The original TIF-IA gene and its two duplicates in the human genome. Exons and introns are marked with numbered boxes and horizontal lines, respectively. Splicing events between exon 1 and 2 are marked with dashed lines. Each of the TIF-IA genes is named according to its relative location on chromosome 16: that is, loci 15, 28, and 21. The relative levels of expression from each locus, as measured by DS Gene®, are given as percent of total TIF-IA mRNA in P69 cells and shown on the left. Locus 15 is the original full-length gene, containing 18 exons, coding for a 75 kDa protein (651 aa) (see Additional file 3). The transcription start site is marked by an arrow above exon 1 and the stop codon by a stop sign above exon 18. The 3'UTR accounts for ~47% of the mRNA molecule. The Alu element is located in intron 1. Locus 28 is a duplication of the original TIF-IA gene containing the promoter region of the original gene (marked by black box). A deletion of 768 nucleotides in the promoter region reduced its transcription activity. Also, this locus contains two additional deletions with respect to the original gene: a deletion of 3517 nucleotides between intron 10 and intron 12 (between LTR16A1 and Alu-Sg transposed elements) and a deletion of the last exon (exon 18). The last two exons of locus 28 probably originated following a duplication event of exons 3 and 4 of BANP gene (96.6% sequence similarity). The complete BANP gene is also located on chromosome 16. The mRNA synthesized from that site has the potential to encode a protein of 514 aa according to a translation-prediction tool, using the same start codon as that of locus 15. A protein corresponding to the predicted molecular weight was not detected by western blotting analysis (see Additional file 3). Locus 21 is presumably a duplication of locus 28, containing the exact major deletion as that of locus 28 and, in addition, a deletion downstream of exon 15. The last two exons originated from exonization events of LINE-LTR and Alu-Sq transposed elements. Alternative poly-adenylation signal in the last two exons is shown. Locus 21 has the potential to encode a 106 aa protein from the third AUG downstream from the transcription start site. The first AUG potentially encodes a 39-aa polypeptide. Analysis of ESTs and RT-PCR revealed that two RNA molecules are generated from locus 21, as shown in the lower panel (data not shown).