The Hoxa1 gene is transcribed to yield mRNA in response to retinoic acid in embryos (Frasch et al. 1995, Dupe et al. 1997), teratocarcinoma cells (Langston and Gudas 1992, Langston et al. 1997, Lee et al. 1997, Kashyap and Gudas 2010), and embryonic stem cells (Chen and Reese 2011, reviewed in Gudas and Wagner 2011). Hoxa1 mRNA is observed in the neural tube, adjacent mesenchyme, paraxial mesoderm, somites, and gut epithelium from rhombomere 4 to the caudal-most region of the embryo (Baron et al. 1987, Sundin et al, 1990, Murphy and Hill 1991, Godwin et al. 1998, Makki and Capecchi 2010). (Rhombomeres are transiently formed segments in the neural tube that will eventually form the hindbrain.)
The long non-coding RNA linc-HOXA1 suppresses transcription of Hoxa1 in embryonic stem cells (Maamar et al. 2013).