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The Jumping Exon

The Jumping Exon. Craig Lowe Rotation Project Working For: Gill Bejerano and David Haussler. Introduction. Jumping exon is an ultra conserved region Blastz finds it in 32 other places in the human genome. Human Occurrences. Distribution. Found in exons, introns, UTRs, and intergenic

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The Jumping Exon

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  1. The Jumping Exon Craig Lowe Rotation Project Working For: Gill Bejerano and David Haussler

  2. Introduction • Jumping exon is an ultra conserved region • Blastz finds it in 32 other places in the human genome

  3. Human Occurrences

  4. Distribution • Found in exons, introns, UTRs, and intergenic • More conserved are in genes • More in genes than random distribution • Instances of varying conservation • Mostly found in genes related to transcription

  5. Secondary Structure • Most conserved instances and ancestor form hairpin structure • DNA/RNA binding • Editing • RNAi • Splicing out

  6. Origin • No instances have been found outside of vertebrates • Furthest species from human containing jumping exon is Coelacanth

  7. Coelacanth • “living fossil” – thought to have changed very little since time of the dinosaurs • Ultra contained in repeated element

  8. Fish Repeat

  9. Alignment • human TAGA-AGGCCAAGAGACTGAAGCCCTCCATTT-TTTCACAGAACAGGTAG---AACATGG • human TGAC-AGCCCTGGAGACTGAAGTCCTCTATTT-ATCCACAGAGCAGACACTGCAGCACGG • human TGA--AGGCGTGGAGACTGAAGTCCTCTCTAT-ATCCACAGAACAGGTAT---GGCACAG • fish TGAC-AGCCCCTGGAGAGGAAGTGTTCCATTT-ATCCACACAACAGGTAT---AGCA-GG • human TGGC-AGCCCCGCAGACTGAAGTCCTCTGTTC-ATCCACAGAACAGGTAC---AGCACGG • fish TGAC-AGCACTAGAGACTGAAGTCTTCTATTT-ATCCAGAGAACGGGTAC---GACACAG • fish TGAT-AGCACCAGAAGCTGAAGTCTATTATCC-TTCCACAGAGCAGGCAC---AGCATGG • fish TAAT-AGCATCAGAGACTAAAGTCCTTTATTT-ATCCACAGGACAGGTAT---AACATGG • fish TAAT-AGTACCAGAGACTAAACTTCTCTATTT-ATCCATAGAGCAAGTAC---AGCACTG • fish TGAC-AACACCTAAGACTGAAGTCCTCTATTT-ATCCACAGGATAGGTAC---AGCATGG • fish TGATTAGCACCAGAGACTGAAATCCTCTACTT-ATCCACAGAATATGTAC---AGCGTGG • human TGAC-AGCCCTGGAGACTGAAATCCTCTATTT-ATCCACAGGACAGGTAC---AGCACAG • fish TGAT-AGCACTGGAGACTGAAGTCCTCTATTT-ATCCACAGGACAGGTAC---AGCACAG • fish TGAT-AGCATCAGAGACTGAAGTCCTCTATTT-ATCCA-----CAGGTAC---AGCACAG • fish TGAT-AGCACCAGAGACTGAAGTCCTCTATTT-ATCCACAGGACAGGTAC---AGCACGG • fish TGAC-AGCACCAGAGACTGAAGTCCT--ATTT-ATTCACAGAACAGGTAC---AGCA--- • fish TGAT-AACACCAGAGACTGAAGTCCTTTATTT-ATTCACAGGACAGGTAC---AGCATGG • fish TGAT-GGCACCAGAGACTGAAGTCCTCTGTTT-ATCCACAAAACAGGAAC---AGCA-GG

  10. Exonic Function • Always natively unfolded • May bind DNA/RNA or Peptide • May be under selection for no function • Contains a NP motif • Possible cleavage • Implicated in nuclear retention • Linked to oral cancer

  11. Thank You • Gill Bejerano • David Haussler • Robert Baertsch • Jim Kent • Mark Diekhans • Patrick Gavin

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