POLYMER GENOMICSchr5·hg38·181.5 Mb
Atlas
Open chr5 in viewer Chromosome 5
A paradox of genomic architecture — the fifth largest chromosome, yet one of the most gene-poor, harboring the engine of telomere immortality and a duplicated death trap at 5q13 that destroys motor neurons.
Physical Properties
Length181.5 Mb
Centromeresubmetacentric
p-arm46.5 Mb
q-arm131.5 Mb
GC content39.5%
Genomic Features
Protein-coding genes923
Gene density5.1 / Mb
CpG islands14,507
EPIC v2 probes51,741
Notable
Largest geneCTNNA1 (385 kb)
Disease associations
Familial adenomatous polyposis
5q- syndrome
Sotos syndrome
· Contains TERT, the catalytic subunit of telomerase
· del(5q) is a defining feature of the 5q- myelodysplastic syndrome
· Home to the APC tumor suppressor
Genomic Architecture
5q13 duplication architecture — The SMA region contains a massive inverted duplication of ~500 kb, producing telomeric and centromeric copies of SMN, NAIP, and other genes. Human-specific — chimpanzees have only a single copy.
Conserved noncoding regions — Gene-poor regions display remarkable conservation with non-mammalian vertebrates (chicken, frog, fish), suggesting deep functional constraint.
Fragile sites — FRA5A at 5p13 and FRA5B at 5q14.
Evolutionary History
Ancestral arrangement — Human represents the ancestral state; the pericentric inversion is chimpanzee-specific.
5q13 duplication is human-specific — The SMN2 duplication occurred after human-chimpanzee divergence. SMA is a uniquely human disease.
Deep Cuts
SMA is a human-only disease — No other species naturally develops SMA because the SMN1/SMN2 duplication is unique to humans.
The single-nucleotide catastrophe — SMN1 and SMN2 differ at one functionally relevant nucleotide, yet this converts a life-sustaining gene into one producing 85-90% defective protein.
TERT at its own telomere — If chromosome 5's telomere erodes, telomere position effect could silence TERT when it's needed most.
§ Deep dive