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After removal of repeats from the spliced sequences, transcripts were obtained of the expected length and size.
For a gene annotated with multiple reference sequences (transcripts) in the same chromosome and strand, the Alu (motif) densities were obtained by calculating the mean.
We identified 97 genes with a single set of MEHEs from among the set of human CCDS (consensus coding sequences) transcripts (see Materials and Methods).
By removing incomplete gene sequences, transcripts of the same genes, and redundant sequences, we identified nineteen non-redundant CDPK genes in the grape genome (Table 1).
When the information was not available in dbTSS for a gene, the 5' end of corresponding NCBI RefSeq sequences (transcripts) was used to represent the TSS position.
Based on the KEGG pathway assignment of the functionally annotated sequences, transcripts coding for most of the enzymes involved in TAG biosynthesis were found in D. tertiolecta.
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Genome sequences, transcript sequences, genome statistics, and annotation are available for download via Genbank (see Table 1 for accession numbers).
Genomic sequences, transcript expression levels, and data from other poeciliids have also not been reported to date.
Currently, ShrimpGPAT holds full-length cDNA sequences, individual EST sequences, transcript contigs and protein sequences for 14 decapod species (>500,000 combined records) together with putative functional annotations.
These gene sequences are called expression sequence transcripts, or ESTs.
Peaks span wider in protein-coding genes and deep sequencing transcripts [40] than in intergenic regions or the few introns in yeast.
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