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)