UCSC Genes, TSS and other annotations for known genes.

Genome annotation from UCSC Known Genes, restricted to gene features such as transcription start and end sites, exon start sites, intron start site and CDS start sites.

• Raw data was downloaded from: UCSC Table Browser
• Input file format: TXT
• Download date: 08-06-2018

From M. musculus (March 2012 GRCm38/mm10).

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	Mm_ucscTSS_mm10.sga	Transcript start sites	TSS	-
2	Mm_ucscTES_mm10.sga	Transcript end sites	TES	-
3	Mm_ucscCDS_mm10.sga	CDS start sites	CDS	-
4	Mm_ucscESS_mm10.sga	Exon start sites	ESS	-
5	Mm_ucscISS_mm10.sga	Intron start sites	ISS	-

All fields from the primary (knownGenes) table were downloaded. Samples were generated from the input TXT file with a custom made awk script.

• O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD
  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45. doi: 10.1093/nar/gkv1189. Epub 2015 Nov 8. 26553804