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How many genes are in mitochondrial DNA?
Human mitochondrial DNA contains 37 genes in a circular genome of 16,569 base pairs. Most human protein-coding genes are instead found in nuclear DNA.
Matic Broz Computational chemist
Human mitochondrial DNA contains 37 genes: 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. They fit into a circular genome of just 16,569 base pairs.
Most human genes are elsewhere. Nuclear DNA contains about 19,400 protein-coding genes and accounts for nearly all of the DNA in a cell.
How many genes are in mitochondrial DNA?
Human mitochondrial DNA contains 37 canonical genes: 13 encode proteins, 22 encode transfer RNAs, and 2 encode ribosomal RNAs.[1][2]
All 13 proteins form parts of the oxidative phosphorylation system that cells use to make ATP. The 24 RNA genes supply the transfer RNAs and ribosomal RNAs needed to translate those proteins inside mitochondria.
The chart divides one complete set of 37 canonical mitochondrial genes by the product each gene encodes.[1][2]
How many genes are in nuclear DNA?
Human nuclear DNA contains about 19,400 protein-coding genes. In GENCODE Release 50, 19,429 of the 19,442 protein-coding genes are nuclear and 13 are mitochondrial.[1][3][4]
That nuclear count is a ProteinIQ calculation. GENCODE counts the mitochondrial chromosome among its reference chromosomes, so subtracting the 13 mtDNA protein-coding genes from its 19,442-gene total leaves 19,429 in nuclear DNA.
GENCODE's broader annotation contains 78,696 nuclear gene entries when non-coding RNA genes, pseudogenes, immune receptor segments, and other annotated gene types are included. This is the 78,733-gene total minus the 37 mitochondrial genes.[1][3][4] The distinction between protein-coding and total annotated genes also explains why estimates of the number of human genes can look inconsistent.
How many base pairs are in mitochondrial DNA?
The human mitochondrial reference genome contains exactly 16,569 base pairs.[2]
By comparison, one set of chromosomes in the human nuclear genome contains about 3.1 billion base pairs. Nuclear DNA is therefore roughly 187,000 times longer than one mitochondrial genome copy.[5] This comparison uses one haploid nuclear genome, rather than the two chromosome sets found in a typical body cell.
Mitochondrial DNA is unusually compact. Some genes even overlap: the protein-coding genes MT-ATP8 and MT-ATP6 share part of the same sequence.[2] Their overlapping reading frames can be inspected with ORF Finder. Mitochondrial sequences also use a modified genetic code, so DNA translation requires the vertebrate mitochondrial code rather than the standard nuclear code.
How many copies of mitochondrial DNA are in a cell?
Most mammalian cells contain roughly 1,000 to 10,000 copies of mitochondrial DNA, but there is no single human-cell average.[7] Copy number changes with cell type, energy demand, development, age, health, and measurement method.
One study of five tissues from 50 people found mean values from 1,259 mtDNA copies per cell in the cerebellar cortex to 9,235 in heart muscle.[6]
These are study means, not fixed values for every person. The measurements also varied widely within tissues. A 2026 analysis of 47 tissue types reports 2 to 10 mtDNA copies per mitochondrion and substantial differences among tissues.[8]
Mitochondrial DNA copy number is not the same as the number of mitochondria. One mitochondrion can hold several genome copies, while mitochondria can fuse into networks or divide into smaller organelles.
Sources▼
- Mitochondrial DNA MedlinePlus Genetics, National Library of Medicine · July 28, 2026. https://medlineplus.gov/genetics/chromosome/mitochondrial-dna/
- Homo sapiens mitochondrion, complete genome NCBI RefSeq · July 28, 2026. https://www.ncbi.nlm.nih.gov/nuccore/NC_012920.1
- Human release statistics (v50) GENCODE · July 28, 2026. https://www.gencodegenes.org/human/stats.html
- Frequently asked questions GENCODE · July 28, 2026. https://www.gencodegenes.org/pages/faq.html
- On the length, weight and GC content of the human genome BMC Research Notes · 2019. https://pmc.ncbi.nlm.nih.gov/articles/PMC6391780/
- Lack of age-related increase of mitochondrial DNA amount in brain, skeletal muscle and human heart Mechanisms of Ageing and Development · 2005. https://pubmed.ncbi.nlm.nih.gov/16099018/
- Release of replication termination controls mitochondrial DNA copy number after depletion with 2′,3′-dideoxycytidine Nucleic Acids Research · 2002. https://academic.oup.com/nar/article/30/9/2004/1088574
- Mitochondrial genetic variation across tissues of the human body Nucleic Acids Research · 2026. https://pubmed.ncbi.nlm.nih.gov/42179041/
Founder and computational chemist, ProteinIQ
Dr. Matic Broz is the founder of ProteinIQ and a computational chemist. He completed a PhD focused on protein structure, molecular dynamics, and neural networks, and writes about structural biology and scientific software.