The chicken homeobox gene Hoxd-11 encodes two alternatively spliced RNA species.

Two forms of cDNA clones corresponding to Hoxd-11 were obtained by screening a chicken limb bud cDNA library. Comparison of the two cDNA sequences with the mouse cDNA and genomic sequence, shows that the shorter cDNA is missing 3 nucleotides, which encode an alanine residue, at the junction between exons 1 and 2. Analysis of the chicken genomic sequence shows two tandem CAG repeats at the intron 1-exon 2 junction, both of which could serve as splice acceptor sequences. Thus we hypothesize that the two spliced forms result from alternative use of two tandem splice acceptor sequences. Using reverse transcription polymerase chain reaction we examined expression of the two forms in 3 to 14-day chick embryos. All samples showed both species of RNA with approximately 2 times more of the larger from compared with the smaller form.