Table 1.

Ultraconserved enhancers deleted from the mouse genome.

Enhancer name (VISTA)	Ultraconserved elements (Bejerano et al.)	Tissue-specific activity	Neighboring genes	Phenotype(s) observed	Reference(s)
Single enhancer deletions
hs112	uc248	Forebrain	Dmrt1/2/3	None	33
hs113	uc329	Dorsal root ganglion	Pax6, Rcn1, Wt1	None	33
hs427	uc482	Forebrain, hindbrain	Sox3, Atp11c	None	33,36
hs121	uc467	Forebrain	Arx, Pola1	None in original study, altered densities of several neuron classes in the brain identified in subsequent study	33,34
hs119	uc463-464-465	Forebrain	Arx, Pola1	Reduced body mass	34
hs122	uc468–469	Forebrain	Arx, Pola1	Defects to hippocampus, decreased Arx expression in developing forebrain	34
hs123	uc470	Forebrain	Arx, Pola1	None	34
hs280	uc019	Limb	Tmem53, Rnf220, Eri3	Reduced body mass and overall body size, decreased expression of Tmem53 and Dmap1 in the limb	35
Compound enhancer deletions
hs119+hs121	uc463-464-465–467	Forebrain	Arx, Pola1	Altered densities of several neuron classes in the brain, reduced body mass, decreased Arx expression in developing forebrain, phenotypes more severe than loss of hs119 or hs121 alone	34
hs122+hs123	uc468-469-470	Forebrain	Arx, Pola1	Defects to hippocampus, decreased Arx expression in developing forebrain, similar to loss of hs122 alone	34

In all cases, homozygous-null (or hemizygous-null for X-linked loci) mice are viable, fertile, and born at Mendelian-expected frequencies. VISTA indicates the name of the enhancer in the VISTA Enhancer Browser⁹⁶.