Strand-specific RNA-seq reveals widespread occurrence of novel cis- natural antisense transcripts in rice

Table 1 Statistics of 3819 cis- NATs identified in rice

Chr.	Transcripts	*cis*-NATs^a	Enclosed^b	3^′-3^′^c	5^′-5^′^d	CDS-p^e vs. ncRNA	CDS-p vs. CDS-n^f	CDS-p vs. CDS-p	CDS-n vs. ncRNA	CDS-n vs. CDS-n	ncRNA vs. ncRNA
1	10,536	558	301	146	11	205	176	92	39	30	16
2	8,527	440	239	115	86	159	141	63	36	30	11
3	9,197	491	296	120	75	175	156	90	29	22	19
4	6,762	361	185	95	81	100	132	55	27	27	20
5	5,940	290	161	71	58	107	108	34	21	11	9
6	6166	299	170	69	60	111	100	38	23	13	14
7	5,862	278	163	63	52	90	96	30	24	19	19
8	5,290	239	138	51	50	103	74	27	19	10	6
9	4,256	189	100	34	55	70	71	10	16	10	12
10	4,144	221	128	41	52	85	74	24	19	10	9
11	4,861	231	139	47	45	92	75	25	23	7	9
12	4,472	222	129	46	47	81	72	24	20	15	10
Total	76,013	3,819	2,149	898	772	1,378	1,275	512	296	204	154

^acis-NAT pairs without transposons.
^b One transcript being entirely reverse-complementarily overlapped by the other.
^c Convergent cis-NAT (with 3^′-ends overlapped).
^d Divergent cis-NAT (with 5^′-ends overlapped).
^e Coding sequence with PFAM domain-containing.
^f Predicted as coding sequence but without any PFAM domain hits.