Daphnia pulex gene annotations.

Gene annotation files for Daphnia pulex strain PA42.

• Gene annotation files were kinldy provided by Zhiqiang Ye (zhiqiang.yes@gmail.com)
• Input file format: GFF3
• Received: 06-01-2021

From D. pulex (Sep 2019 PA42 4.1/dpu2).

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	Daphnia_gene_start_sites.sga	Daphnia|gene starts	GSS	-
2	Daphnia_gene_end_sites.sga	Daphnia|gene ends	GES	-
3	Daphnia_trx_start_sites.sga	daphnia|transcript starts	TSS	-
4	Daphnia_trx_end_sites.sga	Daphnia|transcript ends	TES	-

Notes on samples nomenclature:

• Gene start: beginning of a complete or partial gene annotation. May be anywhere within the gene.
• Gene end: end of a complete or partial gene annotation. May be anywhere within the gene.
• Transcript start: start of an annotated transcript with complete coding region. Must be upstream of translation initiation codon.
• Transcript end: end of an annotated transcript with complete coding region. Must be downstream of translation termination codon.

The source gene annotation file in GFF3 format was converted into UCSC gene prediction format using the UCSC utility /gff3ToGenePred. Gene Features were extracted and converted into SGA format using custom scripts, see: https://epd.expasy.org/mga/dpu2/ye17/scripts/README. SGA files were converted into FPS format using sga2fps.pl (ChIP-Seq v. 1.5.5.

• Ye Z, Xu S, Spitze K, Asselman J, Jiang X, Ackerman MS, Lopez J, Harker B, Raborn RT, Thomas WK, Ramsdell J, Pfrender ME, Lynch M. A. A New Reference Genome Assembly for the Microcrustacean G3 (Bethesda). 2017 May 5;7(5):1405-1416. doi: 10.1534/g3.116.038638. 28235826