Table 3 of
Nickerson, Mol Vis 2006;
12:1565-1585.Table 3 of
Nickerson, Mol Vis 2006;
12:1565-1585.
Table 3. Percent identities and scores comparing Repeat 1 protein orthologs and paralogs
A: Data suggest that the zebrafish and fugu IRBP loci as a pair of orthologs (Z1-F1 and Z2-F2) diverged more recently than Gene 1 and Gene 2 paralogs (Z1-Z2 and F1-F2). The paralogs Z1-F2 and Z2-F1 are consistent with the paralogs Z1-Z2 and F1-F2, in percent identity and score, suggesting that there has been no recent gene conversion. The greater conservation of the orthologs than the paralogs suggests that the divergence of Gene 1 from Gene 2 was an early event in teleost evolution, as the divergence of fugu and zebrafish was in the moderate to distant past in the history of the teleosts. B: Pairwise comparisons between the indicated two versions of Repeat 1 were conducted using BL2SEQ at the Biology Workbench (San Diego Supercomputer Center). The percent identity is indicated in the lower left half of each table. The raw bit score is indicated in the upper left right of the table.
A. Orthologs and paralogs compared in zebrafish and fugu
Repeat 1 gene and species
------------------------------------------
Repeat 1 gene and species Z1 Z2 F1 F2 HR1
---------------------------- ---- -------- ---- ---- ----
zfish Gene 1 Repeat 1 (Z1) --- 337 392 343 326
zfish Gene 2 Repeat 1 (Z2) 52% --- 302 416 289
score
fugu Gene 1 Repeat 1 (F1) 59% 48% --- 306 312 (bits)
fugu Gene 2 Repeat 1 (F2) 52% 63% 49% --- 297
human Repeat 1 (HR1) 53% 42% 51% 47% ---
percent
identity
B. Repeat 1 orthologs compared among teleost fish
Repeat 1 gene and species
--------------------------------------------------------
Repeat 1 gene and species Z2R1 F2R1 MR1 TR1 GR1 SR1 HR1
---------------------------- ---- -------- ---- ---- ----- ---- ----
zfish Gene 2 Repeat 1 (Z2R1) -- 416 384 406 543 402 289
fugu Gene 2 Repeat 1 (Z2R1) 63% -- 488 565 408 515 179
score
Medaka Repeat 1 (MR1) 59% 74% -- 488 379 491 295 (bits)
Tetraodon Repeat 1 (TR1) 63% 89% 75% -- 379 508 298
Goldfish Repeat 1 (GR1) 86% 62% 59% 61% -- 400 281
Stickleback Repeat 1 (SR1) 61% 79% 76% 78% 61% -- 295
Human Repeat 1 (HR1) 42% 47% 45% 47% 42% 46% --
percent
identity
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