noncode

is a Data Source.

A comprehensive database dedicated to long non-coding RNA (lncRNA) annotation in animals and plants, providing systematic nomenclature, sequence information, genome location, expression profiles, functional predictions, and conservation analysis across 39 species (16 animals and 23 plants)

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FAIRsharing ID

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Product Summary

Contacts

Institute of Biophysics, Chinese Academy of Sciences

Email: heshunmin@ibp.ac.cn

Publications

NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants Preferred

Products

From this Resource

ID	Name	URL	Category	Format	Description
noncode.portal	NONCODE Web Portal	www.noncode.org	GraphicalInterface	http	Main web interface for searching, bro...
noncode.browse	Browse NONCODE	browse.php	GraphicalInterface	http	Browse lncRNAs by species and RNA type
noncode.search	Search Gene/Transcript	search.php	GraphicalInterface	http	Search for specific genes or transcri...
noncode.blast	BLAST Similarity Search	blast.php	GraphicalInterface	http	Find similar sequences using BLAST al...
noncode.disease	Disease Information	keyword_dis.php	GraphicalInterface	http	Browse disease-related lncRNA informa...
noncode.genome-browser	Genome Browser	hgTracks?db=hg38	GraphicalInterface	http	View transcript locations in genomic ...
noncode.download	Download Data	download.php	Product	http	Download complete lncRNA annotations ...
noncode.function	Function Prediction	keyword_func.php	GraphicalInterface	http	Predicted functions for plant lncRNAs...
noncode.conservation	Conservation Analysis	keyword_cons.php	GraphicalInterface	http	Cross-species conservation analysis f...
noncode.id-conversion	ID Conversion Tool	id_conversion.php	GraphicalInterface	http	Convert between NONCODE IDs and other...

From other Resources

ID	Name	URL	Category	Format	Relation	Description
rnacentral.portal	RNAcentral Portal	rnacentral.org	GraphicalInterface	http	had primary source	Web portal for searching and browsing...
rnacentral.api	RNAcentral REST API	api	ProgrammingInterface	http	had primary source	REST API for programmatic access to R...
rnacentral.ftp	RNAcentral FTP Archive	RNAcentral	Product	http	had primary source	FTP archive with current and archived...
rnacentral.public-db	RNAcentral Public Postgres Database	public-database	DataModelProduct	postgres	had primary source	Public PostgreSQL database for direct...
lncrnalyzr.graph	lncRNAlyzr Knowledge Graph	lncRNAlyzr	GraphProduct	neo4j	had primary source	Neo4j knowledge graph containing lncR...
genecards.web.interface	GeneCards Web Interface	www.genecards.org	GraphicalInterface	http	had primary source	Web-based interface for searching and...

Relevant Taxa

Green Plants (NCBITaxon:33090)

Details

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 —
  Noncode

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Created: September 09, 2025 | Last modified: July 02, 2026

noncode

Domains

License

Homepage

Repository

Infores ID

FAIRsharing ID

Product Summary

Contacts

Publications

Products

From this Resource

From other Resources

Relevant Taxa

Details

NONCODE

Human and Mouse lncRNAs

Plant lncRNAs

Database Features

Tissue Expression Profiles

Functional Annotation

Conservation Analysis

Disease Associations

Data Processing Pipeline

Nomenclature System

Data Sources

Key Statistics

Database growth: Increased from 548,640 lncRNAs (v5, 2017) to 644,510 lncRNAs (v6, 2021)

Noncode

Is this information incorrect or incomplete? Request an update.