The difference between gene loci with isoform in RNA-seq alternative anlalysis?

[huan]

As I know, 'A locus (plural loci), in genetics, is the specific location or position of a gene, DNA sequence, on a chromosome. Gene loci analysis is generally done in DNA seq. But recently, I have seen the gene loci analysis with RNA-seq data. In the paper, the authour compute the gene loci by mapping the transcript to the reference genome using GMAP. It seems the gene loci counted in the paper is equal to the isoform(like transcripts in gtf files ). So I wonder what's the difference between isoforms and gene loci?
BTW, how can I count the gene loci when a reads mapping to multi-location (like hard clipping )?
Thanks for any advice!