POLYMER GENOMICSchrY·hg38·57.2 Mb
Atlas
Open chrY in viewer Chromosome Y
A chromosome that has been dying for 300 million years, yet refuses to disappear — rescued by palindromes talking to themselves.
Physical Properties
Length57.2 Mb
Centromeresubmetacentric
p-arm10.3 Mb
q-arm46.7 Mb
GC content39.4%
Genomic Features
Protein-coding genes71
Gene density1.2 / Mb
CpG islands491
EPIC v2 probes1,002
Notable
Largest geneRBMY1A1 (40 kb)
Disease associations
46,XY gonadal dysgenesis (Swyer syndrome)
Y chromosome infertility
Turner syndrome mosaicism
· Contains only ~70 protein-coding genes
· SRY triggers male sex determination
· Largely heterochromatic with extensive palindromic repeats
Genomic Architecture
Three euchromatic sequence classes — (Skaletsky et al., 2003):
X-transposed — (3.4 Mb): 99% identical to Xq21, transposed ~3-4 MYA.
X-degenerate — (8.6 Mb): Surviving relics of ancestral autosomes. 16 single-copy genes.
Evolutionary History
Origin — ~300 MYA, SOX3 mutated to create SRY, initiating sex-chromosome differentiation.
97% gene loss — From ~1,000-1,500 ancestral genes. Five evolutionary strata of progressive recombination suppression.
Deep Cuts
Last chromosome sequenced — T2T-Y published August 2023 — over 23 years after chr22. Added >30 Mb of new sequence (more than half the chromosome).
Self-healing chromosome — Palindrome gene conversion is a built-in error-correction system — the Y compares its own palindrome arms and copies the correct version over mutations. Unique among human chromosomes.
Forensic pitfalls — AMELY deleted in ~8% of men in some populations, causing false female results. Multiple wrongful identifications have resulted.
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