wiki:ExampleGenes

Examples of genes with specific features for demo/ testing etc

Ortholog related

  • See List for list of budding yeast genes without an identified fission yeast ortholog, and orthologs with low levels of conservation
  • Orthologs with different functions (my examples appear to be dud, add some after checking NOT annotations)
  • Genes which have equivalent functions (activities) but are not orthologs
    • Ste11 equivalent function in S. cerevisiae is performed by STE12, but this is STE-like not HMG

  • Ortholog prediction false positives
    • DBP is ortholog of S.c YBR278W ...these are not reciprocal best hits. The ortholog predictors predict YER159C
    • see also book chapter

Genome organization related

  • gene duplications in fission yeast
    • cox11 (cox1101 and cox1102)
    • rpn5 proteasome subunit (rpn501, rpn502)
  • possible co-regulated genes arg3/arg11 gal10,gal1

Gene structure related

  • fusion proteins 1 cerevisiae etp1
  • alternative splicing trt1, prp1, zas1
  • multiple transcripts meu1/2
  • snRNA in UTR intron spt20
  • dbp2 Really long intron (longest, this length is conserved between orthologs)

Annotation related

  • A selection of genes with lots of annotation:
    • clp1, mal3, ago1, dcr1, plo1, sre1
  • GO annotation related
    • IC example usp108
    • NOT annotations set9 fap1
    • tps1 has two extensions to +ve reg of trehalose catabolic process that are not pipe-separated, are both displayed?

  • gene with an 'other' allele information entered (check that the text information is displayed in the allele box): myo52 (this session is not loaded as of oct 2012)
  • gene with partial deletion phenotype: cbf12

Gene pages good for..…

  • phenotypes, alleles, evidence crm1, hmt1, pka1, hrk1, all pprs , cdc2, pap1
    • Lots of alleles mcm2

Searching related

  • example searching for function gamma-glutamylcysteine synthetase glutamate-cysteine ligase Gcs1

example component http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0031362#term=ancchart

Last modified 7 years ago Last modified on Jan 23, 2014, 10:21:23 AM