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HOXA6 is 233 amino acids long, weighing approximately 26 kDa, that functions as a sequence-specific transcription factor which focuses on the specific positional identities of cells on the anterior-posterior axis, which is all part of a developmental regulatory system. HOXA4 has also been shown to have interactions with PBX1, PBX3, PKNOX2, POLR2I, and POU2F1.