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Open Access Research article

RsaI repetitive DNA in Buffalo Bubalus bubalis representing retrotransposons, conserved in bovids, are part of the functional genes

Deepali Pathak and Sher Ali*

Author Affiliations

Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi -110 067, India

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BMC Genomics 2011, 12:338  doi:10.1186/1471-2164-12-338

Published: 1 July 2011

Additional files

Additional file 1:

Details of the Blast search. Details of the Blast search of RsaI derived repeat sequences of water buffalo Bubalus Bubalis.

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Open Data

Additional file 2:

Details of ClustalW alignment. ClustalW alignment of buffalo derived RsaI element pDp1, pDp2, pDp3 and pDp4, showing each one as separate entity.

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Open Data

Additional file 3:

ClustalW alignment with transcribing genes. ClustalW alignment of buffalo RsaI pDp1, pDp2 and pDp4 sequences with Bos taurus transcribing genes (A) ACOT11 (B) VPS24 and (C) SLCO1A2. Sequences highlighted in yellow indicate UTR. RsaI sequences are marked in blue.

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Open Data

Additional file 4:

Details of Cross-hybridization studies. Cross-hybridization of RsaI recombinant clones with genomic DNA of different species. Signals were detected only in buffalo, cattle, goat and sheep as shown herein. PC denotes positive control (recombinant plasmids). IDs of the sequences used for hybridization are mentioned on the left.

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Open Data

Additional file 5:

Details of Southern blot hybridization across bovids. Representative blots showing distribution of pDp1 (A) and pDp2 (B) in buffalo, cattle, goat and sheep genome by Southern blot hybridization. Note discernible bands of 1331 and 652 bp in these species.

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Open Data

Additional file 6:

Details of pDp1 alignment across the species. ClustalW nucleotide alignment of buffalo pDp1, 489 bp ORF sequence, with cattle, goat and sheep sequences. Note the close sequence homology among the bovids.

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Open Data

Additional file 7:

Phylogenetic analysis. Phylogram based on percent identity of pDp1, pDp2, pDp3 and pDp4 (A-D) sequence in different species showing close relationship of buffalo with cattle.

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Open Data

Additional file 8:

Details of RT PCR. RT-PCR analysis of RsaI repeat sequences using internal primers and cDNA from different somatic tissues and spermatozoa of buffalo, Sequence IDs are indicated on the left and tissues are mentioned on top of the lanes. β-actin was used a positive control. M denotes 100 base pair marker.

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Open Data

Additional file 9:

Details of copy number calculation with Real time PCR. Standard curve based on 10 fold dilution series of pDp1, pDp2, pDp3, pDp4 and genomic DNA from buffalo, cattle, goat and sheep showing the amplification plot (a-d) panel (A), corresponding slopes of -3.3 to -3.5, panel (B) and a single dissociation peak, panel (C), substantiating maximum efficiency of the PCR reaction and high specificity of the primers with target DNA. Arrow indicates genomic DNA from buffalo, cattle, goat and sheep.

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Open Data

Additional file 10:

Southern hybridization with pDp1 clone. Southern hybridization of Bubalus bubalis RsaI digested genomic DNA with pDp1 clone (A). The strongest isomorphic band corresponds to 1331 bp, indicated by an arrow (B).

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Additional file 11:

Status of Exons in ACOT11 gene. Pictorial representation showing Bos taurus (A) and Bubalus bubalis ACOT11 gene (B) with their representative exons. Nucleotide position 730 to 1331 indicates region of pDp1 showing 92% homology to Bos taurus ACOT11. Full length sequence of Bubalus bubalis ACOT11 gene lacking poly A tail and exons are given in (C).

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Open Data

Additional file 12:

ClustalW alignment of ACOT11 gene. ClustalW alignment of buffalo ACOT11 gene with cattle (NM_001103275.1). Note the high level of sequence homology (92%) between the two species.

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Open Data