Identification of novel protein-coding genes from human fetal hippocampus ESTs database

Abstract

We presented a procedure to identify novel protein-coding genes from human fetal hippocampus ESTs database generated in our previous study. The protocol is involved in searching the GenBank non-redundant (nr) protein database with ESTs coding regions query. We used ESTScan program to detect and reconstruct coding regions in the ESTs sequence data. With almost 10,000 raw ESTs analyzed, 4,061 coding regions were extracted. The corresponding amino acid sequences were then searched against the GenBank nr-protein databases; all the similarity hits were parsed in a homology analysis workbench. 22 ESTs were identified as the “seed” ESTs, which might be the fragment of the novel protein-coding genes. Indeed, further analysis of these ESTs in full-length cDNA cloning in silico, as well as the mapping information in UCSC and the added experimental proof, verified the effectiveness of the strategy. Taking advantage of rare ESTs resources, and the effective strategy, we would explore more novel genes in the human genome. [The ESTs sequence data described in this paper have been submitted to the GenBank data library (http://www.ncbi.nlm.nih.gov/dbEST) under accession nos. BM174886-958, BM259607-9; and the full length cDNA sequence can be obtained in http://www.chgb.org.cn/hippocampus.htm]