Long noncoding RNAs (ncRNAs) are expressed in specific regions and cell types of the adult mouse brain, indicating functional roles rather than being mere transcriptional noise. Using data from the Allen Brain Atlas, researchers identified 849 ncRNAs out of 1,328 examined, showing diverse expression patterns. These ncRNAs are associated with specific neuroanatomical regions, cell types, and subcellular compartments. Their genomic context reveals they are expressed from intergenic, intronic, and imprinted loci, often overlapping or being transcribed antisense to protein-coding genes. Comparisons between ncRNA and protein-coding gene expression profiles show complex relationships, suggesting functional roles. The majority of ncRNAs are expressed in the brain and function intrinsically as RNAs. The study highlights the importance of ncRNAs in brain biology, providing evidence that many of these transcripts are functionally significant. The results suggest that ncRNAs may play a role in regulating gene expression and are involved in various neurological processes. The study also identifies several ncRNAs associated with imprinted genes, which may contribute to the regulation of gene expression in the brain. Additionally, the study reveals that ncRNAs are expressed in specific subcellular locations, indicating regulated expression rather than being artifacts of chromatin remodeling. The findings support the idea that ncRNAs are biologically significant and may contribute to the complexity of the brain. The study provides a comprehensive analysis of ncRNA expression in the mouse brain, highlighting their potential roles in neurological functions and development. The results suggest that ncRNAs are an important component of the transcriptome and may have broader implications for understanding biological processes in mammals. The study also emphasizes the need to consider ncRNAs in genome-scale experiments, as they may play a significant role in various biological functions. The research provides a searchable database for further investigation of ncRNAs in the brain.Long noncoding RNAs (ncRNAs) are expressed in specific regions and cell types of the adult mouse brain, indicating functional roles rather than being mere transcriptional noise. Using data from the Allen Brain Atlas, researchers identified 849 ncRNAs out of 1,328 examined, showing diverse expression patterns. These ncRNAs are associated with specific neuroanatomical regions, cell types, and subcellular compartments. Their genomic context reveals they are expressed from intergenic, intronic, and imprinted loci, often overlapping or being transcribed antisense to protein-coding genes. Comparisons between ncRNA and protein-coding gene expression profiles show complex relationships, suggesting functional roles. The majority of ncRNAs are expressed in the brain and function intrinsically as RNAs. The study highlights the importance of ncRNAs in brain biology, providing evidence that many of these transcripts are functionally significant. The results suggest that ncRNAs may play a role in regulating gene expression and are involved in various neurological processes. The study also identifies several ncRNAs associated with imprinted genes, which may contribute to the regulation of gene expression in the brain. Additionally, the study reveals that ncRNAs are expressed in specific subcellular locations, indicating regulated expression rather than being artifacts of chromatin remodeling. The findings support the idea that ncRNAs are biologically significant and may contribute to the complexity of the brain. The study provides a comprehensive analysis of ncRNA expression in the mouse brain, highlighting their potential roles in neurological functions and development. The results suggest that ncRNAs are an important component of the transcriptome and may have broader implications for understanding biological processes in mammals. The study also emphasizes the need to consider ncRNAs in genome-scale experiments, as they may play a significant role in various biological functions. The research provides a searchable database for further investigation of ncRNAs in the brain.