Cattle EST Project
The W. M. Keck Center for Comparative and Functional Genomics,
A cattle EST project was initiated in order to provide a resource for comparative gene mapping, for evolutionary analysis of genes and gene families and for functional genomics. Three cDNA libraries have been produced for EST sequencing: placenta, ovary and spleen. As part of this project, 12,620 placenta, 726 spleen and 519 ovary cattle ESTs have been deposited into GenBank. Approximately 5000 more spleen ESTs will be deposited soon. These ESTs have proven to be a powerful resource for comparative and functional genome analysis (Band et al., 2000; Ozawa et al., 2000; Rebeiz et al., 2000; Band et al., submitted)
The Cattle EST Database (BOVEST) and accompanying search tools represent a powerful new addition to the arsenal of tools for comparative and functional genomics. Every sequence is annotated with detailed information arising from CAP3 clustering and BLASTN analysis against the human UNIGENE database. The tool allows the user to search by just about any attribute of a sequence or cluster, including GeneOntology (GO) annotation. It is also possible to view the sequence chromatogram, as well as raw and trimmed sequences. To our knowledge, this is the first such publicly available database for any farm animal species. The linkages and associations with GO and LocusLink provide an unprecedented resource to explore orthologous relationships and to begin the process of defining complex phenotypes at the molecular level in cattle.
The placenta library was produced and normalized by M. Bento Soares. The ovary and spleen cDNA libraries were produced by Dr. Runlin Ma and Joshua Larson. Serial subtractions of the placenta and spleen libraries and high throughput sequencing were performed at the UIUC W. M. Keck Center for Comparative and Functional Genomics, High Throughput Sequencing and Genotyping Unit (Dr. Jose Pardinas, Director). The bioinformatics development group is led by Dr. Lei Liu. Microarrays resulting from this work were produced in conjunction with Dr. Mark Band, Director of Functional Genomics at the W. M. Keck Center. Placenta and spleen clones are available from AniGenics, Inc..
This work was supported in part by grants from the USDA/NRI (AG98-35205-4738 and AG99-35205-8534).
Ozawa, A., M. R. Band, J. H. Larson, J. Donovan, C. A. Green, J. E. Womack and H. A. Lewin. 2000. Comparative organization of cattle chromosome 5 revealed by COMPASS and radiation hybrid mapping. Proc. Natl. Acad. Sci. (USA) 11:4150-4155.
Rebeiz, M. and H. A. Lewin. 2000. COMPASS of 47,747 cattle ESTs. Animal Biotechnology 11:75-241.
Band, M. R., J. H. Larson, M. Rebeiz, C. A. Green, D. W. Heyen, J. Donovan, R. Windish, C. Steining, P. Mahyuddin, J. E. Womack and H. A. Lewin. 2000. An ordered comparative map of the cattle and human genomes. Genome Research 10:1359-1368.
Band, M. R., C. Olmstead, R. E. Everts, Z. L. Liu, and H. A. Lewin. 2001. A 3800 gene microarray for cattle functional genomics (submitted).
UIUC Program in Animal Genomics Homepage
Single Sequence COMPASS web site
The EST data can be searched and retrieved using the following search criteria: *
Search by BLAST Cut and paste one or more sequences to BLAST against the two cattle placenta EST data sets, the unique sequence set generated by CAP3 assembly program (cattle_cap.unique), and the high quality EST set (cattle.est).
Search by Keyword Search the database by enering a keyword to retrieve Gene Ontology recognized terms, and retrieve Cattle EST annotation for each of those terms. EST's can have multiple GO terms. To see all possible terms for a particular EST or ID, use the 'Search the Gene Association Database by Id' below. The Gene Ontology Consortium documentation is available at GO documentation.
Search by Sequence ID Enter an EST ID, GENBANK accession ID, or Contig ID to retrieve and download the sequences, view the sequence chromatograph and quality, view contiucture and the consensus sequence.
Search the Gene Association Database by Id Search the database by entering a Sequence ID or Human Unigene Number or Gene Symbol to retrieve annotated ESTs for that ID.
The chromatograms of all ESTs in the BP and BS libraries are available for download. The collected chromatograms are stored in a single TAR file, along with a file listing the conversion from sequence ID to Genbank Accession number.
The BS library is available here [ 1.3 GB]
The BP library is available here [21 MB]
*This website is best viewed using Internet Explorer 4.0 or above, or Netscape Navigator 4.x
This site is maintained by the Bioinformatics Unit
of the W.M. Keck Center for Comparative and Functional Genomics
at the University of Illinois