Long noncoding RNAs (lncRNAs) are transcribed into low potential protein coding RNA molecules, which account for over 70% of mammalian transcriptional products. The role of lncRNAs and their expression is still largely unknown, and the subject of recent investigations. Here, we used bulk RNA sequencing data from the Genotype-Tissue Expression (GTEx) project to investigate the occurrence and specificity of lncRNAs in 13 brain regions (1000 samples). These highly specific lncRNA were co-expressed with previously known mRNA markers in different regions of the brain. Further investigation revealed that splicing could influence the divergent biogenesis and enrichment of lncRNA alleles in different regions. Overall, we demonstrate the use of lncRNA as a potential tool for deconvolving brain regions and further highlights its use for cell-type identification from bulk transcriptome data.