Comparative analysis of 82 expressed sequence tags from a cattle ovary cDNA library

Comparative analysis of 82 expressed sequence tags from a cattle ovary cDNA library In total, 82 ESTs were generated from 51 unique clones randomly selected from a cattle ovary cDNA library. Among these clones, 22 (42.1%) had 5′ and/or 3′ ends that matched with known human or other mammalian coding sequences, 18 (35.3%) matched human or other ESTs, and 11 (21.6%) represented novel transcripts with no significant match to any sequence in the databases. The relatively high frequency of ESTs with no matches in GenBank or dbEST indicates that bovine ovary may be a source of novel candidate genes for loci affecting cattle reproduction traits. Primers were designed for 11 ESTs that had human orthologs in GenBank. These ESTs were mapped to 10 bovine autosomes by PCR screening of a somatic cell hybrid panel. Among these 11 ESTs, 4 corresponded to genes previously mapped in humans and had chromosome assignments on the bovine map that were consistent with available comparative mapping data. Although the human orthologs of the remaining 7 mapped bovine ESTs have not been mapped, the human map location could be predicted on the basis of existing comparative mapping data. Because of the general utility of our approach for comparative genome analysis, we have termed it comparative mapping by annotation and sequence similarity (COMPASS). With the cost of large-scale EST sequencing becoming more affordable, and the rapid expansion of DNA databases, it is likely that COMPASS will be a preferred strategy for high throughput comparative mapping. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Mammalian Genome Springer Journals

Comparative analysis of 82 expressed sequence tags from a cattle ovary cDNA library

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Publisher
Springer-Verlag
Copyright
Copyright © 1998 by Springer-Verlag New York Inc.
Subject
Life Sciences; Cell Biology; Animal Genetics and Genomics; Human Genetics
ISSN
0938-8990
eISSN
1432-1777
D.O.I.
10.1007/s003359900816
Publisher site
See Article on Publisher Site

Abstract

In total, 82 ESTs were generated from 51 unique clones randomly selected from a cattle ovary cDNA library. Among these clones, 22 (42.1%) had 5′ and/or 3′ ends that matched with known human or other mammalian coding sequences, 18 (35.3%) matched human or other ESTs, and 11 (21.6%) represented novel transcripts with no significant match to any sequence in the databases. The relatively high frequency of ESTs with no matches in GenBank or dbEST indicates that bovine ovary may be a source of novel candidate genes for loci affecting cattle reproduction traits. Primers were designed for 11 ESTs that had human orthologs in GenBank. These ESTs were mapped to 10 bovine autosomes by PCR screening of a somatic cell hybrid panel. Among these 11 ESTs, 4 corresponded to genes previously mapped in humans and had chromosome assignments on the bovine map that were consistent with available comparative mapping data. Although the human orthologs of the remaining 7 mapped bovine ESTs have not been mapped, the human map location could be predicted on the basis of existing comparative mapping data. Because of the general utility of our approach for comparative genome analysis, we have termed it comparative mapping by annotation and sequence similarity (COMPASS). With the cost of large-scale EST sequencing becoming more affordable, and the rapid expansion of DNA databases, it is likely that COMPASS will be a preferred strategy for high throughput comparative mapping.

Journal

Mammalian GenomeSpringer Journals

Published: Jul 1, 1998

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