POLYMER GENOMICSchrX·hg38·156.0 Mb
Atlas
Open chrX in viewer Chromosome X
"Every woman is a mosaic" — the only chromosome where an entire copy is silenced, creating two genetically distinct cell populations in every female.
Physical Properties
Length156.0 Mb
Centromeremetacentric
p-arm58.6 Mb
q-arm93.6 Mb
GC content39.5%
Genomic Features
Protein-coding genes842
Gene density5.4 / Mb
CpG islands12,662
EPIC v2 probes38,109
Notable
Largest geneDMD (2.2 Mb)
Disease associations
Duchenne muscular dystrophy
Fragile X syndrome
Hemophilia A
· Subject to X-inactivation in females (Barr body)
· DMD (dystrophin) is the largest known gene at 2.2 Mb
· Contains ~800 protein-coding genes
Genomic Architecture
LINE-1 enrichment — The defining feature — L1 elements cover ~29% (vs 17% genome average). L1-dense regions correlate with efficient X-inactivation; L1-poor regions harbor escape genes. Mary Lyon's "repeat hypothesis" (1998).
Five evolutionary strata — Reflecting stepwise recombination suppression with Y: Stratum 1 (~240-320 MYA, oldest) through Stratum 5 (~30 MYA, youngest, adjacent to PAR1). Escape genes cluster on youngest strata.
PAR1 — (2.6 Mb) and **PAR2** (320 kb): Pseudoautosomal regions still recombining with Y.
Evolutionary History
Ohno's Law — (1967): X gene content conserved across all placental mammals — validated across dog, cow, mouse (>95% shared).
Origin — ~300 MYA from an ordinary autosomal pair when SOX3 mutated to SRY on the proto-Y.
Deep Cuts
Every woman is a chimera — Random X-inactivation makes every 46,XX female a mosaic of two cell populations expressing different X chromosomes.
The LINE hypothesis holds up — 25+ years later — X;autosome translocations silence autosomal genes only in L1-rich regions, and L1-depleted X regions correlate precisely with escape genes.
DMD transcription time — ~16 hours to transcribe. Approaches the limits of what a mammalian cell cycle can accommodate.
§ Deep dive