Sequence of the intergenic spacer between the 28S and 18S rRNA-encoding genes of the crustacean, Daphnia pulex.

The intergenic spacer (IGS) of the ribosomal DNA of the crustacean, Daphnia pulex, is 4819 bp in length, and contains two non-repetitive regions separated by two repetitive regions. The larger repetitive region contains three complete and one truncated copy of a 330-bp sub-repeat. Each sub-repeat contains the sequence, 5'-TATATAGGGAAG, which is very similar to the promoter sequences found in repeated elements in the IGS of other organisms. The 3' non-repetitive region, which separates the repeat elements containing the putative transcription promoter sites from the 18S coding region, is large (2689 bp) compared to those described for other arthropods. A putative transcription start point (tsp) has been identified 1280 bp upstream from the 18S coding region, suggesting that the external transcribed spacer is also large compared to that in other arthropods. The 3' non-repetitive region contains two poly(GT) tracts of 18 and 20 bp. Such sequences, which are capable of forming Z-DNA in vitro, have been found upstream from the transcription units of rRNA and protein-coding genes in human, mouse and rat, and are thought to have a functional role in gene expression.