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MGC Conference Call :Dec 6, 2007

MGC Conference Call :Dec 6, 2007. See BCGSC_MGC_summary_20071201.xls for MGC breakdown. See BCGSC_zebrafish_summary_20071201.xls for Zebrafish breakdown. Finishing complete for MGC targets Validation 1 complete for all Zebrafish targets. MGC Conference Call :Dec 6, 2007.

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MGC Conference Call :Dec 6, 2007

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  1. MGC Conference Call :Dec 6, 2007 • See BCGSC_MGC_summary_20071201.xls for MGC breakdown. • See BCGSC_zebrafish_summary_20071201.xls for Zebrafish breakdown. • Finishing complete for MGC targets • Validation 1 complete for all Zebrafish targets. 1

  2. MGC Conference Call :Dec 6, 2007 Alt splice clone selection 1. BLAT refseq sequence to filter out genes with less than 2 exons. 2. Get all clones of the gene. For each clone, do the following: a) filter out clones that are: "submitted"/"ok to submitted"/"finished"/"ok to finish" b) filter out clones where neither 5' nor 3' end reads match targeted refseq c) trim vector tags and barcode d) find out if the clone is fully sequenced ( phred quality >= 20 at window size 5) e) Any bases with phred quality < 10 are replaced with 'N' 3. BLAT refseq sequence to get gene exons 4. BLAT clone consensus sequence to get clone exons 5. Align clone exons against gene exons a) For clones not fully sequenced (identified in step 2d): go to step 6. b) For clones fully sequenced (identified in step 2d): go to step 7 and the steps after. 6. Identify alt splice clones. exit. No further analysis for clones not fully sequenced. 7. Identify alt splice clones 8. Filter out clones with splice site not in the following list: GTAG, GCAG, GTGG, ATAC, GTNN, NNAG 9. Filter out clones without full ORF (no stop codon found) 10. Report unique full ORF isoforms and submit to NCBI 2

  3. MGC Conference Call :Dec 6, 2007 Alt splice clone set consensus sequence phred quality analysis 3

  4. MGC Progress: December 6, 2007 4

  5. MGC Progress: December 6, 2007 5

  6. MGC Progress: December 6, 2007 Human submission summary • 12 x 384-well plates submitted • 1 x full plate awaiting QC • 1 x partial plate in-progress TOTAL = 14 plates • All 12 remaining difficult-to-sequence clones will be submitted on the in-progress plate 6

  7. MGC Progress: December 6, 2007 Single stranded clone list: Human 7

  8. MGC Progress: December 6, 2007 Mouse submission summary • 14 x 384-well plates submitted to date • 4 plates awaiting QC TOTAL = 18 plates • All 18 remaining difficult-to-sequence clones will be submitted on the in-progress plates 8

  9. MGC Progress: December 6, 2007 Remaining single stranded clones: Mouse 9

  10. Zebrafish progress: Dec 6, 2007 10

  11. Zebrafish progress: Dec 6, 2007 11

  12. Zebrafish progress: Dec 6, 2007 12

  13. Zebrafish finishing examples :Dec 6, 2007 Alt-splite site used in clone at 5’ end of exon, gaining 8bp Refseq Target 13

  14. Zebrafish finishing examples :Dec 6, 2007 Clone retained intron gain 156 bp Refseq Target 14

  15. Zebrafish finishing examples :Dec 6, 2007 alt-splice site used in clone at 5’ end of exon, lose 2bp Refseq Target 15

  16. Zebrafish finishing examples :Dec 6, 2007 Clone Sequences Aiding in Genome Assembly NM_001008484 The first 2400 bases of this clone align to chr 14 The latter 900 bases align to contig Zv7_NA475 16

  17. Zebrafish finishing examples :Dec 6, 2007 Clone Sequences Aiding in Genome Assembly NM_001034975 The first and last sections of this clone align to chr 22 The middle 1100bp align to chr 1 (miss-assembly?) 17

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