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Figure 4 | Genome Biology

Figure 4

From: An Ambystoma mexicanumEST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries

Figure 4

Phylogenetic analysis of the vertebrate cyclin-dependent kinase (CDK) inhibitors (CKIs) p21(Cip1), p27(Kip1) and p57(Kip2). (a) Reference phylogenetic tree of mitochondrial 12S rRNA. The Caudata and Salientia both branch out to build the amphibian group. (b) Unrooted phylogenetic tree of the cyclin B1 gene family. The amphibian cyclin B1 family members form a distinct group. (c) Unrooted phylogenetic tree of the amino-terminal CDK-inhibitory domain of vertebrate p21, p27, p28 and p57, which is conserved between the protein families. p27 of A. mexicanum clearly groups with the p27 proteins from other vertebrates. The amphibian-specific p28-family does not parse with any singe group. Note, however, that unlike the 12S rRNA tree, the A. mexicanum and A. t. tigrinum p27 branch out with that of D. rerio. (d) Unrooted, phylogenetic tree of the full-length kinase inhibitor sequences. Using the full-length protein sequences from the CKI families, the p28 family branches off between the p21 and p27 families. (e) Multiple sequence alignment of the amino-terminal, CDK-inhibitory region of the CKI families. The protein sequence of A. mexicanum p27 is clearly the ortholog of the p27 family, yet displays higher than expected divergence on the protein level. The same divergence is observed for the ambystomatid p57 proteins. The p28 family has extremely high sequence divergence compared to any other CDKN1 family member. Conserved residues between the three CDKN1 families are highlighted in green and the p28-family in light blue. Residues that differ between ambystomatid sequences and the other vertebrate species are highlighted in the ambystomatid sequences in red. Accession numbers are: NM_131513 (D. rerio ccnb1), NM_031966 (H. sapiens ccnb1), BC041302 (X. laevis ccnb1), NM_172301 (M. musculus ccnb1), NM_171991 (R. norvegicus ccnb1), P13351 (X. leavis ccnb2), XP_343420 (R. norvegicus ccnb2), P29332 (G. gallus ccnb2), NP_004692 (H. sapiens ccnb2), NP_031656 (M. musculus ccnb2), CAC24491 (X. laevis ccnb3), P39963 (G. gallus ccnb3), CAC94915 (H. sapiens ccnb3), NP_898836 (M. musculus ccnb3), AAH56746.1 (D. rerio p27A, Drp27A); AAK84219.1 (D. rerio p27, Drp27); CN056871.1 (A. t. tigrinum p27, Attp27); AAM22491.1 (G. gallus p27, Ggp27); NP_004055.1 (H. sapiens p27, Hsp27); P46414 (M. musculus p27, Mmp27); NP_113950.1 (R. norvegicus p27, Rnp27); NP_000067.1 (H. sapiens p57, Hsp57); P49919 (M. musculus p57, Mmp57); XP_341967.1 (R. norvegicus p57, Rnp57); CN039016.1 (A. mexicanum p57, Amp57); BM489375.1 (G. gallus p57, Ggp57); CK697132.1 (D. rerio p57, Drp57); AAH01935.1 (H. sapiens p21, Hsp21); NP_031695.1 (M. musculus p21, Mmp21); NP_542960.1 (R. norvegicus p21, Rnp21); AL639561.2 (X. tropicalis p21, Xtp21); BJ065460.1 (X. laevis p21, Xlp21); AAN63876.1 (G. gallus p21, Ggp21); I51683 (X. laevis Xic1, XlXic1); BX712320.1 (X. tropicalis p28, Xtp28); TNeu143i03.p1cSP6 (X. tropicalis p28A, Xtp28A); CN033557.1 (A. mexicanum p28, Amp28); CN035131.1 (A. mexicanum p28A, Amp28A); CN033708.1 (A. mexicanum p28B, Amp28B). The scale bar indicates substitutions per site.

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