Almost all functional transcripts are derived from known genes. The only exceptions are a small number of transcripts that might play a direct role in regulating gene expression near the prompters of known genes. (See Enhancer RNA.)
Gene occupy most of prokaryotic  genomes so most of their genomes are transcribed. Many eukaryotic genomes are very large and known genes may take up only a fraction of the genome. In mammals, for example, known genes only account for 40-50% of the genome. Nevertheless, identified transcripts often map to a much larger fraction of the genome suggesting that the transcriptome contains spurious transcripts that do not come from genes. Some of these transcripipts are known to be non-functional because they map to transcribed pseudogenes or degenerative transposons and viruses. Others map to unidentified regions of the genome that may be junk DNA.
Spurious transcription is very common in eukaryotes, especially those with large genomes that might contain a lot of junk DNA. Some scientists claim that if a transcript has not been assigned to a known gene then the default assumption must be that it is junk RNA until it has been shown to be functional. This would mean that much of the transcriptome in species with large genomes is probably junk RNA. (See Non-coding RNA)
The transcriptome includes the transcripts of protein-coding genes (mRNA plus introns) as well as the transcripts of non-coding genes (functional RNAs plus introns).
*Ribosomal RNA/rRNA: Usually the most abundant RNA in the transcriptome.
*Long non-coding RNA/lncRNA: Non-coding RNA transcripts that are more than 200 nucleotides long. Members of this group comprise the largest fraction of the non-coding transcriptome other than introns. It is not known how many of these transcripts are functional and how many are junk RNA.
*transfer RNA/tRNA
*micro RNA/miRNA: 19-24 nucleotides (nt) long. Micro RNAs up- or downregulate expression levels of mRNAs by the process of RNA interference at the post-transcriptional level.
*small interfering RNA/siRNA: 20-24 nt
*small nucleolar RNA/snoRNA
*Piwi-interacting RNA/piRNA: 24-31 nt. They interact with Piwi proteins of the Argonaute family and have a function in targeting and cleaving transposons.
*enhancer RNA/eRNA: