Transcriptome studies have revealed that many non-coding RNAs (ncRNAs) are located near the 3' sense terminus of protein-coding genes. However, the transcription and function of these RNAs remain elusive. Here, we identify a 3' sense termini-associated sRNA (TASR) downstream of rpl26 in Schizosaccharomyces pombe (S. pombe). Structure and function assays indicate that the TASR is an H/ACA box snoRNA required for 18S rRNA pseudouridylation at U121 and U305 sites and is therefore a cognate of snR49 from the budding yeast. Transcriptional studies show that pre-snR49 overlaps most of the coding sequence (CDS) of rpl26. Using scanning deletion analysis within promoter region, we show that the rpl26 promoter is required for the 3' TASR transcription. Interestingly, chromosomal synteny of rpl26-snR49 is found in the Schizosaccharomyces groups. Taken together, we have revealed a new transcriptional mechanism for 3' sense TASRs, which are transcribed by the same promoter as their upstream protein genes. These results further suggest that the origin and function of 3' sense ncRNAs are associated with upstream genes in higher eukaryotes. 