Characteristics of a conserved 1,579-bp highly repetitive component in the killer whale, Orcinus orca

A tandemly organized, highly repetitive DNA component of the killer whale was sequenced. The length of the repeat was 1,579 bp. This unit, which characterizes all delphinids, shows stringent hybridization homology with a 1,740-bp repeat that is characteristic of all other cetacean families. The 1,579-bp component comprises approximately 15% of the killer-whale genome, in which it is repeated 4-5 X 10(5) times. Computer analysis of the sequence showed no linear repetition within the component. This indicates that the 1,579-bp unit has not evolved by amplification of shorter repeats. Several inverted repeats of substantial length were found in the 1,579-bp unit. The most conspicuous of these was a 72-bp sequence that deviated from matching in only three positions. The 72-bp sequence occurs within an open reading frame 330 bp in length. Transcriptional activity was registered in the cloned repeat in a cell-free system. The length of the transcript was approximately 340 nucleotides. The chromosomal localization of the 1,579-bp repeat was determined by in situ hybridization. The repeat was present in eight of 21 autosomal pairs and was found in almost all C-band-positive (constitutive heterochromatin) regions of the karyotype.