wiki:AnnotatingInArtemis

Annotating features in Artemis

"gene" features

These are the "feature keys" used for genes

  • CDS
  • CDS with qualifier /pseudo for pseudogene
  • misc_RNA
  • rRNA
  • snoRNA
  • tRNA
  • snRNA

The following qualifiers are available for all genes

names

  • /primary_name cardinal= 0,1
  • /systematic_id cardinal= 1
  • /synonym cardinality 0,1,>1
  • /obsolete_name cardinality 0,1,>1
  • /gene (legacy, deprecated)
  • /product cardinal= 1
  • /reserved_name

other

  • /EC_number
  • /GO
  • /controlled_curation
  • /colour (CDS only)

features associated with genes

  • 3'UTR
  • 5'UTR
  • polyA_Signal
  • promoter
    • Promoter regions; designate name systematic_id-promoter1, 2, 3.....also add a db_xref SO:xxx so that the consensus for that promoter is referenced
  • polyA_site
  • intron
  • /systematic_ID (mandatory the same systematic ID as the gene as CDS as they are part of the same gene)
  • /db_xref Will always have, if from a publication
  • /note (more later)

other features annotated

  • repeat_region (106)
  • LTR (237)
  • rep_origin (16)
  • misc_feature (100)

USE misc feature for any feature type not listed about

  • /SO="SO:0001044"
  • /SO="SO:0000186" (LTR tretrotransposon)
  • /SO="SO:0000577" (centromere) has no label, cent etc add?
  • /SO="SO:0005855" (gene group)

For all above

  • /db_xref Will always have, if from a publication
  • /note (more later)

Ignore these..…

  • CDS_AFTER (1)
  • gap
  • conflict
  • mRNA (3)
Last modified 6 years ago Last modified on Jan 27, 2015, 4:59:24 PM