Sequence-specific DNA-binding transcription factor that binds palindromic sequences within promoters and may activate or repress the transcription of a subset of genes (PubMed:12929931). Most probably regulates the expression of genes involved in the development of mesenchyme-derived craniofacial structures. Early on in development, it plays a role in forebrain mesenchyme survival (PubMed:8673125). May also induce epithelial to mesenchymal transition (EMT) through the expression of SNAI1 (By similarity). Binds DNA as a homodimer; required for transcriptional activation (By similarity). Interacts (via homeobox domain) with EP300; acetylates ALX1 and stimulates its transcriptional activity (PubMed:12929931). At 8.5 dpc and 9.5 dpc expression is restricted to forebrain mesenchymal cells. The OAR motif may negatively regulate DNA-binding and therefore transcriptional activity. It is found in the C-terminal transactivation domain that stimulates transcription. Acetylated at Lys-131 by EP300; increases interaction with EP300 and stimulates ALX1 transcriptional activity. Mice lacking Alx1 die within 24 hours of birth. The overt phenotype is acrania and degeneration of unprotected brain tissues. This is most probably the cause of the death since no other abnormality in limbs and visceral tissues is observed. The defect in cranial bone formation may be a consequence of extensive loss of forebrain head mesenchyme due to cell death and neural tube closure defects earlier during development. The penetrance of the acrania/meroanencephaly phenotype is variable between mice strains. Heterozygous mice appear normal and fertile. Belongs to the paired homeobox family.