Multiple coding and non-coding RNAs in the Hoxb3 locus and their spatial expression patterns during mouse embryogenesis

► Multiple coding and non-coding RNAs are transcribed from the mouse Hoxb3 locus. ► We identified a series of 4 novel Hoxb3 transcription initiation exons. ► We defined a novel promoter P3 in the Hoxb3 locus. ► Sense Hoxb3 transcripts are differentially expressed in the developing hindbrain. ► Anti-sense ncRNAs have rhombomere-specific expression patterns during embryogenesis.