Structures, sequence characteristics, and synteny relationships of the transcription factor E4TF1, the splicing factor U2AF35 and the cystathionine beta synthetase genes from Fugu rubripes

A cosmid containing the beta-amyloid precursor protein (APP) from Fugu rubr ipes has been completely sequenced. In addition to APP, the cosmid contains the E4TF1-60 transcription factor, the U2AF35 pre-mRNA splicing factor, an d the cystathionine beta synthetase (CBS) gene. The human homologues of all four genes map to human chromosome 21 but are not clustered; APP and E4TF1 -60 map within 21q21, whereas U2AF35 and CBS map approximately 20 Mb distal in 21q22.3. The protein sequences of the Fugu genes vary in their overall level of similarity to their mammalian homologues, but several regions of f unctional importance are almost identical. As expected, the intron/exon str uctures of the homologous pairs of genes are highly conserved, but there ar e significant differences in the compaction ratios. The introns of APP and E4TF1-60 are 49- and 24-fold smaller in Fugu than in human, and the interge nic distance is compressed at least 100-fold. For U2AF35 and CBS, the intro ns are compressed only five- to eightfold. These size differences were comp ared with those for a number of previously reported Fugu genes; in general, levels of compaction of Fugu genes are consistent with the isochore locati ons of the human homologues. (C) 1999 Elsevier Science B.V. All rights rese rved.