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Identification and use of conserved noncoding sequences

Inactive Publication Date: 2005-02-10
RGT UNIV OF CALIFORNIA
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0006] In order to meet these needs, the present invention is directed to CNSs (conserved noncoding sequences) and their use in molecular analysis and genetic mapping in any organism. The conserved noncoding sequences (CNSs) of the invention find many applications in mole

Problems solved by technology

Although these methods are powerful, they are useful only within one species or genus because the markers are not from genes shared by larger taxonomic groups.

Method used

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  • Identification and use of conserved noncoding sequences
  • Identification and use of conserved noncoding sequences
  • Identification and use of conserved noncoding sequences

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[0233] Identification of CNSs

[0234] DNA sequences were processed using Perl scripts to automate CNS discovery. Coding regions of maize and rice genes were identified by comparing genomic sequences to predicted protein translations using NCBI's blastx (Altschul, S. F. et al. (1997) Nucleic Acids Research 25, 3389-3402). The coding regions were masked out for further comparisons. The two. masked genomic sequences were then compared using NCBI's bl2seq (Tatusova, T. A. & Madden, T. L. (1999) FEMS Microbiology Letters 174, 247-250), with the following parameters: for finding stringent CNSs (FIG. 1A and Table 2) Word size=7, Gap Penalties: Existence=5, Extension=2; for finding long CNSs (FIG. 6B) Word size=7, Gap Penalties: Existence

[0235] =2, Extension=1. The positions of CNSs relative to intron / exon structure were visualized using Perl scripts to parse the output of both the blastx and bl2seq results.

[0236] Sequence Information

[0237] The Genbank accession number for the rice lg1 co...

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Abstract

The invention is directed to the identification of conserved noncoding sequences in various organisms and the use of those sequences as primers for use in amplifying, mapping and analysis of DNA among different species.

Description

RELATED APPLICATION [0001] This application claims priority to U.S. Provisional Application Ser. No. 60 / 303,356 filed Jul. 6, 2001, which is hereby incorporated by reference in its entirety.[0002] This invention was made with Government support order Grant (Contract) No. R01GM42610 awarded by the National Institutes of Health. The government has certain rights in this invention.FIELD OF THE INVENTION [0003] This invention is in the field of molecular biology. In particular this invention relates to the identification and use of conserved noncoding sequences (CNS) for molecular and genetic analysis. BACKGROUND OF THE INVENTION [0004] While much progress has been made in recent years in traditional molecular and genetic mapping, sequencing of genomes and molecular analysis of gene expression, there is still a tremendous need to develop improved techniques for molecular and genetic analysis within and between species. [0005] Molecular markers are common tools that can reveal polymorphi...

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Application Information

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IPC IPC(8): B42D15/00C12Q1/68C12Q1/6858C12Q1/6876C12Q1/6895G09B29/04G09B29/08
CPCB42D15/008B42D15/0086C12Q1/6858C12Q1/6876C12Q1/6895Y10T428/24008G09B29/08G09B29/04Y10T428/21Y10S40/904C12Q2525/15
Inventor FREELING, MICHAELKAPLINSKY, NICHOLASBRAUN, DAVID
Owner RGT UNIV OF CALIFORNIA