Open Access Research article

ZNF280BY and ZNF280AY: autosome derived Y-chromosome gene families in Bovidae

Yang Yang15, Ti-Cheng Chang12, Hiroshi Yasue3, Arvind K Bharti4, Ernest F Retzel4 and Wan-Sheng Liu12*

  • * Corresponding author: Wan-Sheng Liu wul12@psu.edu

  • † Equal contributors

Author Affiliations

1 Department of Dairy and Animal Science, The Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, University Park, PA 16802, USA

2 The Integrative Biosciences Program, Bioinformatics and Genomics Option, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA

3 National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-0901, Japan

4 National Center for Genome Resources, Santa Fe, NM 87505, USA

5 Current address: Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA

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BMC Genomics 2011, 12:13  doi:10.1186/1471-2164-12-13

Published: 7 January 2011

Additional files

Additional file 1:

A list of the active copies of the bovine ZNF280BY cDNA sequences and the predicted sizes of ZNF280BYpeptides. This file provides a list of the active copies of the bovine ZNF280BY cDNA sequences, the predicted ZNF280BYpeptides, and the information about the ZNF280BY loci were detected in the direct testis cDNA selection.

Format: XLSX Size: 68KB Download file

Open Data

Additional file 2:

Analyses of the ZNF280BY containing BACs. The ZNF280BY genomic structure and clusters of predicted cDNAs and protein isoforms.

Format: XLSX Size: 14KB Download file

Open Data

Additional file 3:

Deep sequence reads count for locus-specific expression of the bovine ZNF280BY and ZNF280AY. Analysis of the locus-specific expression of the bovine ZNF280BY and ZNF280AY using a deep-sequencing approach.

Format: XLSX Size: 17KB Download file

Open Data

Additional file 4:

BTAY-specific BACs used for assembly of the 1.2 Mb contig. A list of BTAY-specific BACs used for assembly of the 1.2 Mb contig.

Format: DOCX Size: 24KB Download file

Open Data

Additional file 5:

Sequence information for the phylogenetic trees. A list of sequences used for phylogenetic analysis.

Format: XLSX Size: 89KB Download file

Open Data

Additional file 6:

The alignment of the ZNF280B/ZNF280A gene block across 17 species. The ZNF280B/ZNF280A gene blocks are conserved in the syntenic regions in most mammals except the rodents, where the block was rearranged in two different chromosomes (Chr4/10 in the mouse and Chr5/20 in the rat). This plot was generated based on the human Chr22 assembly (hg18). The boxes represent ungapped alignments; the lines represent gaps. This plot was generated using lastz alignment from the UCSC genome browser (http://genome.ucsc.edu/ webcite).

Format: PPTX Size: 76KB Download file

Open Data

Additional file 7:

Primer sequences for (RT-) PCR and strand-specific quantitative RT-PCR. Primer sequences designed for (RT-) PCR and strand-specific quantitative RT-PCR.

Format: DOCX Size: 25KB Download file

Open Data

Additional file 8:

Probe sequences for the testis section in situ hybridization. ZNF280BY sense and antisense cRNA probe sequences designed for the testis section in situ hybridization. Probe sequences for the bovine Protamine 1 (PRM1) gene (positive control) and LNE120 (negative control) are also included.

Format: DOCX Size: 24KB Download file

Open Data