BABAM2 (brain and reproductive organ-expressed (TNFRSF1A modulator))

	Generation of the major transcript variant of human BRE. Human BRE gene (not drawn in scale) is consisted of 15 exons, three of which are alternatively spliced. The light green boxes, X - Z, are alternative exons which are not present in the major transcript. The asterisked ATG is the translation start. This transcript encodes the major 383-amino-acid BRE protein isoform 2, that has been studied.
Description	The gene spans 448284 bases, telomere to centromere orientation. The first exon is non-coding. In humans, six transcript variants are produced by alternative splicing predominantly at either end of the gene. All human cells examined co-express all of the splice variants, but at different ratios to one another. The major transcript is αa, also known as variant 3 by NCBI nomenclature. This transcript encodes the ubiquitous 383-amino-acid protein, designated by NCBI as protein isoform 2 (NP_954661.1) (Ching et al., 2001). Functions of all minor transcript variants are undetermined. In mice, alternative splicing occurs only at the 5' region of the gene. The major transcript is variant 5 (NCBI nomenclature), which encodes the ubiquitous 383-amino acid protein that is 99% identical to human BRE. The minor transcript variants, unlike the human counterparts, are expressed differentially among tissues. Their functions are undetermined (Ching et al., 2003).
Transcription	Exon 1 is non-coding; its flanking sequences are embedded in a CpG island of 1216 bases long. Transcription start varies over the region between 35 to 112 bases upstream of the last base of exon 1, with the most common site at 40 bases upstream. No TATA or CAAT box is located within 150 bases upstream of any of the transcription start sites. BRE mRNA is expressed ubiquitously, and was initially found to be highly expressed in brain, and reproductive organs; hence the name "BRE" (Li et al., 1995). Subsequent screens using human multiple-tissue RNA dot blot and Northern blot revealed highest transcript expression in adrenal and heart (Miao et al., 2001).
Pseudogene	No pseudogene found.

Note	According to HapMap genotyped SNP data, there is no SNP polymorphism in any of the coding exons of BRE.
	Copy number polymorphism (CNP) of BRE gene. Regions with CNP are shown in colored boxes. Blue and red indicate copy loss and gain, respectively. Green indicates loss and gain at different segments of the contiguous region. The largest CNP region on the far left spans the first non-coding and the next 3 coding exons (exons 1, 2, 3 and 4) and extends further upstream into the neighboring ribokinase gene. The copy gain variant at the far right spans the alternative exon Z. Data obtained from HapMap.
Germinal	According to the current HapMap_rel27 for all the 4 populations (CEU, CHB, JPT and YRI), the number of nucleotide positions in BRE gene with HapMap genotyped SNP is 453. Given the size of BRE gene of 448284 bases long, the number of bases with SNP fits well to the average genome-wide figure of one SNP per 1000 bases (Dutt and Beroukhim, 2007). It is, however, noteworthy that no SNP has been found in any of the coding exons. All of the SNPs, except one located in the 5' UTR, are present in the introns. Two recombination hotspots are located in the introns, one of which is from position 28271535 to 28276573, located between coding exons 7 and 8. The other one is from position 28338948 to 28341210, located between coding exons 10 and 11. Copy number polymorphisms (CNP) involving a large contiguous region of 163295 bases encompassing the first 3 coding exons and the upstream sequence of the neighbouring ribokinase gene and smaller downstream regions have also been identified (see diagram above) (The International HapMap Consortium, 2003).
Somatic	One R9L mutation was identified in a lung carcinoma cell line, NIH-H2126, and a synonymous mutation S182S in a clear cell renal cell carcinoma sample, PD2198a.

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