Feline spinal muscular atrophy (SMA) is an autosomal recessive juvenile onset lower motor neuron disease caused by an ∼ 140 kb deletion that disrupts expression of 2 genes, limb expression 1 (LIX1) and leucyl/cystinyl aminopeptidase (LNPEP). A previously generated Lnpep knockout (KO) mouse did not demonstrate a neuromuscular phenotype. Little is known about LIX1, except that it is evolutionarily conserved and highly expressed in spinal cord motor neurons. To determine whether loss of LIX1 alone is responsible for the feline SMA phenotype, a Lix1 intron 1 gene trap KO mouse line was obtained from Lexicon Genetics, Inc. Mating of F(1) heterozygotes produced offspring in the expected Mendelian ratios. KO and normal littermates were studied through 2 years of age by hanging latency, rotarod, inked footprint analysis, and histological methods. Disruption of Lix1 expression did not affect survival nor result in any neuromuscular phenotype. Reverse transcriptase-PCR amplification of spinal cord RNA identified a Lix1 alternative transcript beginning in intron 4 and containing exons 5 and 6. The alternative transcript appeared to be rodent specific, and its expression was not disrupted in Lix1 KO mice. Expression of the alternative transcript may have compensated for the loss of Lix1 in the KO mice and thus protected against motor neuron degeneration.