Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6

M. Ali Ansari-Lari, John C. Oeltjen, Scott Schwartz, Zheng Zhang, Donna M. Muzny, Jing Lu, James H. Gorrell, A. Craig Chinault, John W. Belmont, Webb Miller, Richard A. Gibbs

Research output: Contribution to journalArticle

107 Citations (Scopus)

Abstract

The Human Genome Project has created a formidable challenge: the extraction of biological information from extensive amounts of raw sequence. With the increasing availability of genomic sequence from other species, one approach to extracting coding and regulatory element information is through cross-species sequence comparison. To assess the strengths and weaknesses of this methodology for large-scale sequence analysis, 227 kb of mouse sequence syntenic to a gene-rich cluster on human chromosome 12p13 was obtained. Primarily through percent identity plots (PIPs] of SIM comparative sequence alignments, the sequence of coding regions, putative alternative exons, conserved noncoding regions, and correlation in repetitive element insertions were easily determined. The analysis demonstrated that the number, order, and orientation of all 17 genes are conserved between the two species, whereas two human pseudogenes are absent in mouse. In addition, apart from MIRs, no direct correlation of distribution or position of the majority of repetitive elements between the two species is seen. Finally, in examining the synonymous and nonsynonymous substitution rates in the conserved genes, a large variation in nonsynonymous rates is observed indicating that the genes in this region are diverging at different rates. This study indicates the utility and strength of large-scale cross-species sequence comparisons in the extraction of biological information from raw sequence, especially when combined with other computational tools such as GRAIL and BLAST.

Original languageEnglish
Pages (from-to)29-40
Number of pages12
JournalGenome Research
Volume8
Issue number1
StatePublished - Jan 1 1998

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Chromosomes, Human, Pair 6
Human Chromosomes
Multigene Family
Sequence Analysis
Information Storage and Retrieval
Genes
Human Genome Project
Pseudogenes
Sequence Alignment
Exons

ASJC Scopus subject areas

  • Genetics

Cite this

Ansari-Lari, M. A., Oeltjen, J. C., Schwartz, S., Zhang, Z., Muzny, D. M., Lu, J., ... Gibbs, R. A. (1998). Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Research, 8(1), 29-40.

Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. / Ansari-Lari, M. Ali; Oeltjen, John C.; Schwartz, Scott; Zhang, Zheng; Muzny, Donna M.; Lu, Jing; Gorrell, James H.; Chinault, A. Craig; Belmont, John W.; Miller, Webb; Gibbs, Richard A.

In: Genome Research, Vol. 8, No. 1, 01.01.1998, p. 29-40.

Research output: Contribution to journalArticle

Ansari-Lari, MA, Oeltjen, JC, Schwartz, S, Zhang, Z, Muzny, DM, Lu, J, Gorrell, JH, Chinault, AC, Belmont, JW, Miller, W & Gibbs, RA 1998, 'Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6', Genome Research, vol. 8, no. 1, pp. 29-40.
Ansari-Lari MA, Oeltjen JC, Schwartz S, Zhang Z, Muzny DM, Lu J et al. Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. Genome Research. 1998 Jan 1;8(1):29-40.
Ansari-Lari, M. Ali ; Oeltjen, John C. ; Schwartz, Scott ; Zhang, Zheng ; Muzny, Donna M. ; Lu, Jing ; Gorrell, James H. ; Chinault, A. Craig ; Belmont, John W. ; Miller, Webb ; Gibbs, Richard A. / Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6. In: Genome Research. 1998 ; Vol. 8, No. 1. pp. 29-40.
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