ENSEMBL91, gene feature annotations

Gene starts and ends, CDS starts and ends, splice-junctions grouped by coding status and phase of reading frame. The source file was downloaded from the UCSC genome browser.

• Source downloaded via UCSC table browser: http://genome.ucsc.edu/cgi-bin/hgTables
• Input file format: tab-delimited text file
• Download date: 1-6-2018

From G. gallus (Dec 2015 Gallus_gallus-5.0/galGal5).

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	galGal5_ENSEMBL91_TSS.sga	Transcript (cDNA) starts	TSS	-
2	galGal5_ENSEMBL91_TSS_all.sga	Gene starts (all)	TSS	-
3	galGal5_ENSEMBL91_TES.sga	Gene ends	TES	-
4	galGal5_ENSEMBL91_AUG.sga	CDS starts	AUG	-
5	galGal5_ENSEMBL91_Stop.sga	CDS ends	Stop	-
6	galGal5_ENSEMBL91_5INTnc.sga	Splice donor nc	5INTnc	-
7	galGal5_ENSEMBL91_5INT0.sga	Splice donor phase-0	5INT0	-
8	galGal5_ENSEMBL91_5INT1.sga	Spline donor phase-1	5INT1	-
9	galGal5_ENSEMBL91_5INT2.sga	Splice donor phase-2	5INT2	-
10	galGal5_ENSEMBL91_3INTnc.sga	Splice acceptor nc	3INTnc	-
11	galGal5_ENSEMBL91_3INT0.sga	Splice acceptor phase-0	3INT0	-
12	galGal5_ENSEMBL91_3INT1.sga	Splice acceptor phase-1	3INT1	-
13	galGal5_ENSEMBL91_3INT2.sga	Splice acceptor phase-2	3INT2	-

Notes on samples nomenclature:

Transcript (cDNA) starts: includes all ENSEMBL transcript entry starts except those which coincide with the corresponding CDS start annotation

Gene starts (all): includes all ENSEMBL transcript entry starts including those which coincide with the corresponding CDS start annotation

Merged samples:

None

The source data table downloaded from UCSC with the aid of the table browser, includes the following fields:

Table galGal5.ensGene: name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds, name2, exonFrames

Table galGal5.ensemblToGeneName: value

Input filtering criteria:

Table galGal5.ensGene cdsStartStat does match cmpl
Table galGal5.ensGene cdsEndStat does match cmpl
Table galGal5.ensemblSource source does match protein_coding

SGA files were generated with custom Perl scripts available from ( https://epd.expasy.org/ftp/mga/galGal5/ensembl91/scripts/ and format conversion utilities from (ChIP-Seq version 1.5.3).

• Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P
  Ensembl 2018. Nucleic Acids Res. 2018 Jan 4;46(D1):D754-D761. doi: 10.1093/nar/gkx1098. 29155950