Noncoding RNAs

Ribosomal RNA genes

Sequences related to the 5S RNA are found at a number of chromosomal locations. There are two main clusters on chromosome 1. A common repeat unit is about 2.2 kb.

The 18S, 5.8S, and 28S ribosomal RNAs are processed from a large precursor. Sequences related to these genes are dispersed in the genome. There are five major clusters of rRNA genes. These are located on chromosomes 13, 14, 15, 21, and 22. The genes are commonly organized into a 43-kb repeat unit. The nucleotide composition of the repeat is presented below. Note the strong strand bias and compositional differences compared with the complete chromosomes (see Chromosomes and DNA).

                                        Count   Fraction (%)
                              A         6411       14.91
                              G         11491      26.73
                              C         13605      31.65
                              T         11479      26.70

The mitochondrial ribosomal RNA sequences are encoded in the mitochondrial DNA.

tRNA genes

See the section on tRNAs for sequences of tRNAs used in the cytoplasm.

Twenty two mitochondrial tRNAs are encoded by the mitochondrial DNA. Serine and leucine each have two mitochondrial tRNAs.

Additional noncoding RNAs

In addition to the rRNAs and tRNAs involved in translation, the genome encodes a large number of other noncoding RNAs with diverse functions. The following table lists some of their functions and where the RNAs and their protein complexes are described in other sections. The RNA components of these complexes vary greatly in how they are transcribed and processed.

Noncoding RNAs
Function	Sections
rRNA processing	Small RNAs in RNA Processing Nucleus and Nucleolus RNases and RNA Stability
tRNA processing	Small RNAs in RNA Processing Nucleus and Nucleolus RNases and RNA Stability
Formation of histone mRNA 3' ends	Small RNAs in RNA Processing Histones, Related Proteins, and Modifying Enzymes
Telomerase	Telomere Functions
Ro complexes	RNA-binding Proteins
X inactivation	Noncoding RNAs and Development
Transcriptional regulation (CDK9 pathway)	Cyclins and Related Functions
RNA modification (nucleolus and Cajal bodies)	Small RNAs in RNA Processing
Spliceosome (major and minor)	Small RNAs in RNA Processing Capping and Splicing
Signal recognition particle	ER, Golgi, and the Secretory Pathway
Other	Noncoding RNAs and Development

See also the section on microRNAs for examples of these sequences and their their regulatory roles.

Notes and references

For a sample 5S RNA containing repeat unit, see GI:23898. See also GI:396098 for an annotated sequence.

A sample 43-kb rDNA repeat unit is described in GI:555853. The nucleotide composition in the table excludes a small number of ambiguous positions.

See also the additional reading for this chapter.

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