I have recently been playing around with enhancer marks in intergenic regions versus intragenic regions and I have noticed that some of the intronic regions I obtained using this as a guide: http://crazyhottommy.blogspot.com/2013/05/find-exons-introns-and-intergenic.html?showComment=1448033038646#c3246007699340921322 are shown as intergenic regions inside IGV.

Being completely new to bioinformatics, I noticed that when choosing the hg19 genome under IGV, it's detailed as "RefSeq Genes" and I am using the gencode annotation in the above example. Could this be a reason that some intronic regions are being displayed as intergenic? I attempted to build a .genome file using gencode Fasta files and a gff3 file, but I can't seem to load the resulting genome file onto IGV. The program will simply crash, or hang until I force quit it.

Any ideas on either creating the genome file, or whether the RefSeq and Gencode annotations in IGV would look very different?