Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes

Physiol Genomics. 2006 Mar 13;25(1):9-15. doi: 10.1152/physiolgenomics.00121.2005. Epub 2005 Dec 20.


To complement cDNA libraries from the human eye at early gestation and to discover candidate genes associated with early ocular development, we used freshly dissected human eyeballs from week 9-14 of gestation to construct the early human fetal eye cDNA library. A total of 15,809 clones were isolated and sequenced from the unamplified and unnormalized library. We screened 11,246 good-quality ESTs, leading to the identification of 5,534 nonredundant clusters. Among them, 4,010 (72%) genes matched in the human protein database (Ensembl). The remaining 28% (1,524) corresponded to potentially novel or previously unidentified ESTs. We used BLASTX to compare our EST data with eight organisms and found common expression of a high portion of genes: Caenorhabditis briggsae (26%), Caenorhabditis elegans (27%), Anopheles gambiae (37%), Drosophila melanogaster (32%), Danio rerio (42%), Fugu rubripes (49%), Rattus norvegicusvalitus (52%), and Mus musculus (59%). Nevertheless, 48% (2,680 of 5,534) of the genes expressed in the early developing eye were not shared with current NEIBank human eye cDNA data. In addition, eight known retinal disease genes existed in our ESTs. Among them, six (COL11A1, BBS5, PDE6B, OAT, VMD2, and PGK1) were conserved among the genomes of other organisms, indicating that our annotated EST set provides not only a valuable resource for gene discovery and functional genomic analysis but also for phylogenetic analysis. Our foremost early gestation human eye cDNA library could provide detailed comparisons across species to identify physiological functions of genes and to elucidate evolutionary mechanisms.

Publication types

  • Comparative Study

MeSH terms

  • Animals
  • Chromosome Mapping
  • Cluster Analysis
  • Databases, Genetic
  • Expressed Sequence Tags*
  • Eye / embryology
  • Eye / metabolism*
  • Eye Proteins / genetics*
  • Eye Proteins / metabolism
  • Female
  • Fetus / metabolism
  • Gene Expression Regulation, Developmental*
  • Gene Library
  • Gestational Age
  • HSP40 Heat-Shock Proteins / genetics
  • HSP40 Heat-Shock Proteins / metabolism
  • Humans
  • Intramolecular Oxidoreductases / genetics
  • Intramolecular Oxidoreductases / metabolism
  • Pregnancy
  • RNA, Messenger / metabolism
  • Retinal Diseases / genetics
  • Sequence Homology, Nucleic Acid
  • Species Specificity


  • DNAJC3 protein, human
  • Eye Proteins
  • HSP40 Heat-Shock Proteins
  • RNA, Messenger
  • Intramolecular Oxidoreductases
  • dopachrome isomerase