NONCODE
NONCODE is a comprehensive database dedicated to the annotation of long non-coding RNAs (lncRNAs) in both animals and plants. NONCODE v6.0 contains 644,510 lncRNA transcripts from 39 species, including 16 animals and 23 plants.
Human and Mouse lncRNAs
- Human: 173,112 lncRNA transcripts representing 96,411 genes
- Mouse: 131,974 lncRNA transcripts representing 87,890 genes
- Includes expression profiles and predicted functions
- Features 13,749 records of lncRNA-cancer associations from experimentally supported data
Plant lncRNAs
- 23 plant species with 94,697 lncRNAs from 68,808 genes
- Species include: Arabidopsis thaliana, Cucumis sativus, Brassica napus, Brassica rapa, Chenopodium quinoa, Chlamydomonas reinhardtii, Glycine max, Gossypium raimondii, Malus domestica, Manihot esculenta, Medicago truncatula, Musa acuminata, Oryza rufipogon, Oryza sativa, Physcomitrella patens, Populus trichocarpa, Solanum lycopersicum, Solanum tuberosum, Triticum aestivum, Theobroma cacao, Trifolium pratense, Vitis vinifera, Zea mays
Database Features
Tissue Expression Profiles
NONCODE provides tissue-specific expression data for five model plants:
- Arabidopsis thaliana (10 tissues)
- Zea mays (9 tissues)
- Solanum lycopersicum (6 tissues)
- Cucumis sativus (8 tissues)
- Oryza sativa (11 tissues)
Expression levels quantified as transcripts per kilobase million (TPM) using STAR alignment and StringTie quantification.
Functional Annotation
For five plant species, co-expression analysis with coding genes enables functional prediction:
- Pearson correlation coefficients (Pcc) calculated using WGCNA
- Gene pairs with P-value < 0.05 and Pcc > 0.999 or < -0.999 considered co-expressed
- GO term annotation performed using PANTHER classification system
Conservation Analysis
- Transcript-level conservation assessment across 23 plant species
- BLASTn-based pairwise comparisons with E-value threshold of 1e-10
- 122 orthologous lncRNAs identified meeting ≥50% query coverage and E-value ≤1e-10
- Notable conservation in closely related pairs: Brassica napus/Brassica rapa, O. rufipogon/O. sativa, S. lycopersicum/S. tuberosum
Disease Associations
- Focus on lncRNA-cancer relationships in human
- Integration from six databases: LncSpA, LncTarD, Lnc2Cancer, LncRNADisease, LncRNAWiki, MNDR
- Only experimentally supported relationships included (computational predictions excluded)
- Top cancers by number of associated lncRNAs documented
Data Processing Pipeline
- Format normalization: All data converted to bed or gtf formats based on single assembly versions
- Multi-source combination: Normalized data combined using Cuffcompare from Cufflinks suite
- Protein-coding filtration:
- Comparison with RefSeq and Ensembl coding RNAs
- CNIT (Coding-NonCoding Identifying Tool) validation with 99.3% accuracy on plant transcripts
- General information: Location, exons, length, assembly sequence, and source documented
- Conservation analysis: BLAST-based cross-species transcript comparisons
- Web presentation: Comprehensive web interface with visualization tools
Nomenclature System
NONCODE follows a systematic naming convention:
- Transcripts: NON + three species characters + T + six sequential numbers (e.g., NONATHT000001.1)
- Genes: NON + three species characters + G + six sequential numbers
Data Sources
Integration from multiple sources:
- Previous NONCODE versions
- Public literature (57,872 plant articles, 51,771 new human/mouse articles since 2017)
- External lncRNA databases: Ensembl, RefSeq, lncRNAdb, LNCipedia, CANTATAdb, GREENC
Key Statistics
- Total transcripts: 644,510 lncRNAs
- Species coverage: 16 animals, 23 plants
- Plant lncRNAs: Average length 462-1,033 bp; average 1.3-2.3 exons per lncRNA
-
Database growth: Increased from 548,640 lncRNAs (v5, 2017) to 644,510 lncRNAs (v6, 2021)
- category: GraphicalInterface
description: Web portal for searching and browsing ncRNA sequences, structures,
and annotations
format: http
id: rnacentral.portal
name: RNAcentral Portal
original_source:
- 5srrnadb
- crd
- dictybase
- ena
- ensembl
- evlncrnas
- expressionatlas
- flybase
- genecards
- greengenes
- gtrnadb
- hgnc
- intact
- lncbase
- lncbook
- lncipedia
- lncrnadb
- malacards
- mgnify
- mirbase
- mirgenedb
- modomics
- noncode
- pdbe
- pirbase
- plncdb
- pombase
- rdp
- rediportal
- rfam
- rgd
- ribocentre
- ribovision
- sgd
- silva
- snodb
- snopy
- snornadatabase
- srpdb
- tair
- tarbase
- tmrnawebsite
- zfin
- zwd
- rnacentral
product_url: https://rnacentral.org/
- category: ProgrammingInterface
description: REST API for programmatic access to RNAcentral data
format: http
id: rnacentral.api
name: RNAcentral REST API
original_source:
- 5srrnadb
- crd
- dictybase
- ena
- ensembl
- evlncrnas
- expressionatlas
- flybase
- genecards
- greengenes
- gtrnadb
- hgnc
- intact
- lncbase
- lncbook
- lncipedia
- lncrnadb
- malacards
- mgnify
- mirbase
- mirgenedb
- modomics
- noncode
- pdbe
- pirbase
- plncdb
- pombase
- rdp
- rediportal
- rfam
- rgd
- ribocentre
- ribovision
- sgd
- silva
- snodb
- snopy
- snornadatabase
- srpdb
- tair
- tarbase
- tmrnawebsite
- zfin
- zwd
- rnacentral
product_url: https://rnacentral.org/api
- category: Product
description: FTP archive with current and archived release files (sequences and
annotations)
format: http
id: rnacentral.ftp
name: RNAcentral FTP Archive
original_source:
- 5srrnadb
- crd
- dictybase
- ena
- ensembl
- evlncrnas
- expressionatlas
- flybase
- genecards
- greengenes
- gtrnadb
- hgnc
- intact
- lncbase
- lncbook
- lncipedia
- lncrnadb
- malacards
- mgnify
- mirbase
- mirgenedb
- modomics
- noncode
- pdbe
- pirbase
- plncdb
- pombase
- rdp
- rediportal
- rfam
- rgd
- ribocentre
- ribovision
- sgd
- silva
- snodb
- snopy
- snornadatabase
- srpdb
- tair
- tarbase
- tmrnawebsite
- zfin
- zwd
- rnacentral
product_url: https://ftp.ebi.ac.uk/pub/databases/RNAcentral
- category: DataModelProduct
description: Public PostgreSQL database for direct SQL access to RNAcentral data
format: postgres
id: rnacentral.public-db
name: RNAcentral Public Postgres Database
original_source:
- 5srrnadb
- crd
- dictybase
- ena
- ensembl
- evlncrnas
- expressionatlas
- flybase
- genecards
- greengenes
- gtrnadb
- hgnc
- intact
- lncbase
- lncbook
- lncipedia
- lncrnadb
- malacards
- mgnify
- mirbase
- mirgenedb
- modomics
- noncode
- pdbe
- pirbase
- plncdb
- pombase
- rdp
- rediportal
- rfam
- rgd
- ribocentre
- ribovision
- sgd
- silva
- snodb
- snopy
- snornadatabase
- srpdb
- tair
- tarbase
- tmrnawebsite
- zfin
- zwd
- rnacentral
product_url: https://rnacentral.org/help/public-database
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Noncode
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