The Y chromosome is one of the two sex chromosomes in humans. Males normally have one X and one Y chromosome in each cell, and females have two X chromosomes. When a cell divides and the Y is packed most tightly, it is an estimated 2 micrometers long. A micrometer is a millionth of a meter.

Size

One way to measure a chromosome is by the amount of DNA it holds, counted in base pairs, the rungs of the twisted DNA ladder. The first complete reading of a human Y chromosome, published in 2023, found 62,460,029 base pairs. That is almost 2 percent of one full set of human DNA.

Like the other chromosomes, the Y is a long DNA molecule wrapped around proteins. Neighboring base pairs sit 0.34 nanometers apart, and a nanometer is a billionth of a meter. So the DNA of the complete Y chromosome, stretched out, would be about 2.1 centimeters (0.8 inches) long.

As a cell prepares to divide, its chromosomes condense and become about 10,000 times shorter. That gives a rough estimate of 2 micrometers for a tightly packed Y. At that stage each chromosome has been copied, and the two identical copies are joined together. The pair is about 1 micrometer wide, large enough to see with a light microscope.

Size comparisons

A tightly packed Y chromosome, roughly 2 micrometers long, is about as long as an E. coli bacterium.
The X chromosome holds about 155 million base pairs, about two and a half times as much DNA as the Y.
About 40–50 tightly packed Y chromosomes laid end to end would span a human hair, which is 80–100 micrometers wide.
If a packed Y chromosome were enlarged to the height of a person 1.7 meters (5 feet 7 inches) tall, its DNA, stretched out at the same scale, would be about 17 kilometers (11 miles) long.

What the Y chromosome does

The Y chromosome likely holds 70 to 200 genes that carry instructions for making proteins. The estimate varies because researchers use different methods to count genes. Many of these genes are involved in male development. The SRY gene on the Y chromosome causes a developing baby to grow as a male, and other genes are needed to father children.

Not all of the Y is unique. Some regions, called pseudoautosomal regions, carry genes that are also on the X chromosome. As a result, men and women both have two working copies of those genes.

The last chromosome to be read

The Y chromosome was the last human chromosome to be read in full, from one end to the other. Much of it is made of long repeated and mirror-image stretches of DNA, which are hard to put in order. More than half of the Y was missing from the standard reference sequence that scientists had used before.

In 2023, a group of scientists called the Telomere-to-Telomere consortium published the complete sequence of one man's Y chromosome. It added more than 30 million base pairs to the reference, including the repeated region on the long arm.

Y chromosomes differ in size from man to man. A 2023 study of the Y chromosomes of 43 men found sizes from 45.2 to 84.9 million base pairs. The part that varied most was the repeated region on the long arm, which held 17.6 to 37.2 million base pairs where it could be read in full. By the same 10,000-fold estimate, these men's Y chromosomes would be about 1.5 to 3 micrometers long when tightly packed.

Sources

Y chromosome. MedlinePlus Genetics, National Library of Medicine.
X chromosome. MedlinePlus Genetics, National Library of Medicine.
The complete sequence of a human Y chromosome. Rhie et al., Nature, 2023.
Assembly of 43 human Y chromosomes reveals extensive complexity and variation. Hallast et al., Nature, 2023.
Cell Division. In Biology 2e. OpenStax, 2018.
DNA Structure and Sequencing. In Biology 2e. OpenStax, 2018.
Decrease in overall length generated by chromosome condensation during mitosis in animal cells (BNID 105211). BioNumbers, Harvard Medical School, citing D. O. Morgan, The Cell Cycle, 2007.
How big is an E. coli cell and what is its mass?. In Cell Biology by the Numbers. Ron Milo and Rob Phillips, Garland Science.
Just How Small Is "Nano"?. National Nanotechnology Initiative.
SI prefixes. International Bureau of Weights and Measures (BIPM).

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