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JGI JAZZ assembly 2006-09-05 (8/9X) and annotations for Daphnia pulex: http://wfleabase.org/prerelease/dpulex_jgi060905/

est/ EST data set (JGI 2005/2006) :

gff/ Annotations: genome-assembly/ Primary genome assembly data : genome-assembly-full-jazz_20060901/ : Full JGI JAZZ assembler output file set

gene-predictions/ Gene Predictions:

genetic-map/ Genome - Genetic Map correspondence: pasa/ PASA EST assembly analysis results : see PASA_gene_annotation

2008 Dec 09
Find here these various genome features
  http://wfleabase.org/release1/current_release/

This has the official gene predictions with exons,
  gff/dpulex-genepredict-v11.gff.gz  
  and is same as gene-predictions/dpulex_jgi060905_JGI_V11.gff.gz

These introns are computed from the above dpulex_jgi060905_JGI_V11 exons:
  supplement/introns/
    dpulex1_introns.JGI.gff.gz
    and dpulex1_intergene.JGI.gff.gz  for intergenic regions

tRNA genes are listed here 
   trna-ncrna/dpulex-tRNA_analysis2.gff
  
Repeats:
 repeats/dpulex-repeatmasker.gff2  : repeatmasker results from JH Choi
 repeats/dpulex_jgi060905-pilerpred.gff.gz:   770 repeats identified by PILER-DF by Chris Smith
 repeats/daphnia_ltr_table.gff  :  322 LTR transposons from Mike Lynch's colleague

gff/dpulex-polymorphisms_04_2007.gff.gz
 : SNP's from Abe Tucker, UNH
 
gff/dpulex-microsatellite.gff.gz   
 : has identified microsatellites

Here is a full list of ESTs mapped to the genome:
  pasa/pasa_daphc.validated_transcripts.gff3.gz