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Bioinformatics Project

Bioinformatics Project. By: Wiveka Ritzl and Johanna Ödvall. BLAST/BLAT matching. NCBI, Human Genome Browser and Ensamble Human ppp5c gene 13 exons Coding gene length 2060 bp. Serine/Tereonine phosphatase. Serine/Thereonine phosphatase family 11 members (Ensambl)

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Bioinformatics Project

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  1. Bioinformatics Project By: Wiveka Ritzl and Johanna Ödvall

  2. BLAST/BLAT matching • NCBI, Human Genome Browser and Ensamble • Human ppp5c gene • 13 exons • Coding gene length 2060 bp

  3. Serine/Tereonine phosphatase • Serine/Thereonine phosphatase family • 11 members (Ensambl) • Tetratricopeptide repeats and active site (PROSITE)

  4. Function • Dephosphorylation • Regulation of RNA biogenesis • Regulation of mitosis • Magnesium and iron ions cofactors

  5. Genomic location • Chromosome 19q13 • HIF3A upstream (same direction) • CCDC8 downstream (opposite direction)

  6. Cleavage with restriction enzymes

  7. Gene propertiesESTs, SNPs, Repeats and GC content

  8. Repetitive elements

  9. Homologies in mouse and rat

  10. Phylogeny based on cDNA • Sequences from NCBI • ednacomp, Emboss • Lycopersicon as out-group

  11. Phylogeny based on protein sequences • eprotpair, Emboss • Tryptanosoma as out-group • Highly conserved between plants and animals

  12. Promoter region • Binding sites for known transcription factors • 0-400bp upstream • rVista

  13. Tetrameric ppp5c (PDB)

  14. Miscellaneous • The protein is localised to the cell nucleus • Is not known to be involved in deceases (OMIM) • The gene is expressed in all human tissues (Xu et al., 1996) • Interaction with CDC16 and CDC27

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