Genic regions of a large salamander genome contain long introns and novel genes

doi:10.1186/1471-2164-10-19

BMC Genomics

Volume 10

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Smith JJ
Putta S
Zhu W
Pao GM
Verma IM
Hunter T
Bryant SV
Gardiner DM
Harkins TT
Voss SR

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Smith JJ
Putta S
Zhu W
Pao GM
Verma IM
Hunter T
Bryant SV
Gardiner DM
Harkins TT
Voss SR
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Research article

Genic regions of a large salamander genome contain long introns and novel genes

Jeramiah J Smith¹^,6^,7 , Srikrishna Putta¹ , Wei Zhu² , Gerald M Pao² , Inder M Verma² , Tony Hunter² , Susan V Bryant³^,4 , David M Gardiner³^,4 , Timothy T Harkins⁵ and S Randal Voss¹

¹Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40506, USA

²The Salk Institute for Biological Studies, La Jolla, CA 92037, USA

³Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA

⁴The Developmental Biology Center, University of California Irvine, Irvine, CA 92697, USA

⁵Roche Applied Science, Indianapolis, IN 46250, USA

⁶University of Washington, Department of Genome Sciences, Seattle, WA 98195, USA

⁷Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA

author email corresponding author email

BMC Genomics 2009, 10:19doi:10.1186/1471-2164-10-19


Published:	13 January 2009

Additional files

Additional file 1:

Comparative data for exons and introns. A table containing exon alignment statistics and corresponding intron lengths for salamander, human, chicken, and frog.

Format: XLS Size: 31KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Self-self sequence alignments. Plots showing representative self-self sequence alignments for the 4 longest introns that were isolated from A. mexicanum.

Format: DOC Size: 404KB Download file

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Additional file 3:

Alignment of all salamander introns. A plot showing the self-alignment of concatenated intronic sequence sampled from A. mexicanum.

Format: DOC Size: 166KB Download file

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Additional file 4:

miRNAs predicted for axolotl and human. A table containing positional and statistical information for miRNAs predicted for axolotl and human.

Format: XLS Size: 37KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 5:

snoRNAs predicted for axolotl and human. A table containing positional and statistical information for snoRNAs predicted for axolotl and human.

Format: XLS Size: 21KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 6:

Human-axolotl 1: 1 orthologs. A table containing identities and alignment summary statistics for human-axolotl 1: 1 orthologs.

Format: XLS Size: 112KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 7:

Human-axolotl many: many paralogs. A table containing identities and alignment summary statistics for human-axolotl many: many paralogs predicted for both human and axolotl.

Format: XLS Size: 21KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 8:

Human-axolotl many: 1 paralogs. A table containing identities and alignment summary statistics for human-axolotl many: 1 paralogs predicted for both human and axolotl.

Format: XLS Size: 18KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 9:

Human-axolotl 1: many paralogs. A table containing identities and alignment summary statistics for human-axolotl 1: many paralogs predicted for both human and axolotl.

Format: XLS Size: 24KB Download file

This file can be viewed with: Microsoft Excel Viewer