The t complex on chromosome 17 of the house mouse is an exceptional model for studying the genetic control of transmission ratio, gametogenesis, and embryogenesis. Partial haplotypes derived through rare recombination between a t haplotype and its wild-type homolog have been essential in the genetic analysis of these various properties of the t complex. A new partial t haplotype, which was derived from the complete tw71 haplotype and which is called tw71Jr1, was shown to have unexpected effects on tail length and unique recombination breakpoints. This haplotype, either when homozygous or when heterozygous with the progenitor tw71 haplotype, produced short-tailed rather than normal-tailed mice on certain genetic backgrounds. Genetic analysis of this exceptional haplotype showed that the recombination breakpoints were different from those leading to any other partial t haplotype. Based on this haplotype, a model is proposed that accounts for genetic interactions between the brachyury locus (T), the t complex tail interaction (tct) locus, and their wild-type homolog(s) that determine tail length. An important part of this model is the hypothesis that the tct locus, which enhances the tail-shortening effect of T mutations, is in fact at least two, genetically separable genes with different genetic activities. Genetic analysis of parental and recombinant haplotypes also suggests that intrachromosomal recombination involving an inverted duplicated segment can account for the variable orientation of loci within an inverted duplication on wild-type homologs of the t haplotype.