Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription

Amano, Takanori, Sagai, Tomoko, Tanabe, Hideyuki, Mizushina, Yoichi, Nakazawa, Hiromi, Shiroishi, Toshihiko·2009·Developmental Cell

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  25. Limb Development Anomalies: Genetics
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