A nuclear gene is a gene located in the cell nucleus of a eukaryote. The term is used to distinguish nuclear genes from the genes in the mitochondrion, and in case of plants, also the chloroplast, which host their own genetic system and can produce proteins from scratch. The term "gene" most often refers to nuclear genes.
The distinct genomes of eukaryotes are thought to have arisen through symbiotic relationships. The mitochondrion represents a eubacterium that integrated into its archaeal host cell's physiology to such an extent that it became an integral cell component, or organelle. The process repeated in plants, with a cyanobacterial symbiont in a eukaryote host becoming the chloroplast. The nuclear genes represent the genome of the original host cell, while both of these organelles still retain a small genome, although many of the genes of the organelles have moved to the nucleus during the course of evolution.
The majority of the proteins of a cell are the product of messenger RNA transcribed from nuclear genes, including most of the proteins of the organelles, which are produced in the cytoplasm like all nuclear gene products and then transported to the organelle. In addition, there are nuclear genes that encode non-translated regulatory RNAs. Genes in the nucleus are arranged in a linear fashion upon chromosomes, which serve as the scaffold for replication and the regulation of gene expression. As such, they are usually under strict copy-number control, and replicate a single time per cell cycle.