to be the source of the EST. For each of the genes used in the gene families on this page, the presence of an EST that best matched the gene is given in the gene family's table. If the BLAST score was worse than 10-30, it is listed as a "weak" match.
If a gene contained introns, any corresponding EST or Ceres cDNA clones were examined to see if intron sequences had been removed. If evidence exists for all the introns, the table entry for the gene is "yes"; if only some introns are confirmed, the answer is given as "some"; if the EST sequences didn't cross the exon-intron boundaries, the answer was given as "no". It is important to note that "no" does not imply an experimental contradiction of the predicted introns, but instead it implies a lack of confirmatory evidence. In rare cases where an EST contradicted a predicted intron boundary, a correction was made in the diagram.
As a simple and general measure of similarity, the genetic distance between each pair of family members was calculated. To compare the genes, the aligned sequences were trimmed at the 5' and 3' ends to a common length, and all intron sequences were removed. The resulting trimmed sequences can be seen under the "Exon sequences" link for each family. The exon sequences were then analyzed using the Jukes-Cantor distance method, the default with the GCG "Distances" program. This method calculates the number of mismatched bases, then applies a simple correction factor for multiple substitutions at a single site. Gaps are not penalized, and no distinction is made between transitions and transversions. Distances are expressed as the number of base substitutions per 100 bases). (Jukes T.H. and C. R. Kantor, 1969. Evolution of protein molecules. vol. 3, pp. 21-132. In H.N. Munro (ed.), Mammalian Protein Metabolism. Academic Press, New York)
The percentage of amino acids that are identical in the aligned peptide sequences was also calculated with the "Distances" program, using the uncorrected distance option. This gives the percentage of amino acids that differ between pairs of peptides, which was converted to percentage similarity by subtracting it from 100.
If two similar genes are both being subjected to selection pressure, due to the contribution of their protein products to the organism's fitness, non-synonymous base substitutions should be rarer than synonymous substitutions. Non-synonymous substitutions alter the amino acid sequence and potentially affect the protein's activity, and so they should be subjected to greater constraints than synonymous substitutions that don't change the protein sequence. Based on this prinicple, Li et al. (1985) developed a method that uses the ratio of synonymous to non-synonymous substitutions as evidence that a given portion of a gene has functional significance for the organism. This method, slightly modified, is the basis of the GCG "Diverge" program. It measures the corrected frequency of substitutions on aligned DNA sequences, and reports the ratio of synonymous to synonymous substitutions, Ks/Ka. A ratio greater than 1.0 implies that selection pressure exists for both genes. Thus, if both genes are active, the Ks/Ka ratio will be high, but if one or both genes is a pseudogene (selectively neutral), the ratio will be approximately 1.0. (Li, W.-H., C.-I. Wu, and C.-C. Luo. (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.)
Dotplots provide a graphical comparison of 2 DNA or protein sequences. They provide a rapid visual method of seeing major structural differences between genes, such as the presence and absence of introns. It is not necessary to align the sequences in advance; dotplots can be used as an aid to producing the alignments. In the simplest conception, one sequence is plotted on the x-axis and the other sequence is plotted on the y-axis, and a dot is placed at each point of intersection if the two sequences match. This results in a diagonal line for the areas where the genes are similar. The noise level is reduced by using a sliding window, and placing a dot if a given number of matches occur within the window. Here, the "Dotplots" link shows the DNA sequences (showing introns) and the peptide sequences (without introns). Also, displayed are the similarites of the 500 bp upstream from the start of the coding sequence, and 500 bp downstream from the end of the coding sequences. The plots were produced using the GCG "Compare" and "Dotplot" programs. (Maizel, R.P. and Lenk, J.V. (1981) "Enhanced Graphic Matrix Analysis of Nucleic Acid and Protein Sequences" Proc. Natl. Acad. Sci. USA 78; 7665-7669 )
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g20960 | yes | no |
| at2g42270 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g20960 | at2g42270 |
| at1g20960 | -- | 17.85 | 83.0% |
| at2g42270 | 5.068 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g31470 | yes | no |
| at3g01630 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g31470 | at3g01630 |
| at1g31470 | -- | 42.39 | 66.2% |
| at3g01630 | 5.291 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at5g40880 | no | -- |
| at5g49200 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at5g40880 | at5g49200 |
| at5g40880 | -- | 13.94 | 79.8% |
| at5g49200 | 1.859 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g18310 | no | -- |
| at5g15870 | weak | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g18310 | at5g15870 |
| at1g18310 | -- | 26.55 | 79.0% |
| at5g15870 | 5.622 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at3g56630 | no | -- |
| at1g34540 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at3g56630 | at1g34540 |
| at3g56630 | -- | 9.91 | 88.6% |
| at1g34540 | 3.792 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at4g02500 | yes | no |
| at3g62720 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at4g02500 | at3g62720 |
| at4g02500 | -- | 26.39 | 84.0% |
| at3g62720 | 11.225 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at3g10280 | no | -- |
| at2g46720 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at3g10280 | at2g46720 |
| at3g10280 | -- | 1.08 | 99.1% |
| at2g46720 | 8.718 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at2g39210 | no | -- |
| at2g28120 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at2g39210 | at2g28120 |
| at2g39210 | -- | 53.83 | 61.6% |
| at2g28120 | 6.763 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at4g05540 | no | -- |
| at5g52090 | weak | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at4g05540 | at5g52090 |
| at4g05540 | -- | 28.63 | 65.3% |
| at5g52090 | 1.383 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g72810 | yes | no |
| at4g29840 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g72810 | at4g29840 |
| at1g72810 | -- | 35.30 | 79.8% |
| at4g29840 | 9.129 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at4g21120 | no | -- |
| at1g17120 | yes | -- |
| at2g34960 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at4g21120 | at1g17120 | at2g34960 |
| at4g21120 | -- | 78.97 | 54.3% | 71.15 | 61.5% |
| at1g17120 | ND | -- | 50.81 | 60.7% |
| at2g34960 | ND | ND | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g04180 | yes | no |
| at4g28720 | no | -- |
| at5g43890 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g04180 | at4g28720 | at5g43890 |
| at1g04180 | -- | 45.67 | 73.6% | 22.70 | 83.9% |
| at4g28720 | 5.853 | -- | 47.41 | 74.8% |
| at5g43890 | 9.118 | 5.970 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at5g01320 | no | -- |
| at5g01330 | no | -- |
| at4g33070 | yes | some |
| at5g54960 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at5g01320 | at5g01330 | at4g33070 | at5g54960 |
| at5g01320 | -- | 7.31 | 92.5% | 14.16 | 89.2% | 28.42 | 81.6% |
| at5g01330 | 5.465 | -- | 15.01 | 87.0% | 30.35 | 79.9% |
| at4g33070 | 8.511 | 5.921 | -- | 29.68 | 82.2% |
| at5g54960 | 10.179 | 10.185 | 11.650 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g01600 | yes | yes |
| at4g00360 | yes | yes |
| at2g45970 | weak | -- |
| at1g63710 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g01600 | at4g00360 | at2g45970 | at1g63710 |
| at1g01600 | -- | 18.61 | 88.8% | 31.61 | 77.0% | 39.64 | 70.3% |
| at4g00360 | 10.859 | -- | 31.32 | 76.6% | 41.72 | 70.5% |
| at2g45970 | 7.255 | 6.363 | -- | 39.10 | 71.2% |
| at1g63710 | 5.423 | 6.908 | 6.151 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at2g44450 | yes | some |
| at3g60130 | yes | some |
| at2g25630 | yes | -- |
| at5g44640 | yes | -- |
| at5g42260 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at2g44450 | at3g60130 | at2g25630 | at5g44640 | at5g42260 |
| at2g44450 | -- | 30.36 | 71.2% | 14.57 | 89.1% | 14.14 | 89.3% | 14.62 | 88.6% |
| at3g60130 | 4.457 | -- | 31.48 | 71.3% | 30.68 | 73.0% | 31.08 | 73.2% |
| at2g25630 | 7.211 | 5.259 | -- | 12.80 | 93.8% | 12.96 | 92.5% |
| at5g44640 | 8.047 | 5.082 | 9.724 | -- | 3.97 | 96.3% |
| at5g42260 | 7.862 | 5.205 | 8.717 | 5.330 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at5g45530 | no | -- |
| at5g45470 | yes | -- |
| at5g45460 | yes | -- |
| at5g45480 | yes | -- |
| at5g45540 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at5g45530 | at5g45470 | at5g45460 | at5g45480 | at5g45540 |
| at5g45530 | -- | 54.23 | 58.0% | -- | 52.1% | 64.92 | 43.3% | 57.99 | 52.3% |
| at5g45470 | 6.079 | -- | -- | 77.7% | 60.13 | 42.1% | 58.41 | 50.3% |
| at5g45460 | -- | -- | -- | -- | 44.1% | -- | 43.0% |
| at5g45480 | ND | 3.341 | -- | -- | 44.24 | 60.1% |
| at5g45540 | 4.642 | 3.934 | -- | 3.881 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at4g33260 | yes | some |
| at4g33270 | yes | some |
| at5g27080 | no | -- |
| at5g26900 | no | -- |
| at5g27570 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at4g33260 | at4g33270 | at5g27080 | at5g26900 | at5g27570 |
| at4g33260 | -- | 2.53 | 98.7% | 19.49 | 78.5% | 19.59 | 77.6% | -- | 80.2% |
| at4g33270 | 12.781 | -- | 19.19 | 78.0% | 19.29 | 76.8% | -- | 80.5% |
| at5g27080 | 3.295 | 3.280 | -- | 2.71 | 93.7% | -- | 92.0% |
| at5g26900 | 2.965 | 2.940 | 1.503 | -- | -- | 91.2% |
| at5g27570 | -- | -- | -- | -- | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g21530 | no | -- |
| at1g21540 | yes | no |
| at5g16340 | no | -- |
| at5g16370 | yes | -- |
| at1g75960 | no | -- |
| at1g77240 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g21530 | at1g21540 | at5g16340 | at5g16370 | at1g75960 | at1g77240 |
| at1g21530 | -- | 15.82 | 89.4% | 46.90 | 62.3% | 47.60 | 61.2% | 51.05 | 60.8% | 28.03 | 59.8% |
| at1g21540 | 8.671 | -- | 47.94 | 62.2% | 48.52 | 61.7% | 54.01 | 60.5% | 26.44 | 80.0% |
| at5g16340 | 4.575 | 4.983 | -- | 6.85 | 91.8% | 22.56 | 79.6% | 51.12 | 59.3% |
| at5g16370 | 4.343 | 5.123 | 4.504 | -- | 23.48 | 79.8% | 52.36 | 60.2% |
| at1g75960 | 4.641 | 5.648 | 4.776 | 5.094 | -- | 54.40 | 59.8% |
| at1g77240 | 7.803 | 7.919 | 5.756 | 6.822 | 5.564 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at2g32830 | no | -- |
| at5g43350 | yes | no |
| at5g43360 | no | -- |
| at5g43370 | yes | yes |
| at5g43340 | weak | -- |
| at2g38940 | yes | -- |
| at3g54700 | weak | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at2g32830 | at5g43350 | at5g43360 | at5g43370 | at5g43340 | at2g38940 | at3g54700 |
| at2g32830 | -- | 43.39 | 76.0% | 45.37 | 77.2% | 43.04 | 75.2% | 55.13 | 65.3% | 42.36 | 75.9% | 41.33 | 75.9% |
| at5g43350 | 10.541 | -- | 10.67 | 93.7% | 2.30 | 98.9% | 51.68 | 67.8% | 37.09 | 77.7% | 37.04 | 78.3% |
| at5g43360 | ND | 10.046 | -- | 11.35 | 93.5% | 51.42 | 68.8% | 35.52 | 78.6% | 36.30 | 79.3% |
| at5g43370 | 9.541 | 10.286 | 10.089 | -- | 51.42 | 67.7% | 36.46 | 77.7% | 36.62 | 78.1% |
| at5g43340 | 4.461 | ND | ND | ND | -- | 50.77 | 67.0% | 46.34 | 69.1% |
| at2g38940 | 12.176 | 12.862 | 12.111 | 12.830 | ND | -- | 20.41 | 88.7% |
| at3g54700 | 12.912 | 11.457 | 16.432 | 11.632 | 6.028 | 15.087 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g01900 | yes | no |
| at2g05920 | yes | yes |
| at1g04110 | no | -- |
| at5g51750 | yes | -- |
| at3g14240 | yes | -- |
| at4g34980 | yes | -- |
| at5g67360 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g01900 | at2g05920 | at1g04110 | at5g51750 | at3g14240 | at4g34980 | at5g67360 |
| at1g01900 | -- | 78.74 | 45.8% | 81.07 | 43.9% | 78.75 | 45.6% | 77.82 | 44.7% | 76.80 | 45.0% | 73.44 | 46.8% |
| at2g05920 | 4.670 | -- | 73.44 | 48.7% | 69.99 | 49.6% | 67.24 | 50.5% | 69.35 | 49.3% | 62.37 | 55.6% |
| at1g04110 | ND | 4.940 | -- | 78.30 | 43.2% | 76.67 | 44.7% | 77.44 | 43.5% | 75.02 | 46.1% |
| at5g51750 | ND | 5.101 | 5.258 | -- | 72.45 | 47.7% | 70.62 | 49.4% | 64.64 | 53.1% |
| at3g14240 | 5.029 | 3.243 | ND | 5.761 | -- | 58.54 | 56.1% | 63.13 | 51.8% |
| at4g34980 | 3.618 | 5.329 | ND | 5.222 | 4.010 | -- | 63.10 | 51.1% |
| at5g67360 | 4.065 | 4.022 | 3.695 | 4.802 | 3.431 | 3.677 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at5g56350 | yes | yes |
| at4g26390 | no | -- |
| at5g63680 | yes | yes |
| at5g08570 | yes | yes |
| at3g04050 | no | -- |
| at3g55650 | no | -- |
| at3g55810 | no | -- |
| at3g25960 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at5g56350 | at4g26390 | at5g63680 | at5g08570 | at3g04050 | at3g55650 | at3g55810 | at3g25960 |
| at5g56350 | -- | 20.77 | 90.4% | 34.48 | 79.0% | 36.31 | 79.0% | 41.71 | 73.0% | 41.83 | 71.5% | 42.10 | 70.9% | 40.35 | 73.9% |
| at4g26390 | 18.943 | -- | 38.29 | 77.1% | 40.10 | 76.7% | 42.06 | 72.3% | 43.60 | 69.1% | 43.64 | 69.0% | 43.96 | 71.6% |
| at5g63680 | 10.733 | 10.943 | -- | 16.73 | 92.8% | 44.33 | 69.4% | 45.18 | 68.0% | 44.85 | 67.3% | 42.86 | 70.5% |
| at5g08570 | 10.157 | 11.304 | 15.247 | -- | 45.54 | 69.2% | 46.41 | 68.0% | 46.08 | 67.3% | 45.45 | 69.9% |
| at3g04050 | 8.787 | 8.526 | 8.484 | 9.707 | -- | 17.41 | 84.9% | 17.42 | 84.6% | 18.54 | 86.5% |
| at3g55650 | 7.383 | 6.948 | 8.193 | 10.983 | 5.653 | -- | 2.02 | 97.2% | 8.28 | 91.6% |
| at3g55810 | 7.802 | 7.459 | 8.342 | ND | 6.116 | 4.219 | -- | 8.13 | 91.7% |
| at3g25960 | 7.000 | 8.901 | 8.398 | 10.362 | 8.159 | 4.594 | 5.443 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at5g28540 | yes | some |
| at5g42020 | yes | some |
| at1g09080 | no | -- |
| at1g56410 | no | -- |
| at3g09440 | yes | yes |
| at3g12580 | yes | no |
| at5g02490 | yes | no |
| at5g02500 | yes | no |
| at1g16030 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at5g28540 | at5g42020 | at1g09080 | at1g56410 | at3g09440 | at3g12580 | at5g02490 | at5g02500 | at1g16030 |
| at5g28540 | -- | 2.36 | 98.8% | 34.43 | 77.4% | 48.09 | 62.3% | 46.15 | 64.0% | 46.96 | 62.9% | 47.47 | 62.9% | 47.16 | 62.8% | 51.02 | 62.8% |
| at5g42020 | 18.314 | -- | 35.29 | 77.2% | 47.78 | 62.0% | 45.16 | 63.8% | 47.87 | 62.5% | 47.16 | 62.7% | 46.66 | 62.5% | 51.13 | 62.5% |
| at1g09080 | 12.583 | 13.473 | -- | 52.01 | 60.1% | 49.96 | 61.8% | 50.80 | 61.2% | 51.99 | 59.8% | 51.48 | 60.5% | 49.86 | 61.9% |
| at1g56410 | 5.042 | 5.003 | 7.248 | -- | 21.03 | 87.5% | 26.28 | 86.9% | 13.43 | 89.6% | 18.36 | 89.3% | 33.91 | 79.5% |
| at3g09440 | 4.660 | 4.448 | 7.722 | 12.285 | -- | 23.48 | 90.9% | 17.96 | 91.7% | 17.21 | 93.1% | 31.83 | 81.7% |
| at3g12580 | 5.904 | 5.866 | 8.716 | 12.047 | 20.412 | -- | 23.48 | 90.2% | 23.33 | 91.2% | 28.40 | 84.5% |
| at5g02490 | 5.133 | 5.047 | 8.993 | 7.051 | 18.321 | 17.458 | -- | 14.22 | 94.2% | 31.28 | 81.0% |
| at5g02500 | 4.904 | 4.740 | 7.622 | 11.192 | 19.371 | 19.694 | 15.272 | -- | 32.35 | 81.9% |
| at1g16030 | 7.085 | 6.601 | 5.960 | 12.415 | 13.285 | 15.672 | 15.142 | 15.142 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at5g42280 | no | -- |
| at1g55410 | no | -- |
| at1g55380 | no | -- |
| at1g55390 | weak | -- |
| at1g55420 | weak | -- |
| at1g55430 | no | -- |
| at1g55440 | no | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at5g42280 | at1g55410 | at1g55380 | at1g55390 | at1g55420 | at1g55430 | at1g55440 |
| at5g42280 | -- | 23.50 | 64.9% | 22.03 | 70.2% | 21.60 | 67.9% | 21.76 | 66.8% | 23.31 | 64.2% | 24.50 | 65.8% |
| at1g55410 | 1.872 | -- | 24.24 | 70.2% | 24.37 | 67.6% | 24.16 | 66.7% | 26.37 | 64.2% | 27.02 | 65.2% |
| at1g55380 | 2.175 | 1.881 | -- | 20.46 | 70.6% | 8.41 | 81.8% | 18.99 | 71.8% | 23.89 | 66.8% |
| at1g55390 | 2.183 | 1.811 | 2.142 | -- | 21.21 | 66.9% | 22.40 | 66.9% | 22.98 | 67.6% |
| at1g55420 | 2.045 | 1.817 | 2.181 | 2.049 | -- | 18.27 | 69.4% | 23.76 | 65.9% |
| at1g55430 | 1.604 | 1.373 | 1.481 | 1.486 | 1.366 | -- | 25.06 | 64.1% |
| at1g55440 | 1.631 | 1.483 | 1.664 | 1.613 | 1.687 | 1.241 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g04220 | yes | yes |
| at5g43760 | yes | yes |
| at1g25450 | yes | yes |
| at1g68530 | yes | yes |
| at1g01120 | yes | -- |
| at1g19440 | yes | -- |
| at2g15090 | yes | -- |
| at2g16280 | yes | -- |
| at2g26640 | yes | -- |
| at4g34250 | yes | -- |
| at4g34510 | yes | -- |
| at4g34520 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g04220 | at5g43760 | at1g25450 | at1g68530 | at1g01120 | at1g19440 | at2g15090 | at2g16280 | at2g26640 | at4g34250 | at4g34510 | at4g34520 |
| at1g04220 | -- | 19.76 | 88.1% | 60.22 | 57.5% | 57.10 | 57.7% | 53.19 | 58.9% | 54.40 | 62.3% | 57.01 | 57.4% | 52.51 | 62.8% | 44.08 | 72.2% | 58.02 | 54.9% | 51.14 | 61.3% | 57.37 | 52.6% |
| at5g43760 | 9.170 | -- | 56.92 | 58.9% | 54.96 | 58.5% | 54.04 | 59.5% | 52.77 | 62.7% | 53.25 | 57.6% | 51.21 | 62.1% | 42.19 | 70.7% | 56.46 | 54.9% | 49.44 | 59.5% | 55.98 | 54.9% |
| at1g25450 | 7.117 | 6.400 | -- | 21.27 | 88.6% | 62.93 | 55.9% | 54.82 | 61.5% | 61.39 | 54.0% | 53.21 | 62.3% | 62.28 | 57.3% | 64.77 | 50.9% | 54.49 | 57.4% | 63.93 | 50.8% |
| at1g68530 | ND | 5.915 | 14.994 | -- | 63.10 | 55.5% | 55.26 | 61.9% | 64.70 | 54.2% | 54.67 | 62.7% | 61.63 | 57.3% | 65.79 | 51.4% | 58.62 | 58.3% | 66.48 | 51.7% |
| at1g01120 | 5.225 | 6.493 | 5.832 | ND | -- | 59.86 | 57.5% | 60.38 | 54.2% | 58.30 | 55.3% | 58.11 | 61.0% | 63.93 | 51.7% | 60.86 | 55.0% | 63.76 | 51.6% |
| at1g19440 | 7.721 | 10.133 | 7.305 | 8.866 | ND | -- | 47.37 | 63.9% | 31.16 | 76.2% | 50.64 | 65.3% | 47.90 | 62.7% | 37.16 | 70.8% | 46.30 | 63.8% |
| at2g15090 | 6.063 | 4.326 | 6.044 | ND | 6.164 | 7.121 | -- | 43.70 | 62.6% | 59.31 | 57.4% | 27.30 | 75.7% | 43.05 | 61.8% | 43.08 | 65.5% |
| at2g16280 | 6.418 | 7.155 | ND | ND | ND | 8.233 | 5.519 | -- | 48.98 | 63.9% | 42.94 | 61.4% | 25.27 | 79.7% | 39.61 | 66.7% |
| at2g26640 | 11.625 | 9.749 | ND | ND | ND | 9.521 | ND | 7.089 | -- | 60.98 | 55.9% | 51.72 | 60.3% | 59.86 | 56.0% |
| at4g34250 | 5.043 | 4.151 | ND | ND | 5.185 | 6.533 | 5.162 | 4.815 | ND | -- | 44.47 | 61.2% | 40.74 | 64.8% |
| at4g34510 | 5.899 | 5.335 | ND | ND | 7.169 | 7.695 | 4.778 | 6.428 | 5.515 | 4.382 | -- | 39.81 | 64.2% |
| at4g34520 | 5.511 | 9.170 | ND | ND | 4.316 | 8.241 | 5.153 | 5.544 | 7.413 | 4.490 | 4.880 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends
EST Information
| Gene | ESTs exist? | ESTs confirm introns? |
| at1g70110 | no | -- |
| at1g70130 | no | -- |
| at2g37710 | yes | -- |
| at2g43690 | no | -- |
| at2g43700 | no | -- |
| at3g55550 | no | -- |
| at3g59700 | yes | -- |
| at3g59730 | no | -- |
| at3g59740 | yes | -- |
| at3g59750 | no | -- |
| at4g02410 | no | -- |
| at4g02420 | weak | -- |
| at4g29050 | yes | -- |
Genetic distances | Percent peptide similarity (upper) and Ks/Ka ratios (lower)
| -- | at1g70110 | at1g70130 | at2g37710 | at2g43690 | at2g43700 | at2g59730 | at3g55550 | at3g59700 | at3g59740 | at3g59750 | at4g02410 | at4g02420 | at4g29050 |
| at1g70110 | -- | 40.06 | 61.5% | 72.18 | 46.8% | 60.96 | 49.8% | 60.01 | 51.7% | -- | 46.5% | 73.90 | 43.2% | 61.23 | 52.3% | 61.81 | 50.6% | 60.37 | 50.3% | 71.75 | 44.0% | 75.49 | 46.5% | 32.95 | 69.4% |
| at1g70130 | 3.458 | -- | 73.89 | 44.0% | 66.57 | 46.3% | 64.27 | 49.0% | -- | 47.4% | 78.30 | 42.3% | 64.47 | 48.1% | 66.87 | 47.0% | 67.27 | 46.5% | 73.45 | 43.1% | 75.35 | 43.2% | 37.42 | 65.3% |
| at2g37710 | ND | 4.943 | -- | 75.904 | 42.7% | 73.09 | 44.7% | -- | 46.5% | 69.94 | 48.5% | 73.92 | 45.2% | 77.47 | 43.7% | 76.41 | 42.4% | 26.69 | 73.6% | 26.62 | 76.8% | 70.49 | 48.9% |
| at2g43690 | 3.882 | 3.611 | 4.753 | -- | 26.57 | 70.5% | -- | 64.5% | 80.16 | 42.0% | 41.70 | 62.2% | 42.43 | 60.5% | 41.17 | 60.5% | 75.29 | 41.3% | 75.59 | 42.1% | 57.09 | 50.5% |
| at2g43700 | 4.840 | 4.917 | 4.432 | 3.185 | -- | -- | 66.5% | 77.56 | 43.5% | 38.61 | 67.5% | 39.22 | 65.3% | 39.39 | 64.1% | 72.02 | 44.0% | 72.34 | 45.3% | 58.64 | 52.7% |
| at2g59730 | -- | -- | -- | -- | -- | -- | -- | 45.4% | -- | 79.1% | -- | 78.3% | -- | 77.7% | -- | 44.4% | -- | 46.1% | -- | 52.8% |
| at3g55550 | 4.402 | 4.115 | 4.868 | 4.699 | 4.877 | -- | -- | 79.55 | 43.0% | 78.43 | 42.8% | 78.54 | 42.3% | 69.96 | 47.2% | 71.15 | 48.9% | 75.31 | 45.6% |
| at3g59700 | 4.436 | 3.658 | 3.811 | 4.024 | 5.059 | -- | 7.743 | -- | 17.01 | 78.9% | 19.19 | 77.0% | 73.04 | 44.1% | 74.67 | 44.5% | 56.34 | 53.0% |
| at3g59740 | 4.601 | 3.811 | 3.960 | 3.533 | 4.135 | -- | ND | 2.344 | -- | 14.89 | 82.1% | 75.29 | 43.4% | 76.24 | 44.0% | 57.90 | 51.6% |
| at3g59750 | 4.054 | 3.769 | 3.519 | 3.738 | 4.044 | -- | 5.292 | 2.529 | 2.431 | -- | 74.66 | 42.3% | 74.73 | 43.1% | 58.61 | 51.6% |
| at4g02410 | ND | 4.060 | 3.898 | 6.348 | 4.596 | -- | 5.000 | 3.990 | 4.289 | 3.826 | -- | 19.27 | 78.0% | 69.21 | 47.5% |
| at4g02420 | ND | 5.958 | 4.507 | 5.218 | ND | -- | 5.288 | 6.174 | 5.181 | 4.029 | 3.561 | -- | 69.23 | 49.1% |
| at4g29050 | 3.479 | 3.681 | 7.658 | 3.437 | 4.941 | -- | 4.723 | 4.125 | 4.447 | 4.257 | 6.326 | 7.382 | -- |
Aligned DNA and peptide sequences
Exon sequences (used for distance and Ks/Ka calculations)
Dotplots for pairs of genes in the family, including DNA, peptides, 5' and 3' ends