Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, limited effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Here we reveal, in the plant model Arabidopsis thaliana, that the PIN7 gene, which encodes a polarly localized transporter for the phytohormone auxin, produces two evolutionarily conserved

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... s. These isoforms PIN7a and PIN7b, differing in a 4 amino acid motif, are present at nearly equal levels in most cells, except some early developing tissues where the expression of PIN7b is moderately prevalent. Both proteins also transport auxin with similar capacity and directionality. However, only PIN7a but not PIN7b cDNA rescues the phenotypes associated with the pin7 knock-out mutation, consistent with their differences in the subcellular trafficking and dynamics at the plasma membrane. Further phenotypic analyses suggested a joint, mutually opposing activity of both isoforms as being required for correct seedling apical hook formation and auxin-mediated tropic responses. These results establish alternative splicing of the PIN family as an evolutionary conserved, functionally relevant mechanism, taking part in the auxin-mediated plant development.