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Transcriptome- The complete set of RNA molecules produced by the genome is, usually, referred to as transcriptome. In case of eukaryotes, a single gene can produce more than one type of mature mRNA by a phenomenon called alternative splicing. Splicing describes the removal of introns from RNA transcripts, and the linking together all the exons in the correct order to yield a mature functional mRNA.

In alternative splicing, the splicing a single primary RNA transcript occurs in two or more different but well defined patterns. In each splicing pattern, a defined set of exons is joined together to yield a functional mRNA molecule. The net effect of alternative splicing is the generation of a large number of different proteins from a relatively smaller number of genes.

If each human gene was alternatively processed to yield an average of 3 different proteins, the estimated 35,000 human genes would produce 105,000 different proteins. An extreme case of alternative processing is provided by the Drosophila gene Dscam.

This gene can generate nearly 40,000 different mRNAs, each of which could be translated into a distinct receptor protein. Thus the transcriptome is bound to be much more complex (i.e., variable) than the transcribed portion of the genome.

In addition, none of the tissues of a multicellular organism will express all the genes, and genes expressed in one tissue will differ from those in another tissue. In other words, the transcriptome obtained from one tissue will differ in some respects from that obtained from another tissue. Therefore, it is customary to refer to the transcriptomes as 'human brain transcriptome', 'mouse liver transcriptome', etc.