A copy number variation in human NCF1 and its pseudogenes

Additional file 1:

Genotyped positions of cDNA amplicons used in copy number variation analysis. A) Amplicon generated at the exon-1 exon-2 boundary. B) Amplicon generated in exons 8 and 9. Genotyped locations are bold and underlined. Red base represents the end of an exon and blue represents the start of the neighboring exon.

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Additional file 2:

Representative pyrograms showing low pyrosequencing noise. a) The 2-bp GT deletion in exon 2. b) The A/G substitution in exon 9.

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Additional file 3:

CNV allele frequencies in three populations. Totally 86 non-related individuals (32 African-Americans, 30 Caucasians and 24 Mexicans) were genotyped at this CNV.

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Additional file 4:

Copy number variation at the NCF1 locus observed in genomic DNA samples extracted directly from peripheral white blood cells. In order to eliminate the possibility that this CNV is an artefact caused by chromosomal instability in lymphoblastoid cell lines, we analyzed 48 genomic DNA samples directly extracted from human peripheral white blood cells. Means of 3 independent experiments performed in duplicate.

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Additional file 5:

cDNA sequences of alternatively spliced exons. By PCR, cloning and direct DNA sequencing, we have experimentally discovered two novel alternative exons (GenBank: GU215077, GU215078) located in the intron-1. Neither of these two transcripts used the GT-containing exon-2.

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Additional file 6:

Putative open reading frames of alternative spliced transcripts. The open reading frame (ORF) of two alternative spliced products, sub1 and sub2, were predicted with the NCBI ORF Finder.

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Additional file 7:

Putative transcription factor binding sites (TFBS) of the human NCF1 gene and its pseudogenes. A 20 kb sequence of 5'-flanking region of each of NCF1 and its pseudogenes (immediately upstream to exon 1) was retrieved from UCSC Genome Browser. Sequence alignment was performed with EMBL-EBI CLUSTAL 2.0.12 (Larkin et al., 2007). Putative TFBS was predicted with rVISTA (Loots et al., 2002) using the vertebrates TRANSFAC matrices and cut-off 1.0 for both matrix similarity and core similarity.

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Additional file 8:

Primers used in this study. This table provides the detailed sequence information of oligonucleotides that were used in this study.

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Additional file 9:

Melting curves of quantitative real-time PCR (RT-qPCR) using primers specific for the true p47^phox mRNA. The specificity of this primer set is indicated the single sharp peak. The negative control is indicated by the straight line.

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