The semaphorins comprise a large family of membrane-bound and secreted proteins, some of which have been shown to function in axon guidance. We have cloned a transmembrane semaphorin, Sema W, that belongs to the class IV subgroup of the semaphorin family. The mouse and rat forms of Sema W show 97% amino acid sequence identity with each other, and each shows about 91% identity with the human form. The gene for Sema W is divided into 15 exons, up to 4 of which are absent in the human cDNAs that we sequenced. Unlike many other semaphorins, Sema W is expressed at low levels in the developing embryo but was found to be expressed at high levels in the adult central nervous system and lung. Functional studies with purified membrane fractions from COS7 cells transfected with a Sema W expression plasmid showed that Sema W has growth-cone collapse activity against retinal ganglion-cell axons, indicating that vertebrate transmembrane semaphorins, like secreted semaphorins, can collapse growth cones. Genetic mapping of human SEMAW with human͞hamster radiation hybrids localized the gene to chromosome 2p13. Genetic mapping of mouse Semaw with mouse͞hamster radiation hybrids localized the gene to chromosome 6, and physical mapping placed the gene on bacteria artificial chromosomes carrying microsatellite markers D6Mit70 and D6Mit189. This localization places Semaw within the locus for motor neuron degeneration 2, making it an attractive candidate gene for this disease.Development of the nervous system requires that axonal projections reach the correct targets. Within the last few years, a number of molecules have been found that have the ability to guide axonal growth by providing a repulsive signal that inhibits axons from straying outside of their correct paths. Most of these repellant molecules identified to date belong to the semaphorin family. In vitro, semaphorin family members collapsin 1 (1) and Sema D (2) can repel axons and cause growth-cone collapse. In vivo, grasshopper and Drosophila Sema I (3, 4) and Drosophila Sema II (5) can influence axon trajectories, and targeted disruption of the gene for Sema D, or its receptor neuropilin 1, leads to severe abnormalities in peripheral nerve projection (6, 7). Recently, new members of the semaphorin family have been described that have effects outside of the nervous system. Human CD100, known as Sema J in the mouse, has been found to function in T cell and B cell aggregation and activation (8, 9). Human Sema E has been found to be involved in the resistance of cancers to radiation and chemotherapeutic drugs (10), and mouse Sema H expression has been found to correlate with the metastatic ability of tumor cell lines (11). In addition, two viral genes bearing significant homology to semaphorin have been described in alcelaphine herpesvirus 1 and vaccinia virus, although the function of these genes is not yet known.In mammals, 15 members of the semaphorin family of molecules have been described to date and, together with avian and insect semaphorins, can be grouped int...