Homeobox genes encode homeodomain (HD) proteins which function as transcription factors and play an important role in plant and animal development by controlling cell specification and pattern formation. (Knotted1 in Arabidopsis thaliana) KNAT1-like mRNAs referred to as PtKN1(HD+) and mRNA sequences which lack HD region referred as PtKN1(hd-) were cloned from embryos of loblolly pine (Pinus taeda L.). Production of PtKN1(hd-) mRNAs is developmentally regulated and their encoded protein is abundant in mature pine embryos. Both forms of PtKN1 are produced by the same gene which has 5 exons; the regulatory dynamic is between cleavage-polyadenylation or termination within intron 3 to produce PtKN1 mRNA lacking HD sequences and splicing of exon 3 to exon 4 which excludes the 3'UTR/exon3 sequence to create an mRNA which encodes a HD. KNAT1 mRNA in Arabidopsis which lacks HD sequences was identified and characterized. While KNAT1 has been studied for many years, this is the first report of a KNAT1 mRNA lacking HD. KNAT1 mRNA lacking HD sequences was identified for the RS1 gene of maize, a monocotyledon. This is the first report of splicing of KNAT1 genes to produce mRNAs lacking HD sequences. The phenomenon appears to be ubiquitous as it is observed in gymnosperms, and both dicotyledonous and monocotyledonous angiosperms.