14Orthopedia homeobox (OTP) gene encodes a homeodomain-containing transcription 15 factor involved in brain development. OTP is mapped to human chromosome 5q14.1. Earlier we 16 described transcription in the second intron of this gene in wide variety of tumors, but among 17 normal tissues only in testis. In GeneBank these transcripts are presented by several 300-400 18 nucleotides long AI267901-like ESTs. 19 We assumed that AI267901-like ESTs belong to longer transcript(s). We used the Rapid 20 Amplification of cDNA Ends (RACE) approach and other methods to find the full-length 21 transcript. The found transcript was 2436 nucleotides long polyadenylated sequence in antisense 22 48 (tumor-specifically expressed, evolutionary novel) genes described by the authors in previous 49 papers. 50 51 131 samples of endometrial adenocarcinoma (156, 270), meningiomas (45, 63); and in all lymphoma 132 samples (31, 67, 82, 92, 102, 94, 113) (Fig 8b). Weak signals corresponding to the studied 157 chromosome and consists of 3 exons and 2 introns.

The phenomenon of evolutionary fixation of agrobacterial sequences (cT-DNA or cellular transferred DNA) in plant genomes is well known in nature. It was previously considered, that all of cT-DNA-containing species, except Linaria vulgaris, have multiple inverted cT-DNA repeats. Deep studying of general features of cT-DNA brings us closer to understanding the causes and mechanisms of its fixation in plants genomes. We combined multiple long-range PCR with genome walking for studying extended structure of cT-DNA. Using digital PCR method, we estimated copy number of cT-DNA elements. NGS with low covering allows us to develop a set of microsatellite markers, also used for copy number estimation. According to new data, cT-DNA elements in L. vulgaris form an inverted complex repeat of two simple direct repeats. After cT-DNA integration, cT-DNA sequence duplication events took place at least two times. The phenomenon of concerted evolution of cT-DNA sequences as well as some details of this process have been shown for the first time.We have shown, that L. vulgaris, as well as other cT-DNA containing species, has inverted structure of repeats. This fact indicates possible existence of some general causes and mechanisms of cT-DNA fixation in plant genomes during evolution.

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