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Biotechnology

Year: 2007 | Volume: 6 | Issue: 3 | Page No.: 393-407
DOI: 10.3923/biotech.2007.393.407
Identification and Assignment of Human Superoxide Dismutase-1 Retropseudogenes Using Comparative Mapping and Bioinformatic Analysis
Ahlam A. Abou Mossallam

Abstract: In the course of studying the natural immunity of cattle and other rural ruminants in Egypt, SOD1 was one of the genes under investigation. The nucleotide sequence analysis of the obtained SOD1 amplified segments of cattle lead to the identification and assignment of SOD1 retropseudogenes Ψ 71.4 and 69.1 on human chromosome 8 and 16, respectively. Sequencing and Blast analysis for SOD1 amplified segments (370 nt) of Egyptian native cattle cDNA and genomic DNA revealed that these segments have 97% similarity. Blast analysis showed that the amplified sequence of cattle genomic DNA has great similarity with Bos taurus SOD-1 mRNA; with four separate segments of Bos taurus chromosome 1 genomic superoxide dismutase 1 and showed high identities with DNA of Bos taurus chromosome 13 similar to SOD1. These results indicate that cattle genomic DNA has intronless pseudogene on Bos taurus chromosome 13. The amplified sequence of cattle genomic DNA also showed a high similarity with three separate segments of human chromosome 21 on which the SOD1 gene is known to be located. In addition, four interesting alignments were also observed; it showed high alignment with a segment of human chromosome 16; a segment of human chromosome 8 and with human SOD1 processed pseudogenes Ψ 69.1 and 71.4. The SOD1 processed pseudogene Ψ 69.1 can be assigned to human chromosome 16 and the SOD1 processed pseudogene Ψ 71.4 can be assigned to chromosome 8. Two segments of 2000 nt from both human chromosome 16 and 8 were used for homology search. The maches obtained have high identities with the whole length of human SOD1 processed pseudogenes Ψ 69.1 and 71.4, respectively. These results identify the complete SOD-1 retropseudogenes sequence and their location on human chromosome 16 and 8, respectively. They bear the structural hallmarks of processed pseudogene; they lack introns; the 5’ and 3’ direct repeats are presented. They also contain TATA box upstream from the 5’ direct repeat in a position almost identical to the functional TATA box. They also contain a 3’ poly (A or T)-rich stretch and are flanked by short direct repeat sequences. The presence of SOD1 retropseudogenes on human chromosome 16 and 8 reported in this study explain the reported FALS and other diseases in individuals with a normal chromosome 21.

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How to cite this article
Ahlam A. Abou Mossallam , 2007. Identification and Assignment of Human Superoxide Dismutase-1 Retropseudogenes Using Comparative Mapping and Bioinformatic Analysis. Biotechnology, 6: 393-407.

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