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Conserved synteny and gene prediction

Conserved synteny and gene prediction. Jeltje – January 21 2004. What is synteny?. Synteny the occurrence of two or more genes on the same chromosome within one species - Conserved Synteny

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Conserved synteny and gene prediction

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  1. Conserved syntenyand gene prediction Jeltje – January 21 2004

  2. What is synteny? • Synteny the occurrence of two or more genes on the same chromosome within one species • -Conserved Synteny • The occurrence of synteny of orthologous genes in two different organisms. human chr7 mouse chr5 conserved synteny

  3. How not to think about conserved synteny human chr7 mouse chr1 chr5 chr3 chr18

  4. Rearrangements in evolution cause insertions human mouse

  5. Genes do not cross breaks?

  6. Pseudogenes and conserved synteny human mouse pseudogene? Could be a human-derived pseudogene that maps elsewhere in the mouse however it is unlikely that the green fragment contains an exon of the surrounding gene

  7. pseudogene finding?

  8. How many genes overlap a synteny break? • Get synteny tables from UCSC • For every exon in a gene, see to which chromosome(s) it maps • If a common chromosome cannot be found: list gene

  9. Unfortunately… • Results: 100 RefSeqs • 387 Twinscan genes

  10. Conserved synteny fragments per chromosome • 536766 chr1 • 295425 chr2 • 424573 chr3 • 322412 chr4 • 384215 chr5 • 353938 chr6 • 965845 chr7 • 358521 chr8 • 581427 chr9 • 388673 chr10 • 536356 chr11 • 279668 chr12 • 84576 chr13 • 125128 chr14 • 116420 chr15 • 311749 chr16 • 345482 chr17 • 191502 chr18 • 6527678 chr19 • 126663 chr20 • 80734 chr21 • 97941 chr22 • 302460 chrX • 150707 chrY • 13971696 total almost half!

  11. Synteny and gene length Average gene size on chromosome 19: 15187 (lowest of all chromosomes, avg total is 47807) Is the conserved-synteny fragment size smaller in chr19 and is the gene size smaller because of that? BUT: The median gene length is 312552 AND: >90% of conserved-synteny-fragments is found in 17 1 Mb fragments - many containing zinc finger genes.

  12. Using conserved synteny in gene prediction • HOW?

  13. Using conserved synteny in pseudogene finding • Bork et al.: Whole-genome pseudogene finding: • Use intergenic regions for BLASTX vs human proteins • Map hits to mouse and human genome • If there is a better hit in the human genome than in the mouse conserved syntenic region: possible pseudogene human mouse ?

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