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these cleaned reads are presented in Table 1 and Fig. 1. It is notable that a substantial number of cleaned reads were longer than 400 bp. CAP3 assembling resulted in 63,581 contigs of an average length of 480. 6 and a median length of 417 bp. N50 was 477 bp, The maximum length of a contig was 13,292 bp, and the length of a substantial number of con tigs Purmorphamine exceeded 2 kb, The 10% of lon gest contigs accommodated almost 60% of all assembled bases, Contigs were composed on average of 10. 5 reads, however the median number of reads per contig was three, Very high coverage of cer tain contigs should be noted, with the maximum reaching 23,367 reads per contig and the maximum average per base coverage of 2,770.

We detected in our trimmed reads 5,763 microsatellite repeats, the majority of them con taining dinucleotide motifs, followed by tetra and trinucleotide repeats, Functional annotation of the transcriptome Searching the SwissProt database revealed that 18,470 contigs and 44,823 singletons showed similarity to proteins D4476 in the database at an E value thresh old 10 5, In total, we identified significant similarity to 11,181 genes. Many more sequences exhibited similarity to sequences from the ENSEMBL collection of mouse transcripts. 27,283 contigs and Purmorphamine 92,957 singletons rep resenting 14,051 ENSEMBL genes, Interestingly, a number of contigs and singletons, that did not have hits in ECMT did have hits in SwissProt. Over mouse genome had hits in the AceView although this database covers only less than 10% of the mouse genome.

Messenger RNA Thus, sequences that did not match ECMT but matched genomes were highly enriched in sequences known to be 60% of such sequences showed homology to viral or transposon proteins, Contigs and singletons Purmorphamine without hits in ECMT were blasted against the mouse and rat genomes as well as the AceView nonredun dant database of mouse transcripts. A substantial propor tion of contigs showed similarity to the mouse or rat genome, and two thirds of them had hits in both genomes, A qualitatively similar picture was obtained for singletons, although the proportion of sequences with hits was lower than for contigs, The absolute number of singletons with hits to genomes was higher Purmorphamine than the number of singletons with hits to ECMT. A remarkable result is that a large number of sequences, Several conclu sions may be drawn from the inspection of this table.

Genes for all proteins encoded in mitochondrial and for both mitochondrial ribosomal RNAs were among the high coverage contigs. A number of nuclear genes encod ing mitochondrial proteins were present as well. In con trast, only five genes encoding structural cardiac muscle proteins or proteins involved Purmorphamine in the cardiac muscle con traction were detected among the most abundant genes. Overall, although the Purmorphamine normalization procedure was suc cessful, as judged from the gel images before and after normalization, the dynamic range of library, expressed as the total number of bases matching a transcript divided by the transcript length, still spanned six orders of magni tude, Completeness of the transcriptome To evaluate the completeness of the transcriptome, we checked whether transcripts of all genes normally present in most mammalian cells could be detected.

We tested for the presence of genes encoding proteins Purmorphamine forming selected macromolecular complexes and genes encoding proteins involved in basic metabolic pathways. In five of six mac romolecular complexes and all four evaluated metabolic pathways, all of the involved genes were identified in the bank vole heart transcriptome, We also evaluated the presence of genes that should be expressed in the heart because their products are struc tural and functional components of the cardiac muscle or are involved in regulation of heart function. We selected five GeneOntology categories related to cardiac muscle organization and contraction. 1 contractile fiber part, 2 myofibril, 3 cardiac myofibril assembly, 4 sacrcomere organi zation, 5 cardiac muscle