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In order to identify novel homeobox-containing genes involved in early embryonic development, we conducted a degenerate oligonucleotide polymerase chain reaction (PCR) screening of a murine embryonic stem (ES) cell cDNA library. ENK (early embryo specific expression NK family) was one of several genes isolated that was found to exhibit early embryo stage-specific expression. The full-length ENK cDNA was cloned and its genomic organization was characterized. Murine ENK spans 7.1 kb, encodes four exons and maps to mouse chromosome 6F2. Reverse transcriptase–PCR and Northern blot analyses show that ENK is preferentially expressed in pre-implantation mouse embryos and a higher level in blastocysts. Whole-mount in situ hybridization analysis further demonstrates that ENK mRNA is present predominantly in the inner cell mass of blastocysts. The expression of ENK is markedly higher in undifferentiated ES cells than in retinoic acid differentiated ES cells and embryonic bodies. ENK expression slightly decreased in early primitive ectoderm-like (EPL) cells and was absent after the 9.5-day embryo stages. ENK is one of the few homeobox-encoding genes preferentially expressed in ES cells during mammalian embryogenesis. [Copyright &y& Elsevier]