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Long non-coding RNA databases | Non-coding RNA data analysis

Long non-coding RNAs (lncRNAs) form the largest class of non-protein coding genes in the human genome. While a small subset of well-characterized lncRNAs has demonstrated their significant role in diverse biological functions like chromatin…
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LNCediting
Dataset

LNCediting Long Non Coding editing

A database of comprehensive information about Adenosine-to-Inosine editing…

A database of comprehensive information about Adenosine-to-Inosine editing sites in long non-coding RNAs (lncRNAs) across human, rhesus, mouse, and fly, to explore their potential functions.…

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NONCODE
Dataset

NONCODE

An interactive database that aims to present the most complete collection and…

An interactive database that aims to present the most complete collection and annotation of non-coding RNAs, especially long non-coding RNAs (lncRNAs). In this update, NONCODE has added six new…

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lncRNAdb
Dataset

lncRNAdb long noncoding RNA database

A database providing comprehensive annotations of eukaryotic long non-coding…

A database providing comprehensive annotations of eukaryotic long non-coding RNAs (lncRNAs). In addition to capturing a great proportion of the recent literature describing functions for individual…

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fRNAdb
Dataset

fRNAdb Functional RNA Database

A database service that hosts a large collection of non-coding transcripts…

A database service that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences from the H-inv database, NONCODE and RNAdb. fRNAdb provides an efficient…

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NSDNA
Dataset

NSDNA Nervous System Disease NcRNAome Atlas

A manually curated database that provides comprehensive experimentally…

A manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDNA database documents 24713…

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DeCoN
Web

DeCoN Developing Cortical Neuron Transcriptome Resource

Enables multidimensional data mining, exploration, and dissemination that is…

Enables multidimensional data mining, exploration, and dissemination that is scalable and designed to integrate future data on additional neuronal classes and different species. DeCoN enables…

ChIPBase
Dataset

ChIPBase

Enables to explore the transcriptional regulatory networks of noncoding RNAs…

Enables to explore the transcriptional regulatory networks of noncoding RNAs (ncRNAs) and protein-coding genes (PCGs). ChIPBase is an open database that integrates many ChIPseq peak datasets of…

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ncRDeathDB
Dataset

ncRDeathDB

A comprehensive bioinformatics resource to archive non-coding RNA…

A comprehensive bioinformatics resource to archive non-coding RNA (ncRNA)-associated cell death interactions. ncRDeathDB documents a total of more than 4600 ncRNA-mediated programmed cell death (PCD)…

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LNCat
Dataset

LNCat

Stores the information of 24 currently available long noncoding RNAs (lncRNA)…

Stores the information of 24 currently available long noncoding RNAs (lncRNA) annotation resources. LNCat provides a genome browser of lncRNA structures, visualization of different resources from…

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NRED
Dataset

NRED Noncoding RNA Expression Database

Provides gene expression information for thousands of long ncRNAs in human and…

Provides gene expression information for thousands of long ncRNAs in human and mouse. The database contains both microarray and in situ hybridization data, much of which is described here for the…

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GREENC
Dataset

GREENC Green Non-Coding Database

A repository of lncRNAs annotated in 37 plant species and six algae. By using…

A repository of lncRNAs annotated in 37 plant species and six algae. By using the same pipeline to annotate lncRNAs we make it possible to compare lncRNA sequences and distribution from different…

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LNCipedia
Dataset

LNCipedia

A database for human long non-coding RNA (lncRNA) transcripts and genes. In…

A database for human long non-coding RNA (lncRNA) transcripts and genes. In addition to basic transcript information and structure, several statistics are calculated for each entry in the database,…

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PeTMbase
Dataset

PeTMbase

A living plant endogenous target mimicry dataset. PeTMbase enables a highly…

A living plant endogenous target mimicry dataset. PeTMbase enables a highly flexible user interface to retrieve endogenous Target Mimicry (eTM) sequences by choosing the plant species. It also…

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DsTRD
Dataset

DsTRD Danshen Transcriptional Resource Database

A comprehensive transcript resource for Salvia miltiorrhiza. DsTRD contains…

A comprehensive transcript resource for Salvia miltiorrhiza. DsTRD contains 76531 transcribed sequences assembled from the RNA-seq data. DsTRD provides information regarding the sequences and…

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LncRNAs2Pathway…
Desktop

LncRNAs2Pathways

Identifies pathways synergistically regulated by the interested long noncoding…

Identifies pathways synergistically regulated by the interested long noncoding RNA (lncRNA) sets based on an lncRNA-mRNA (messenger RNA) interaction network. LncRNAs2Pathways is a software which draw…

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BmncRNAdb
Dataset

BmncRNAdb Bombyx mori non-coding RNA database

A comprehensive and web-based database of the silkworm lncRNAs and miRNAs.…

A comprehensive and web-based database of the silkworm lncRNAs and miRNAs. BmncRNAdb offers a user-friendly interface for data browse and online analysis as well as the three online tools for users…

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PNRD
Dataset

PNRD Plant Non-coding RNA Database

It is the updated version of PMRD. PNRD mainly focuses on plant species. A…

It is the updated version of PMRD. PNRD mainly focuses on plant species. A total of 25739 entries of 11 different types of ncRNAs from 150 plant species were collected. Targets of miRNAs were…

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lncRNASNP
Dataset

lncRNASNP

A database providing comprehensive resources of single nucleotide polymorphisms…

A database providing comprehensive resources of single nucleotide polymorphisms (SNPs) in human/mouse lncRNAs. It contains SNPs in lncRNAs, SNP effects on lncRNA structure and lncRNA:miRNA binding.…

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LncRNAWiki
Dataset

LncRNAWiki

A wiki-based platform that is open-content and publicly editable and aimed at…

A wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related databases are dependent…

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ViRBase
Dataset

ViRBase

Aims to provide the scientific community with a resource for efficient browsing…

Aims to provide the scientific community with a resource for efficient browsing and visualization of virus-host ncRNA-associated interactions and interaction networks in viral infection. Users can…

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lncRNA-screen
Desktop

lncRNA-screen

A comprehensive pipeline for computationally screening putative long non-coding…

A comprehensive pipeline for computationally screening putative long non-coding RNA (lncRNA) transcripts over large multimodal datasets. lncRNA-screen main objective is to facilitate the…

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IRNdb
Dataset

IRNdb Immunologically Relevant Non-coding RNAs database

Combines microRNA, PIWI-interacting RNAs, and long non-coding RNA information…

Combines microRNA, PIWI-interacting RNAs, and long non-coding RNA information with immunologically relevant target genes. IRNdb is intended to advance research on the influence of ncRNAs on…

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LncVar
Dataset

LncVar Long noncoding Variation

A database of genetic variation associated with long noncoding genes in 6…

A database of genetic variation associated with long noncoding genes in 6 species. The LncVar database can be used as a resource to evaluate the effects of the variations on the biological function…

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CANTATAdb
Dataset

CANTATAdb

An online database of long non-coding RNAs (lncRNAs) in 10 model plant species.…

An online database of long non-coding RNAs (lncRNAs) in 10 model plant species. The lncRNAs were identified computationally using dozens of publicly available RNA sequencing (RNA-Seq) libraries.…

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AnnoLnc
Web

AnnoLnc

An online portal for systematically annotating newly identified human lncRNAs.…

An online portal for systematically annotating newly identified human lncRNAs. AnnoLnc offers a full spectrum of annotations covering genomic location, RNA secondary structure, expression,…

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LncRBase
Dataset

LncRBase

A comprehensive database for long noncoding RNA (lncRNA) in Human and Mouse.…

A comprehensive database for long noncoding RNA (lncRNA) in Human and Mouse. LncRBase hosts information on basic lncRNA transcript features, with additional details on genomic location, overlapping…

GENCODE
Dataset

GENCODE

Aims to identify all gene features in the human genome using a combination of…

Aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation…

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exoRBase
Dataset

exoRBase

Gathers long RNA species derived from RNA-seq data analyses of human blood…

Gathers long RNA species derived from RNA-seq data analyses of human blood exosomes. exoRBase is a manually curated database which allows integration and visualization of RNA expression profiles…

ncDR
Dataset

ncDR

Provides experimentally validated ncRNAs involved in drug resistance that were…

Provides experimentally validated ncRNAs involved in drug resistance that were curated from a large-scale of literature. ncDR offers computationally predicted drug resistance-ncRNA associations based…

LeishDB
Dataset

LeishDB

Provides leishmania genomic information. LeishDB contains prediction and…

Provides leishmania genomic information. LeishDB contains prediction and annotation of L. braziliensis protein-coding genes and non-coding RNAs. It is able to store a myriad of annotation data from…

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LncATLAS
Dataset

LncATLAS

Localizes lncRNA in human cells based on RNA-sequencing datasets. LncATLAS…

Localizes lncRNA in human cells based on RNA-sequencing datasets. LncATLAS enables non-expert users to rapidly access a rich variety of easily-interpreted data on their 39 lncRNA of interest. It is…

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LongTarget
Web

LongTarget

A computational method and program to predict lncRNA DNA-binding motifs and…

A computational method and program to predict lncRNA DNA-binding motifs and binding sites. LongTarget is used to analyse multiple antisense lncRNAs, including those that control well-known imprinting…

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LncRNA2Function
Dataset

LncRNA2Function

Facilitates researchers to search the functions of a specific lncRNA or the…

Facilitates researchers to search the functions of a specific lncRNA or the lncRNAs associated with a given functional term, or annotate functionally a set of human lncRNAs of interest. The…

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PLNlncRbase
Dataset

PLNlncRbase

Provides detailed information for experimentally identified plant lncRNAs. In…

Provides detailed information for experimentally identified plant lncRNAs. In the current version, PLNlncRbase has manually collected data from nearly 200 published literature, covering a total of…

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lncRScan-SVM
Desktop

lncRScan-SVM

Classifies protein coding and long non-coding RNA (lncRNA) transcripts using…

Classifies protein coding and long non-coding RNA (lncRNA) transcripts using support vector machine (SVM). lncRScan-SVM is a python package for lncRNA prediction that aims at classifying PCTs and…

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zflncRNApedia
Dataset

zflncRNApedia

A comprehensive resource which houses the annotation of lncRNAs as well as…

A comprehensive resource which houses the annotation of lncRNAs as well as associated information including expression levels, promoter epigenetic marks, genomic variants and retroviral insertion…

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ALDB
Dataset

ALDB

Enables the exploration and comparative analysis of lncRNAs in domestic…

Enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB…

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FARNA
Dataset

FARNA Function Annotation of human non-coding RNA transcripts

Integrates ncRNA information related to expression, pathways and diseases in a…

Integrates ncRNA information related to expression, pathways and diseases in a large number of human tissues and primary cells. FARNA is a knowledgebase of inferred functions of 10,289 human ncRNA…

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lncRNAtor
Web

lncRNAtor

Aims to be the long non-coding RNA portal encompassing expression profile,…

Aims to be the long non-coding RNA portal encompassing expression profile, interacting (binding) protein, integrated sequence curation, evolutionary scores, and coding potential. Data sets were…

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lnCeDB
Dataset

lnCeDB

Provides a database of human lncRNAs (from GENCODE 19 version) that can…

Provides a database of human lncRNAs (from GENCODE 19 version) that can potentially act as ceRNAs. In lnCeDB one can not only browse for lncRNA-mRNA pairs having common targeting miRNAs, but also…

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Co-LncRNA
Web

Co-LncRNA

Allows identification and annotations of human long non-coding RNAs. Co-LncRNA…

Allows identification and annotations of human long non-coding RNAs. Co-LncRNA is a web application allowing users to study gene ontology (GO) annotations and KEGG pathways. It uses genome-scale…

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LncReg
Dataset

LncReg

Provides regulatory information about lncRNAs, such as targets, regulatory…

Provides regulatory information about lncRNAs, such as targets, regulatory mechanisms, and experimental evidences for regulation and key molecules participating in regulation. LncReg is developed by…

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GermlncRNA
Dataset

GermlncRNA

Provides the first comprehensive web-based and open-access lncRNA catalogue for…

Provides the first comprehensive web-based and open-access lncRNA catalogue for three key male germ cell stages, including type A spermatogonia, pachytene spermatocytes and round spermatids. This…

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PLncDB
Dataset

PLncDB Plant long non-coding RNA database

Attempts to provide the following functions related to long non-coding RNAs…

Attempts to provide the following functions related to long non-coding RNAs (lncRNAs): (i) Genomic information for a large number of lncRNAs collected from various resources; (ii) an online genome…

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The Functional…
Dataset

The Functional lncRNA Database

A repository of mammalian long non-protein-coding transcripts that have been…

A repository of mammalian long non-protein-coding transcripts that have been experimentally shown to be both non-coding and functional. To search for a specific lncRNA, enter its name and choose the…

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lncRNAMap
Dataset

lncRNAMap

An integrated and comprehensive database relating to exploration of the…

An integrated and comprehensive database relating to exploration of the putative regulatory functions of human lncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA…

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lncPro
Desktop
Web

lncPro

A web app for predicting the interaction between long noncoding RNAs and…

A web app for predicting the interaction between long noncoding RNAs and proteins. By coding RNA and protein sequences into vectors, a matrix multiplication is used to give score to each RNA-protein…

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lncAMLdb
Dataset

lncAMLdb

Allows to consult IncRNAs in Acute Myeloid Leukemia. IncAMLdb contains 2616…

Allows to consult IncRNAs in Acute Myeloid Leukemia. IncAMLdb contains 2616 items.

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PlncRNADB
Dataset

PlncRNADB

A searchable database of lncRNA sequences and annotation in plants. PlncRNADB…

A searchable database of lncRNA sequences and annotation in plants. PlncRNADB includes about 5100 lncRNAs from A. thaliana, A. lyrata, P. trichocarpa and Z. mays. The sequences were obtained either…

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lncRNome
Dataset

lncRNome

A comprehensive searchable biologically oriented knowledgebase for long…

A comprehensive searchable biologically oriented knowledgebase for long noncoding RNAs in Humans. lncRNome hosts information on over 17,000 long noncoding RNAs in Human. The resource provides…

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ncFANs
Web

ncFANs non-coding RNA Function ANnotation server

Annotates human and mouse long non-coding RNA (lncRNA). ncFANs, on the basis of…

Annotates human and mouse long non-coding RNA (lncRNA). ncFANs, on the basis of the re-annotated Affymetrix microarray data, provides two alternative strategies for lncRNA functional annotation: one…

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EVLncRNAs
Dataset

EVLncRNAs Experimentally Validated lncRNAs

Provides all species and covers functional and disease-specific roles for all…

Provides all species and covers functional and disease-specific roles for all long non-coding RNAs (lncRNAs) validated. EVLncRNAs contains about 1543 lncRNAs from 77 species along with their…

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PhyloNONCODE
Dataset

PhyloNONCODE

A publicly available repository dedicated to the evolutionarily conservation…

A publicly available repository dedicated to the evolutionarily conservation annotation of lncRNAs. PhyloNONCODE starts to place mammalian lncRNAs in an evolutionary context and represent a rich…

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Linc2GO
Dataset

Linc2GO

A web resource that aims to provide comprehensive functional annotations for…

A web resource that aims to provide comprehensive functional annotations for human lincRNA. MicroRNA-mRNA and microRNA-lincRNA interaction data were integrated to generate lincRNA functional…

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