Abstract The heterochromatic Y chromosomes of several Drosophila species harbor a small number of male fertility genes (fertility factors) with several unusual features. Expression of their megabase-sized loci is restricted to primary spermatocytes and correlates with the unfolding of species-specific lampbrush loop-like structures resulting from huge transcripts mainly derived from clusters of loop-specific Y chromosomal satellites. Otherwise, there is evidence from genetic mapping and biochemical experiments that at least two of these loops, Threads in Drosophila hydei and kl-5 in D. melanogaster, colocalize with the genes for the axonemal dynein β heavy chain proteins DhDhc7(Y) and Dhc-Yh3, respectively. Here, we make use of particular Threads mutants with megabase-sized deletions for direct mapping of DhDhc7(Y)-specific exons among the large clusters of satellite DNA within the 5.1-Mb Threads transcription unit. PCR experiments with exon-specific primer pairs, in combination with hybridization experiments with exon- and satellite-specific probes on filters with large PFGE-generated DNA fragments, offer a simple solution for the long-lasting paradox between megabase-sized loops and protein-encoding transcription units; the lampbrush loops Threads and the DhDhc7(Y) gene are one and the same transcription unit, and the giant size of the DhDhc7(Y) gene as well as its appearance as a giant lampbrush loop are merely the result of transcription of huge clusters of satellite DNA within some of its 20 introns.