Table 1  Noncoding RNAs predicted by RNA-Seq data
RNA Blot Estimated Band Sizes (kb)
ncRNA designationAntisense GeneaStartbStopbStrandcRT-PCRWTpnp1-1
1trnH18125++1.6, 1.81.6, 1.8, 3.7
2matK29463086++
3rps1648145371++1.30.8, 1.2,1.3
4rps16i-154265581++0.8, 1.1,1.30.8, 0.9, 1.1,1.3
5rps16i-256325875+NTNTNT
6trnQ65216646++1.0, 1.21.1, 1.2
7psbK68827462+1.2, 3.3, 3.41.3, 3.4, 3.5
8psbI76117691NTNT
9trnS.178177984++1.8, 3.0, 3.21.9, 3.1, 3.3
10trnG-5′86449004+1.1, 1.81.1, 1.8, 3.7
11trnG-3′92449484+0.5, 0.6, 1.0, 3.3, 3.7
12trnR.195559858+0.2, 0.3
13atpA1034210536NTNTNT
14atpI1408814182++0.6, 1.00.2, 0.4, 0.6, 1.0, 1.2
15rpoC2-11698417163+NTNTNT
16rpoC2-21723317410+NTNTNT
17trnC2744627666+0.6, 1.1, 1.70.5, 0.6, 1.1, 1.7
18trnC-ycf6int2780727956+
19trnD2962729825+NTNTNT
20trnD-trnYint2993930070+NTNTNT
21trnT.13140831518+0.3, 0.9
22psbD3310633456+
23trnS.23531235409++3.3, 3.43.1, 3.4, 3.7
24ycf93582036116+0.3, 0.9, 2.00.4, 0.8, 1.0, 2.3
25trnfM3664236862++0.1, 0.3, 0.40.8-1.0 smear
26rps14-psaBint3725037327+NTNT
27ycf3-3′4254242629++
28trnS.34482745050+1.11.2, 1.4, 1.5, 3.0
29rps4-3′4529445358++1.91.9
30rps4-5′4574745929+
31trnT.24602646338+
32trnL-3′4741747670NTNTNT
33ndhK4926049386++
34ndhC-5′5026950469++
35ndhC-trnV.1int5076250916++0.4, 0.7, 0.8, 1.3
36trnVi5168851884+NTNTNT
37trnM5195052128NTNTNT
38rbcL-accDint5658456822+0.5, 0.6, 1.00.4, 0.5, 3.0
39accD5794958056+0.7, 0.8, 1.0, 1.90.4, 0.7, 1.9
40accD-psaIint-15877658869+1.1, 1.80.4, 0.6, 0.7, 1.1, 1.9
41accD-psaIint-25903059096NTNT
42ycf10-5′6075660963+
43ycf106098361159+1.3, 1.7, 1.81.1, 1.3, 1.7, 1.9
44ycf10-petAint6140961529+1.0, 1.6, 1.80.9, 1.0, 1.6, 1.8
45petA6204562271+0.5, 1.70.5, 1.2, 1.4, 1.8
46psbJ6347963648+NTNTNT
47psbL-psbF6380564018+NTNTNT
48orf316570865805+
49trnW6624866330++0.9, 1.3, 1.80.8, 0.9, 1.2, 1.3, 1.9, 2.9
50trnP6633066701++1.0, 1.11.0, 1.1, 1.9
51psaJ6692067113NTNTNT
52psaJ-rpl33int6715467304+0.3, 0.7, 1.3, 1.41.2, 1.3, 1.4, 3.0
53rpl336733467594+0.7, 1.3, 1.4, 2.7, 3.11.2, 1.3, 1.4, 3.0
54rps186778468222+1.0, 1.4, 1.9, 3.01.2, 1.8, 1.9, 2.8, 3.7
55rpl206851268680+NTNTNT
56psbB7367773837+1.70.9, 1.0, 1.7
57psbB-psbTint7392774077+0.60.6, 0.7, 0.9
58psbT7413674184NTNTNT
59psbN7424974380++2.0, 3.3, 3.52.0, 3.3, 3.6
60psbH7460174726+1.1, 1.91.9
61petBi7496775151+
62petD-3′7743177604+
63rpoA-3′7796778098++1.2, 1.3, 3.3
64rpoA7832078768+NTNTNT
65rpoA-5′7882778957++
66rps117916679359+NTNTNT
67rpl367950279858+NTNTNT
68rpl148072380895+NTNTNT
69rpl2i8527185419+NTNTNT
70trnI.18620386389++0.30.35, 0.4, 0.5
71ycf2.1-18664486764+0.70.75
72ycf2.1-28794888212+1.2, 1.3, 3.5
73ycf2.1-38845188564+
74ycf2.1-48896089328+
75ycf2.1-58944590769+1.0
76ycf2.1-69115891564+1.2, 1.7
77ycf2.1-79170392005+
78ycf2.1-89230992432+1.8, 3.71.1, 1.2, 1.8, 3.8
79ycf2.1-99297993113+1.20.6, 0.7, 1.25, 1.6, 1.7
80ycf2.1-109317893281+
81trnL-ndhBint9437794967++0.4, 1.7, 3.70.6, 1.6, 1.7, 3.7
82ndhB-3′9511195707++
83ndhBi9591096164+NTNTNT
84rps12-5′9871898822+NTNTNT
85rrn4.5-rrn5int107905107963+
86ycf1.1-1109354109553NTNTNT
87ycf1.1-2109923110387+0.8, 0.9, 1.3, 3.30.85, 1.3, 3.2, 3.3
88ndhF-3′110389110488+NTNT
89ndhF-5′-1112345112435++1.7, 1.8, 3.81.7, 1.8, 3.8
90ndhF-5′-2112475112665++1.65, 1.71.75, 1.8
91ycf5-1114738114982NTNTNT
92ycf5-2115138115220+
93ndhD-1115897116043++1.60.3, 1.3, 1.8
94ndhD-2116137116437++1.31.35
95ndhD-3116467116567++
96ndhD-4116627116785+NTNT
97ndhA-3′119774119911+NTNTNT
98ndhAi120852120948++0.3, 0.5
99ndhAi-2121194121344+NTNTNT
100ndhA-5′121398121822+NTNTNT
101ycf1.2-1124129124265+NTNTNT
102ycf1.2-2124605124768+NTNTNT
103ycf1.2-3125263125448+NTNTNT
104ycf1.2-4127146127277++2.00.8, 2.0, 3.7
105ycf1.2-5127626127788++
106ycf1.2-6127788128098+NTNT
107ycf1.2-7128220129004+NTNTNT
  • NT, not tested.

  • a Gene or genes encoded on complementary strand. 5′ or 3′ indicates which part of the coding region is complementary to the ncRNA. Some ncRNAs are between two coding regions (int) or opposite an intron (i).

  • b ncRNA termini as predicted by RNA-Seq from WT, except for the NT samples, which were defined from pnp1-1 RNA-Seq data based on the criteria given in the text.

  • c Strand is + or – for the ncRNA according to the GenBank accession for Arabidopsis cpDNA.