Database Commons
Database Commons

a catalog of worldwide biological databases

Database Profile

General information

URL: http://www.nipgr.ac.in/AlnC
Full name: Angiosperms long non-coding RNAs catalogue
Description: AlnC is an extensive database of long non-coding RNAs (lncRNAs) in Angiosperms. Here, we have incorporated a total of 10,855,598 lncRNAs, annotated in 809 RNA-seq samples of 682 flowering plants by using machine learning approach previously described by Singh et al., 2017. All transcriptome data available at 1KP project initiative was processed and used to annotate the lncRNAs.
Year founded: 2021
Last update:
Version: 1.0
Accessibility:
Manual:
Accessible
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Country/Region: India

Classification and Labelling

Data type:
RNA
Data object:
Database category:
Major species:
NA
Keywords:

Contact information

University/Institution: National Institute of Plant Genome Research
Address:
City:
Province/State:
Country/Region: India
Contact name (PI/Team): Ajeet Singh
Contact email (PI/Helpdesk): singh.ajeet@nipgr.ac.in

Publications

33852582
AlnC: An extensive database of long non-coding RNAs in angiosperms. [PMID: 33852582]
Ajeet Singh, A T Vivek, Shailesh Kumar

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.

PLoS One. 2021:16(4) | 1 Citations (from Europe PMC, 2022-07-02)

Ranking

All databases:
3995/5381 (25.776%)
Raw bio-data:
347/505 (31.485%)
Metadata:
391/547 (28.702%)
Expression:
779/1006 (22.664%)
3995
Total Rank
1
Citations
1
z-index

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Record metadata

Created on: 2022-04-20
Curated by:
Lin Liu [2022-06-23]
Jing Wei [2022-05-12]
Yuxin Qin [2022-04-20]