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We have isolated and characterized portions of the alpha 1 (IX) collagen gene from mouse and human DNA. Nucleotide sequence analysis and comparison with the chicken gene suggest that the mammalian genes contain an alternative exon that is located within the intron between exons 6 and 7. Using oligonucleotide primers specific for exons 4, 8, and the alternative exon (exon 1*), we demonstrated by the polymerase chain reaction that embryonic mouse and fetal human RNAs contain two types of alpha 1(IX) collagen transcripts. One type of transcript does not contain the sequence encoded by exon 1*; the second type of transcript contains this exon. Both mouse and human alpha 1(IX) collagen genes give rise, therefore, to (at least) two mRNA transcripts.

The alpha 1 (IX) collagen gene gives rise to two different transcripts in both mouse embryonic and human fetal RNA.