Table 1.

Structured Allen Mouse Brain Atlas riboprobes

	Only	Only	Overlap	Overlap
	Intergenic	Intronic	5’ UTR	3’ UTR	Total
Expressed structured ncRNAs	141	10			151
Expressed structured UTRs			817	4,502	5,126
Expressed Atlas probes	462	15	2,492	8,108	16,483

Structured Allen Mouse Brain Atlas riboprobes have RNA secondary structures predicted by , are expressed above background in the adult mouse brain and are mapped to the mouse genome (mm8). We subdivided structured probes into two genomic locations: (1) structured (long) noncoding RNAs (ncRNAs) have no protein coding potential and the entire probe is intergenic or intronic, and (2) structured UTRs are probes overlapping a UTR exon annotated in UCSC or RefSeq gene tracks with an RNA structure prediction. Total numbers of expressed Allen Mouse Brain Atlas probes (structured and non-structured) are listed. Detailed information about probes and structures are contained in Additional file 1.