Open Access Research article

Characterization of the ovine ribosomal protein SA gene and its pseudogenes

Alice Van den Broeke1, Mario Van Poucke1, Ane Marcos-Carcavilla2, Karine Hugot3, Hélène Hayes3, Maud Bertaud3, Alex Van Zeveren1 and Luc J Peelman1*

Author Affiliations

1 Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium

2 Departamento de Mejora Genética Animal, INIA, Ctra La Coruña Km 7.5, Madrid 28040, Spain

3 INRA, UMR 1313 Génétique Animale et Biologie Intégrative, F78350 Jouy-en-Josas, France

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BMC Genomics 2010, 11:179  doi:10.1186/1471-2164-11-179

Published: 16 March 2010

Additional files

Additional file 1:

Primers used for screening of the INRA BAC library. Characteristics of primers used for screening of the INRA BAC library: sequence, location, melting temperature and amplicon length.

Format: XLSX Size: 11KB Download file

Open Data

Additional file 2:

STS primers BES. Characteristics of primers used for STS content mapping: sequence, annealing temperature and amplicon length.

Format: XLSX Size: 15KB Download file

Open Data

Additional file 3:

Alignment of the mRNA of the ovine RPSA gene with 11 RPSA pseudogenes. The startcodon, stopcodon, poly-adenylation signal exon-exon junctions and interspersed repeats are highlighted in yellow. The primers used to screen the INRA BAC library are highlighted in green.

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Additional file 4:

In silico promoter prediction. The in silico predicted promoter sequence is shown with the transcription start site highlighted in red. Furthermore, the score of the prediction, identification of the promoter and location of the transcription start site in the sequence is shown.

Format: XLSX Size: 10KB Download file

Open Data

Additional file 5:

Characteristics BES. Characteristics of the 68 BES: BES length, orthologous sequences and genes, and repeats present in the BES.

Format: XLSX Size: 17KB Download file

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Additional file 6:

Primers used to annotate the mini-contigs. Characteristics of primers used to annotate the mini-contig: sequence, annealing temperature, amplicon size and annotation information.

Format: XLSX Size: 16KB Download file

Open Data

Additional file 7:

FISH experiments. Pictures of FISH experiments of the 11 RPSA pseudogenes.

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Additional file 8:

Bovine RPSA pseudogenes. Characteristics of bovine RPSA pseudogenes predicted in silico by BLAST analysis of the bovine genome (reference assembly, based on Btau_4.0). In yellow are the pseudogenes that are annotated as 'similar to Ribosomal protein SA pseudogene'. The bovine pseudogene RPSAP1 is highlighted in blue and the pseudogenes that aren't annotated yet in white.

Format: XLSX Size: 13KB Download file

Open Data

Additional file 9:

minus-RT PCR control on RNA isolated from blood. RT-PCR with ACTB primers. Marker (M) is the Hyperladder V (Bioline). Samples are RNA isolated from blood, genomic DNA and water (-).

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Additional file 10:

Specificity of the expression primer for RPSAP6. PCR with expression primer for RPSAP6. Marker (M) is the Hyperladder IV (Bioline). Samples are the respective unique BAC clones of all RPSA family members, genomic DNA and water (-).

Format: PDF Size: 85KB Download file

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