UCSC, TSS and other annotations for known genes.

Transcription start sites inferred form dm3 KnownGenes track from UCSC Genome Browser.

• Raw data was downloaded from: UCSC Table Browser
• Input file format: TXT
• Download date: n/a

From D. melanogaster (Apr 2006 BDGP R5/dm3).

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	ucsc_promoter_list.sga	TSS from UCSC known genes	TSS	-
2	ucsc_CDSstart_list.sga	CDS start sites	CDS_start	-
3	ucsc_exonStart_list.sga	Exon start sites	exon_start	-
4	ucsc_intronStart_list.sga	Intron start sites	intron_start	-
5	ucsc_transcriptEnd_list.sga	Transcript end sites	polyA_site	-

Genes were retained if annotated as "protein coding" or if they had a protein ID or a refSeq status.

• Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ
  The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6. 14681465