Research article
Duplication and relocation of the functional DPY19L2 gene within low copy repeats
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* Corresponding author: Stephen W Scherer swscherer@sickkids.ca
1 Department of Genetics and Genomic Biology, Hospital for Sick Children, Toronto, Ontario, Canada
2 Department of Medical and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
BMC Genomics 2006, 7:45 doi:10.1186/1471-2164-7-45
Published: 9 March 2006Additional files
Additional File 1:
Supplementary Table 1: Coordinates of low copy repeats. This file lists the coordinates, in both NCBI Build 35 (hg17) and CRA_TCAGchr7.v2, of each LCR described in these analyses. Underlined coordinates indicate sequences used in the analyses, with the size of the region in brackets.
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Additional File 2:
Supplementary Table 2: Pairwise identity comparisons between the eight LCR regions. This table lists the modified percent match value calculated between each identified LCR in this analysis.
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Additional File 3:
Supplementary Table 3: Nucleotide identity comparisons. This file shows the nucleotide identities calculated from mVISTA (using SLAGAN alignment program) for the human genes (DPY19L1 through DPY19L4) and the C. elegans gene (DPY-19).
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Additional File 4:
Supplementary Table 4: Amino acid identity comparisons. This file shows the amino acid identities and positives from Blast 2 Sequences for the human proteins (DPY19L1 through DPY19L4) and the C. elegans protein (DPY-19).
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Additional File 5:
Supplementary Figure 1: DNA-based phylogeny of the gene and pseudogene transcripts. This file shows a maximum likelihood tree that was created in PAUP using a general time reversible plus gamma (α = 1.5090) model of sequence evolution. DPY19L3 was used as an outgroup to root the tree. Bootstrap values were calculated using 100 replicates and are shown at the nodes.
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Additional File 6:
Supplementary Figure 2: Putative novel domain identified by MEME. This file shows one of three motifs identified by MEME. This is the only motif that does not contain a transmembrane domain. Amino acids conserved in >90% of the proteins (at least 38 of 42 sequences) are shaded (grey when similarity groups are used). Asterisks (*) denote the 23 amino acids that have >90% identity without using similarity groups.
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