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Open Access Research article

Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles

Li-Fang Kang1, Zheng-Lin Zhu1*, Qian Zhao1, Li-Yong Chen2* and Ze Zhang1

Author Affiliations

1 College of Life Sciences, Chongqing University, Chongqing, 400044, China

2 Department of Anesthesiology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, 10 Changjiang Zhilu, Chongqing, 400042, China

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BMC Evolutionary Biology 2012, 12:128  doi:10.1186/1471-2148-12-128

Published: 28 July 2012

Additional files

Additional file 1:

Transcripts uniquely mapped to retrogenes. This file lists transcripts that spanned the introns of their mapped retrogenes

Format: DOC Size: 43KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 2:

Evidence for transcription of retrogene introns (from the UCSC Genome Browser database). This file contains snapshots from the UCSC Genome Browser database that displays the transcription of retrogenes that gained introns

Format: DOC Size: 803KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 3:

List of human tissues sampled for the experiments. This file lists the human tissues that we used for the experiments to validate the existence of retrogene introns

Format: DOC Size: 34KB Download file

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Open Data

Additional file 4:

Experimental validation of retrogene introns in TMEM14D and HSP90AA4P. This file shows the experimental results for validating the existence of retrogene introns

Format: DOC Size: 57KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 5:

Phylogenetic tree for vertebrates. A diagram of the phylogenetic tree for vertebrates

Format: DOC Size: 127KB Download file

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Open Data

Additional file 6:

Chromosome and time of origin of intronized retrogenes. This file shows the origination times of intronized retrogenes

Format: DOC Size: 33KB Download file

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Open Data

Additional file 7:

Chromosome and time of origin of retrogenes that gained introns by chimerization. This file shows the origination times of retrogenes that gained introns by chimerization

Format: DOC Size: 54KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 8:

Transcription annotations (from the UCSC Genome Browser database) of retrogene introns in the parental gene. This file contains snapshots from the UCSC Genome Browser database displaying transcription annotations of retrogene introns in the parental gene

Format: DOC Size: 3.5MB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 9:

Sequences of primer pairs used to amplify the retrogenes and their parents. A table that lists primer pairs we used to amplify the retrogenes and their parents

Format: DOC Size: 29KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 10:

Protein-level alignments of intron-gain retrogenes (“Sbjct”) and their parents (“Query”) by GeneWise. This file contains alignments of intron-gain retrogenes and their parents in protein level

Format: PDF Size: 100KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 11:

Nucleotide-level alignments of retrogene introns (‘Sbjct’, blue and red, splice sites) and parental genes (‘Query’, program NCBI-BLAST). This file contains alignments of intron-gain retrogens and their parents in DNA level

Format: PDF Size: 229KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 12:

Positions of three retrogenes (XXyac-R12DG2.2, CSMD3 and WBP2NL) in the human genome (from the UCSC Genome Browser database). This file contains snapshots from the UCSC Genome Browser Database displaying the positions of three retrogenes

Format: DOC Size: 443KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 13:

Comparison of splicing signals (percentile score) in the corresponding region of the new intron in the parental gene and neighboring introns. This file shows the results for the comparison of splicing signals in the corresponding region of the new intron in the parental gene and neighboring introns

Format: DOC Size: 35KB Download file

This file can be viewed with: Microsoft Word Viewer

Open Data

Additional file 14:

Genetic variation of four retrogenes in different human populations. This file displays alignments of genomes of different human populations in the region of four retrogenes.

Format: TXT Size: 195KB Download file

Open Data