Reference Genome sequence annotation (Retired)

The Reference Genome initiative will foster SO compliant annotations. The sequences will be available using the file format GFF3.

For discussion on standardizing URLs for accessing this information please see the GMOD wiki page Standard URL

Where to find SO compliant GFF3 annotations for the Reference Genome sequences. ( * means that the presented file is not yet SO compliant)

Organism	Organization	Download	Date
Drosophila melanogaster (Fruitfly)	FlyBase	ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/current/gff	9/12/07
Caenorhabditis elegans (Worm)	WormBase	ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF3	?
Saccharomyces cerevisiae (Budding yeast)	SGD	ftp://genome-ftp.stanford.edu/pub/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff	updated nightly
Dictyostelium (cellular slime mold)	dictyBase	http://www.dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=gff3&ID=dicty_gff3.zip	updated weekly
Arabidopsis thaliana	TAIR	ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR7_genome_release/TAIR7_gff3	8/15/07
Danio rerio (Zebrafish)	ZFIN Sanger Institute	Vega: ftp://ftp.sanger.ac.uk/pub/vega/danio/gff3/vega_danio_rerio_20070803.gff3 Ensembl*: ftp://ftp.ensembl.org/pub/current_gtf/Danio_rerio.ZFISH7.47.gtf.gz	With new releases
Mouse	MGI	?	?
Human	GOA	ftp://ftp.ensembl.org/pub/current_gtf/Homo_sapiens.NCBI36.47.gtf.gz	?
Schizosaccharomyces pombe (Fission yeast)	Sanger Centre	* ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF/	7/17/08
E.coli	ASAP	https://asap.ahabs.wisc.edu/asap/download_gff3.php?LocationID=&SequenceVersionID=&GenomeID=	?
Rat	RGD	ftp://ftp.ensembl.org/pub/current_gtf/Rattus_norvegicus.RGSC3.4.47.gtf.gz	?

Nota bene

1. The human and zebrafish Ensembl data is in GTF (not GFF3)
2. The rat Ensembl data (link provided) is also in GTF format
3. The pombe files are not (yet) valid GFF3. The known problems are:
   • extra column 10 "Name"
   • extra column 11 "orf_classification"
   • extra column 12 "gene"
   • extra column 13 "chr"
   • the mandatory "phase" column isn't filled in.
   • and the attributes" column may not be formatted correctly.

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