An example of an overwhelmingly up-regulated cis- NAT under abiotic stresses. (A) Expressions of a cis- NAT pair of an annotated gene Os09t0482800-02 and a novel ncRNA CUFF.14823.1 are dramatically up-regulated under cold-stress conditions. Expression levels of this cis- NAT pair under normal, cold, salt and drought conditions are relatively low and displayed. (B) The unique small RNAs that are generated mainly from the plus strand (short blue lines) of the cis- NAT pair of the gene Os09t0482800-02 and the ncRNA CUFF.14823.1 are shown. (C) Expressions of this cis-NAT pair were detected through semi-quantitative RT-PCR analysis. Rice actin expression was used as a control. The PCR products of the cis- NAT were amplified by 36 cycles, while actin products were amplified by 26 cycles. Real-time RT-PCR analysis of the cis- NATs was used to confirm the differential expressed genes under normal and cold conditions. Expression data from ssRNA-seq (FPKM, Fragments Per Kilobase of exon Models) are represented as gray blocks; and the data from real-time RT-PCR are indicated as orange lines.