Table 2.

Novel non-coding RNA (ncRNA) candidates (150 in total) based on transcriptome sequencing and ribosomal profiling. ncRNAs are identified by their start position on the genome given in the name (abbreviated as ncR#)

Name	Length	Max. ORF (nt)	Strand	Number of transcriptome reads	Number of footprint reads	RPKM transcriptome	RPKM footprints	RCV	Northern Blot	CopraRNA	CopraRNA term
ncR1085800	72	-	+	11274	532	8857	898	0.1	positive
ncR1481381	99	9	+	11208	516	6404	634	0.1	positive
ncR3690952	145	54	-	4898	26	1911	22	0.01	negative	1.18	ecc00620:Pyruvate metabolism
ncR1636218	78	27	-	1034	22	750	34	0.05	negative	1.31a	GO:0042364~water-soluble vitamin biosynthetic process
ncR3545929	41	-	+	542	2	748	6	0.01
ncR3665651	109	45	-	1442	2	748	2	0	negative	1.24	GO:0045426~quinone cofactor biosynthetic process
ncR3860554	73	24	-	637	3	494	5	0.01		0.98	2Fe-2S
ncR1088953	37	-	+	295	4	451	13	0.03
ncR3066135	48	-	+	354	0	417	0	0
ncR1484560	42	-	+	294	0	396	0	0
ncR5355946	47	21	-	246	4	296	10	0.04
ncR16920	36	-	-	164	4	258	14	0.05
ncR165975	49	9	+	216	4	249	10	0.04	negative
ncR5223290	66	-	+	265	3	227	6	0.02
ncR1641710	114	105	-	430	28	213	30	0.14
ncR1765944	114	54	+	406	33	201	35	0.18		5.48a	membrane
ncR2358348	45	-	-	151	1	190	3	0.01
ncR1888606	46	18	-	147	4	181	11	0.06
ncR2530362	64	6	-	196	0	173	0	0
ncR5133665	29	-	-	86	0	168	0	0
ncR2638864	38	-	-	100	2	149	6	0.04
ncR326492	42	-	+	110	9	148	26	0.18
ncR622277	95	63	+	248	1	148	1	0.01	negative
ncR2549762	59	45	-	150	2	144	4	0.03
ncR2287	90	45	-	218	8	137	11	0.08
ncR1019437	57	-	-	130	2	129	4	0.03
ncR1694864	51	18	+	116	1	129	2	0.02
ncR1864748	174	105	-	370	32	120	22	0.19		4.00a	cell membrane
ncR3526958	96	45	-	193	9	114	11	0.1		2.92a	ecd00190:Oxidative phosphorylation
ncR867065	45	21	-	76	1	96	3	0.03
ncR1079732	27	-	-	41	2	86	9	0.11
ncR3020266	116	57	+	168	9	82	9	0.12
ncR1328373	40	21	-	55	1	78	3	0.04
ncR3094200	36	9	+	47	3	74	10	0.14
ncR774709	58	39	+	74	1	72	2	0.03
ncR3725111	44	-	-	52	1	67	3	0.04
ncR451977	43	21	-	50	3	66	8	0.13
ncR4881271	105	75	+	123	7	66	8	0.12		1.70a	GO:0022900~electron transport chain
ncR4922734	44	27	+	49	2	63	6	0.09
ncR1748457	38	9	-	40	0	60	0	0
ncR4393950	74	-	-	78	5	60	8	0.14
ncR5324582	92	24	+	94	4	58	5	0.09
ncR1847082	38	-	+	38	1	57	3	0.06
ncR2820623	107	66	-	105	9	56	10	0.18		1.89a	lipoprotein
ncR1114186	94	60	-	91	3	55	4	0.07
ncR3583650	35	-	-	34	1	55	3	0.06
ncR1509794	96	60	-	91	5	54	6	0.12
ncR4391372	28	-	-	26	2	53	9	0.17
ncR4546182	36	12	-	34	2	53	7	0.13
ncR612919	36	-	+	32	0	50	0	0
ncR426804	47	-	+	41	3	49	8	0.16
ncR3164662	66	9	+	56	3	48	6	0.12
ncR2585184	44	-	+	36	1	46	3	0.06
ncR2930972	38	6	-	30	2	45	6	0.14
ncR3527530	119	51	-	95	4	45	4	0.09		1.97a	GO:0046395~carboxylic acid catabolic process
ncR4520884	50	24	+	40	3	45	7	0.16
ncR2498369	53	33	-	41	1	44	2	0.05
ncR4161484	42	39	+	33	1	44	3	0.07
ncR2699447	35	18	+	26	1	42	3	0.08
ncR5210782	28	18	+	21	0	42	0	0
ncR205409	74	45	-	53	0	41	0	0		1.02	IPR014021:Helicase, superfamily 1 and 2, ATP-binding
ncR1868696	103	30	-	72	6	40	7	0.18
ncR3915561	37	-	-	26	2	40	7	0.17
ncR1462015	40	21	-	27	0	38	0	0
ncR1475353	73	-	-	48	4	37	7	0.18
ncR397399	68	-	-	44	0	37	0	0
ncR4645569	57	15	-	36	0	36	0	0
ncR1239030	54	-	+	33	1	35	2	0.07
ncR1645154	42	-	-	26	1	35	3	0.08
ncR3553461	57	33	+	35	1	35	2	0.06
ncR4853400	65	15	+	40	3	35	6	0.16
ncR1143400	43	18	+	25	2	33	6	0.17
ncR2693045	49	6	-	29	2	33	5	0.15
ncR3735643	69	45	+	40	2	33	4	0.11
ncR3991822	44	9	-	26	0	33	0	0
ncR4714439	67	6	-	39	2	33	4	0.11
ncR1960332	35	-	+	20	1	32	3	0.11		1.96a	GO:0034660~ncRNA metabolic process
ncR2885483	44	-	-	25	1	32	3	0.09
ncR4463425	63	12	-	36	1	32	2	0.06
ncR501481	70	21	+	39	0	32	0	0
ncR963596	50	9	-	28	1	32	2	0.08
ncR1152534	90	51	+	50	4	31	5	0.17		0.84	ecq00052:Galactose metabolism
ncR2602372	62	12	-	34	2	31	4	0.13
ncR2062548	38	-	+	20	0	30	0	0
ncR4770438	40	12	+	21	1	30	3	0.1
ncR865067	103	51	-	54	1	30	1	0.04
ncR11537	73	48	+	37	2	29	3	0.12
ncR3040352	77	18	-	40	3	29	5	0.16
ncR4249267	64	9	+	33	2	29	4	0.13
ncR1592436	48	9	-	24	1	28	3	0.09
ncR3583545	40	-	-	20	1	28	3	0.11
ncR725615	61	-	+	30	2	28	4	0.14
ncR1066434	66	21	-	32	1	27	2	0.07
ncR4163613	125	45	+	59	5	27	5	0.18		1.29	antibiotic resistance
ncR15950	44	18	+	20	0	26	0	0
ncR2452385	45	18	-	21	0	26	0	0
ncR2841773	79	18	+	37	0	26	0	0
ncR3320428	75	51	+	34	1	26	2	0.06
ncR2903620	140	33	-	61	3	25	3	0.11
ncR3042903	164	57	-	69	3	24	2	0.09
ncR543583	67	51	+	29	0	24	0	0
ncR1585703	88	48	+	36	2	23	3	0.12
ncR1999946	51	15	+	21	0	23	0	0
ncR5077759	50	6	-	20	1	23	2	0.11
ncR1640190	56	-	-	22	2	22	4	0.2
ncR1752346	64	-	+	25	0	22	0	0
ncR3074598	54	36	-	21	0	22	0	0
ncR3320341	85	18	+	33	0	22	0	0
ncR3330508	57	-	-	22	0	22	0	0
ncR4096595	60	-	-	23	2	22	4	0.19
ncR4137844	268	195	-	102	7	22	3	0.15
ncR4414172	53	-	-	21	0	22	0	0
ncR492696	51	-	-	20	0	22	0	0
ncR1215540	74	21	+	28	2	21	3	0.15
ncR2254917	76	-	+	28	2	21	3	0.15
ncR2902855	104	-	-	39	3	21	4	0.17
ncR752395	172	66	+	64	2	21	1	0.07
ncR283226	71	27	+	25	0	20	0	0
ncR1049002	77	48	-	26	1	19	2	0.08		1.84a	GO:0050890~cognition
ncR1216838	100	12	-	33	1	19	1	0.07
ncR4829752	78	-	-	26	1	19	2	0.08
ncR1483108	77	63	+	23	1	17	2	0.09
ncR155024	78	18	+	23	0	17	0	0
ncR4156147	78	-	-	23	1	17	2	0.09		1.75a	GO:0032196~transposition
ncR4788281	97	78	-	30	0	17	0	0		0.99	topological domain:Periplasmic
ncR1854285	91	48	-	25	1	16	1	0.09
ncR1942672	85	-	+	24	1	16	1	0.09		2.09a	GO:0015031~protein transport
ncR2614043	86	57	-	25	0	16	0	0
ncR4741832	75	30	-	21	0	16	0	0
ncR484751	94	51	-	27	2	16	3	0.16
ncR5283975	98	84	-	28	0	16	0	0		2.14a	GO:0009386~translational attenuation
ncR1314229	101	48	+	26	2	15	2	0.17
ncR1893573	187	87	-	48	4	15	3	0.18
ncR3609575	74	-	+	20	0	15	0	0		1.72a	eum00660:C5-Branched dibasic acid metabolism
ncR3724967	105	42	-	28	0	15	0	0
ncR4245110	118	48	+	30	1	14	1	0.07
ncR866957	79	42	-	20	0	14	0	0
ncR336953	96	27	+	22	2	13	3	0.2
ncR3997954	104	81	+	23	2	13	2	0.19
ncR411208	99	6	-	22	2	13	2	0.2		2.64a	GO:0015980~energy derivation by oxidation of organic compounds
ncR1736783	100	57	-	22	1	12	1	0.1
ncR745748	107	54	+	23	1	12	1	0.09
ncR3609372	201	-	+	38	1	11	1	0.06			Rfam match: tRNA RF00005b
ncR3890479	104	51	-	20	1	11	1	0.11
ncR1087411	224	135	+	41	2	10	1	0.11
ncR3874837	127	48	-	22	2	10	2	0.2
ncR4187491	122	9	-	22	0	10	0	0
ncR769665	198	102	+	34	2	10	1	0.13
ncR5157894	218	114	+	33	3	9	2	0.2
ncR196880	135	81	-	20	1	8	1	0.11		1.23	ecc00330:Arginine and proline metabolism

^aDAVID enrich. score; signif. ≥ 1.3. ^btRNA

The longest potential ORF is indicated for each ncRNA. RPKM values of transcriptome and translatome are shown, as well as the ribosome coverage value (RCV). A transcript is considered non-coding if it has at least 20 reads in the transcriptome data and the RCV is below 0.197 (α = 0.01). Transcripts examined via Northern blots are indicated and CopraRNA functional enrichments are shown