JustRNA is an expression profiling resource for plant lncRNAs. The platform currently contains 1 088 565 lncRNA annotations for 80 plant species (Table 1 and Fig. 1). In addition, it includes 3692 RNA-seq samples derived from 825 conditions in six model plants (Table 2). ChIP-seq data of transcription factors and histone modifications were integrated into the JustRNA platform to identify the transcriptional regulation of lncRNAs (Table 3).


Table 1. Numbers of lncRNAs contained in different databases.

Species JustRNA RNAcentral GreeNC CANTATAdb NONCODE PLncDB RiceNCexp
A. chinensis 13178 0 961 0 0 13178 0
A. trichopoda 6135 10 0 5511 0 8215 0
A. comosus 47662 0 0 10404 0 52201 0
A. coerulea 3333 0 4868 0 0 3333 0
A. lyrata 4703 0 2676 7593 0 8901 0
A. thaliana 7213 3958 2254 4373 4046 13599 0
A. ipaensis 3004 0 0 0 0 17088 0
B. distachyon 7271 4 0 4945 0 12821 0
B. napus 31843 1 9060 12010 8212 49250 0
B. rapa 10453 1 2674 8501 6457 17519 0
C. grandiflora 2746 0 0 0 0 2746 0
C. rubella 5926 0 1812 0 0 8012 0
C. annuum 27073 0 2124 0 0 35503 0
C. papaya 18038 0 0 0 0 20210 0
C. reinhardtii 2639 0 0 3425 783 2639 0
C. arietinum 4816 0 2004 0 0 8002 0
C. clementina 9766 11 0 0 0 10943 0
C. maxima 6959 0 0 0 0 6959 0
C. sinensis 8713 0 0 0 0 12405 0
C. subellipsoidae 809 0 0 0 0 809 0
C. arabica 10919 0 0 0 0 16424 0
C. sativus 5212 0 9659 7348 2550 8753 0
D. carota 10122 0 0 0 0 15096 0
D. salina 584 0 0 0 0 584 0
D. zibethinus 2932 0 0 0 0 4469 0
E. guineensis 83874 0 0 0 0 86852 0
E. guttata 4854 0 0 0 0 6891 0
E. grandis 9674 0 0 0 0 18062 0
E. salsugineum 3381 0 0 0 0 4366 0
F. vesca 8439 0 0 0 0 12237 0
G. lucidum 56 0 0 0 0 60 0
G. max 11591 47 5978 3096 2242 12577 0
G. barbadense 32191 2 8720 0 0 32192 0
G. raimondii 13161 9 4555 0 1247 21101 0
H. vulgare 25881 0 23867 7970 0 25884 0
J. curcas 4994 0 0 0 0 6793 0
L. sativa 13394 0 5395 0 0 13394 0
L. usitatissimum 10451 0 0 0 0 10451 0
L. japonicus 2936 1 0 0 0 2936 0
L. angustifolius 4597 2 1686 0 0 7407 0
M. domestica 26421 0 0 10924 0 33706 0
M. esculenta 16076 0 2655 9504 5601 18515 0
M. truncatula 6815 3877 9093 3590 2258 17449 0
M. commoda 758 0 0 0 0 758 0
M. pusilla 332 0 0 0 0 332 0
M. acuminata 15546 1 2214 3001 1809 15546 0
N. benthamiana 48045 0 0 0 0 48045 0
N. tabacum 31026 0 0 0 0 31028 0
O. europaea 18397 0 5516 0 0 23961 0
O. brachyantha 3873 0 4575 6004 0 5574 0
O. sativa 20820 2 5724 0 1190 11565 15914
O. lucimarinus 83 0 0 0 0 83 0
P. ginseng 23015 1 0 0 0 23016 0
P. hallii 1155 0 3643 0 0 4212 0
P. vulgaris 7801 1 0 0 0 7801 0
P. dactylifera 24484 0 0 0 0 27894 0
P. patens 16211 0 0 0 471 19319 0
P. sativum 45728 0 0 0 0 45728 0
P. tremula 4621 0 0 0 0 4622 0
P. trichocarpa 6879 4 1795 4322 0 10571 0
P. persica 10920 0 0 2902 0 13022 0
R. communis 4374 0 0 0 0 5322 0
S. miltiorrhiza 17817 7 0 0 0 17834 0
S. moellendorffii 3628 1 0 2267 0 5615 0
S. italica 9170 3 0 4208 0 12425 0
S. viridis 13482 0 5427 0 0 18106 0
S. lycopersicum 20365 564 4242 4716 3822 8741 0
S. melongena 332 0 0 0 0 332 0
S. pimpinellifolium 419 0 0 0 0 419 0
S. tuberosum 16483 2 8005 5790 3069 16485 0
S. bicolor 21725 3 5107 2600 0 27623 0
S. polyrhiza 3364 0 0 0 0 3364 0
T. cacao 8940 0 0 5256 3532 11340 0
T. pratense 17733 0 5402 10179 5278 17733 0
T. aestivum 43645 43 6710 0 12427 43659 0
V. radiata 20556 0 1268 0 0 20557 0
V. vinifera 13279 10 2978 4542 3351 16209 0
V. carteri 6207 0 0 0 0 6207 0
Z. mays 48123 3477 13430 10761 4717 32397 0
Z. marina 8394 0 0 0 0 8394 0




Figure 1. Numbers of overlap lncRNAs between different databases.


Table 2. Numbers of RNA-seq samples contained in different databases.

Species JustRNA CANTATAdb 2.0 NONCODE V6 PLncDB V2.0 RiceNCexp
A. thaliana 2920 10 37 376 0
G. max 6 8 0 160 0
M. truncatula 18 10 0 564 0
O. sativa 468 10 30 98 491
S. lycopersicum 93 9 28 43 0
Z. mays 187 8 31 166 0
Total 3692 55 126 1407 491

Table 3. Numbers of ChIP-seq samples contained in different databases.

Species JustRNA CANTATAdb 2.0 NONCODE V6 PLncDB V2.0 RiceNCexp
A. thaliana 2920 0 0 0 0
G. max 6 0 0 21 0
M. truncatula 18 0 0 0 0
O. sativa 468 0 0 318 0
S. lycopersicum 93 0 0 43 0
Z. mays 187 0 0 2 0
Total 3692 0 0 384 0