AlnC: An extensive database of long non-coding RNAs in angiosperms.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2021
2021
Historique:
received:
02
02
2021
accepted:
27
03
2021
entrez:
14
4
2021
pubmed:
15
4
2021
medline:
18
9
2021
Statut:
epublish
Résumé
Long non-coding RNAs (lncRNAs) are defined as transcripts of greater than 200 nucleotides that play a crucial role in various cellular processes such as the development, differentiation and gene regulation across all eukaryotes, including plant cells. Since the last decade, there has been a significant rise in our understanding of lncRNA molecular functions in plants, resulting in an exponential increase in lncRNA transcripts, while these went unannounced from the major Angiosperm plant species despite the availability of large-scale high throughput sequencing data in public repositories. We, therefore, developed a user-friendly, open-access web interface, AlnC (Angiosperm lncRNA Catalogue) for the exploration of lncRNAs in diverse Angiosperm plant species using recent 1000 plant (1KP) trancriptomes data. The current version of AlnC offers 10,855,598 annotated lncRNA transcripts across 682 Angiosperm plant species encompassing 809 tissues. To improve the user interface, we added features for browsing, searching, and downloading lncRNA data, interactive graphs, and an online BLAST service. Additionally, each lncRNA record is annotated with possible small open reading frames (sORFs) to facilitate the study of peptides encoded within lncRNAs. With this user-friendly interface, we anticipate that AlnC will provide a rich source of lncRNAs for small-and large-scale studies in a variety of flowering plants, as well as aid in the improvement of key characteristics in relevance to their economic importance. Database URL: http://www.nipgr.ac.in/AlnC.
Identifiants
pubmed: 33852582
doi: 10.1371/journal.pone.0247215
pii: PONE-D-21-03595
pmc: PMC8046212
doi:
Substances chimiques
RNA, Long Noncoding
0
RNA, Plant
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0247215Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Front Plant Sci. 2020 Mar 12;11:276
pubmed: 32226437
BMC Bioinformatics. 2014 Sep 19;15:311
pubmed: 25239089
Trends Genet. 2018 Sep;34(9):704-721
pubmed: 30017313
Planta. 2020 Oct 24;252(5):92
pubmed: 33099688
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515
pubmed: 30395287
Sci Rep. 2020 Feb 10;10(1):2194
pubmed: 32042035
Science. 2016 Jan 15;351(6270):271-5
pubmed: 26816378
Methods Mol Biol. 2019;1933:415-429
pubmed: 30945201
PLoS One. 2014 Jun 03;9(6):e98958
pubmed: 24892290
Gene. 2002 Jan 9;282(1-2):33-41
pubmed: 11814675
Cell. 2018 Jan 25;172(3):393-407
pubmed: 29373828
Cell. 2014 Mar 27;157(1):77-94
pubmed: 24679528
Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68
pubmed: 25355905
Nucleic Acids Res. 2016 Jan 4;44(D1):D1161-6
pubmed: 26578586
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Gene. 2015 Dec 1;573(2):328-32
pubmed: 26211629
Genome Biol. 2014 Dec 03;15(12):512
pubmed: 25517485
Nat Struct Mol Biol. 2015 Jan;22(1):5-7
pubmed: 25565026
Nucleic Acids Res. 2015 Jan;43(Database issue):D168-73
pubmed: 25332394
Algorithms Mol Biol. 2011 Nov 24;6:26
pubmed: 22115189
Plant Cell. 2012 Nov;24(11):4333-45
pubmed: 23136377
Curr Opin Plant Biol. 2015 Oct;27:207-16
pubmed: 26342908
Gigascience. 2019 Oct 1;8(10):
pubmed: 31644802
Sci Rep. 2019 Oct 16;9(1):14876
pubmed: 31619732
Nucleic Acids Res. 2016 Jan 4;44(D1):D203-8
pubmed: 26586799
Brief Bioinform. 2017 Jan;18(1):9-27
pubmed: 26839320
Brief Bioinform. 2020 Dec 18;:
pubmed: 33333550
Nucleic Acids Res. 2021 Jan 8;49(D1):D1489-D1495
pubmed: 33079992
Nucleic Acids Res. 2017 Dec 15;45(22):e183
pubmed: 29036354
Annu Rev Cell Dev Biol. 2019 Oct 6;35:407-431
pubmed: 31403819