The Drosophila chromosome 4, known as the “dot chromosome” or Müller F element is predominantly heterochromatic. There is evidence however that 80 genes are actively transcribed in this region. The mechanism by which active transcription is carried out in this environment is under investigation. It is hypothesized that chromosome 4 genes share common elements in their transcriptional start sites that may explain their levels of transcription in this highly compacted environment similar to the other euchromatic autosomes. As part of the Genomics Education Partnership (GEP) undergraduate research initiative, the goal of this study was to annotate all features in Contig 5 of Drosophila ficusphila chromosome 4 utilizing a comparative genomics approach and several bioinformatics tools including the Basic Local Alignment Search Tool (BLAST), the UCSC Genome Browser, and gene predictors such as GENSCAN and N-SCAN, as well as RNA-Seq data and TopHat junctions. The Drosophila melanogaster genome was used as a reference for gene orthology. It was found that three genes, pan, ank, and ank2, with orthologs in D. melanogaster are located in contig.5. Gene models were proposed based on all gathered evidence that allowed for annotation of exact coordinates for each intron and exon of all isoforms for each gene homolog. We are currently analyzing the transcriptional start sites that may shed light on how these genes can be expressed in such a highly heterochromatic environment.