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<p>Abstract</p> <p>Background</p> <p>Mucolipidosis type IV (MLIV) is an autosomal recessive lysosomal storage disorder characterized by severe neurologic and ophthalmologic abnormalities. Recently the MLIV gene, <it>MCOLN1,</it> has been identified as a new member of the transient receptor potential (TRP) cation channel superfamily. Here we report the cloning and characterization of the mouse homologue, <it>Mcoln1,</it> and report a novel splice variant that is not seen in humans.</p> <p>Results</p> <p>The human and mouse genes display a high degree of synteny. <it>Mcoln1</it> shows 91% amino acid and 86% nucleotide identity to <it>MCOLN1.</it> Also, <it>Mcoln1</it> maps to chromosome 8 and contains an open reading frame of 580 amino acids, with a transcript length of approximately 2 kb encoded by 14 exons, similar to its human counterpart. The transcript that results from murine specific alternative splicing encodes a 611 amino acid protein that differs at the c-terminus.</p> <p>Conclusions</p> <p><it>Mcoln1</it> is highly similar to <it>MCOLN1,</it> especially in the transmembrane domains and ion pore region. Also, the late endosomal/lysosomal targeting signal is conserved, supporting the hypothesis that the protein is localized to these vesicle membranes. To date, there are very few reports describing species-specific splice variants. While identification of <it>Mcoln1</it> is crucial to the development of mouse models for MLIV, the fact that there are two transcripts in mice suggests an additional or alternate function of the gene that may complicate phenotypic assessment.</p>