Traced orthologous amplified sequence tags (TOASTs) and mammalian comparative maps

Traced orthologous amplified sequence tags (TOASTs) and mammalian comparative maps Progress on mammalian comparative maps could be significantly accelerated by developing reagents defining orthologous landmarks in the genome of many mammalian species. Using the large databases of gene sequences, we designed 225 orthologous gene-specific primer pairs corresponding to 146 functional genes. Of these 225 primer pairs, 155 (68.9%), 182 (80.9%), 126 (56.0%), and 82 (36.4%) produced a single PCR product when tested against human, pig, dog, and hamster genomic DNA, respectively. In addition to the general rules of primer designing, particular factors must be taken into consideration when choosing gene-specific universal primers—for instance, preference for single-exon regions or highly conserved segments among species, avoidance of GC-rich regions. Sequencing all the canine PCR products traced by these primers demonstrated that of 123 traced canine fragments with readable and reliable sequences, 121 (98.4%) were found to match the GenBank orthologous sequences used for designing the primers, after a BLAST search. Comparative characterization of PCR fragments among human, pig, dog, and hamster revealed that the length of a single exon was much conserved among species, with few exceptions. As the fragments were traced with amplification by orthologous gene-specific primers, we suggest they be termed Traced Orthologous Amplified Sequence Tags (TOASTs). http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Mammalian Genome Springer Journals

Traced orthologous amplified sequence tags (TOASTs) and mammalian comparative maps

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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/s003359900821
Publisher site
See Article on Publisher Site

Abstract

Progress on mammalian comparative maps could be significantly accelerated by developing reagents defining orthologous landmarks in the genome of many mammalian species. Using the large databases of gene sequences, we designed 225 orthologous gene-specific primer pairs corresponding to 146 functional genes. Of these 225 primer pairs, 155 (68.9%), 182 (80.9%), 126 (56.0%), and 82 (36.4%) produced a single PCR product when tested against human, pig, dog, and hamster genomic DNA, respectively. In addition to the general rules of primer designing, particular factors must be taken into consideration when choosing gene-specific universal primers—for instance, preference for single-exon regions or highly conserved segments among species, avoidance of GC-rich regions. Sequencing all the canine PCR products traced by these primers demonstrated that of 123 traced canine fragments with readable and reliable sequences, 121 (98.4%) were found to match the GenBank orthologous sequences used for designing the primers, after a BLAST search. Comparative characterization of PCR fragments among human, pig, dog, and hamster revealed that the length of a single exon was much conserved among species, with few exceptions. As the fragments were traced with amplification by orthologous gene-specific primers, we suggest they be termed Traced Orthologous Amplified Sequence Tags (TOASTs).

Journal

Mammalian GenomeSpringer Journals

Published: Jul 1, 1998

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