recent whole transcriptome studies have revealed that about three quarters of the human genome is capable of being transcribed , while protein - coding regions account for just 2% of the genome ( 13 ) . therefore , the vast majority of transcribed sequences do not encode proteins , and are called non - coding rna ( ncrna ) . accumulating evidence shows that non - coding rnas play key roles in various biological processes , such as imprinting control , the circuitry controlling pluripotency and differentiation , immune responses , and chromosome dynamics ( 4 ) . ncrnas are as important as protein - coding genes to cellular functions ( 5,6 ) . notably , a growing number of long ncrnas ( lncrnas ) , which are considered to be > 200 nt in length and are often multiexonic ( 7 ) , have been implicated in disease etiology ( 810 ) . it is therefore of great importance to collect lncrna information and store this information in a one - stop knowledge gateway for lncrnas , the noncode database . the development of high - throughput sequencing methodologies has reduced the cost of rna sequencing , and as a result there has been an explosive rise in the number of newly identified lncrnas . established a consensus set of 384 066 predicted transcripts from 7256 rna - seq libraries , which were designated as the mitranscriptome assembly ( 11 ) . since then the revolutionary advancement of sequencing methods , such as single - molecule long - read techniques , leads us closer to the real lncrna transcriptome . given sufficient material , amplification - free sequencing of full - length cdna molecules noncode has collected data from literature published since the last update and includes the latest versions of several public databases ( ensembl ( 13 ) , refseq(14 ) , lncrnadb ( 15 ) and gencode ( 16 ) ) . after the removal of false and redundant lncrnas , noncode contains a total of 527,336 transcripts . in addition to the identification of new lncrnas , data on the genetics and biochemical properties of lncrnas has accumulated rapidly . of the papers retrieved from pubmed for lncrnas , we found that the vast majority studied lncrna function , especially the relationship between lncrnas and disease ( 810 ) . in large - scale searches for single - base differences between diseased and healthy individuals , about 40% of the disease - related differences show up in genomic regions outside of protein - coding genes . this implicates non - coding regions as vital for genetic risk factors of disease ( 2 ) . in order to enable a systematic compilation and integration of this information the sources for these annotations were derived from literature mining , differential lncrna analysis utilizing public rna - seq data and microarray data and mutation analysis from public genome - wide association study ( gwas ) data . along with the ever increasing number of lncrnas and the amount and functional study data , genome - wide conservation information is required for biologists to study the mechanisms of lncrna actions . in order to explore the conservation information of lncrnas , noncode collected six new mammalian species ( chimpanzee , gorilla , orangutan , rhesus macaque , opossum and platypus ) ( 17 ) . users can browse the conserved counterparts of any human lncrna gene in other species through a phylogenetic tree layout . similar to the former iterations of noncode ( 1821 ) , the source of noncode 2016 includes the previous versions of noncode , the collated literature and other public databases . noncoding ,  non - coding ,  no code ,  non - code ,  lncrna and  lincrna , and found 6532 new articles since 1 june 2013 ( the last collection date for noncode ) . we retrieved the newly identified lncrnas and their annotations from the supplementary material or web site of these articles . together with the newest data from ensembl , refseq , lncrnadb , gencode and the old versions of noncode data , literature data were processed through a standard pipeline for each species . all of the input data were processed into bed or gtf formats based on one assembly version , for example , hg38 for human and mm10 for mouse.combination . all of the normalized data files were combined together using the cuffcompare program in the cufinks suite ( 22 ) . after eliminating redundancy , every new transcript i d and the accompanying resources were extracted.filtering protein - coding rna . firstly , the rna was compared with the coding rna in refseq and ensembl , and the  =  and  c transcripts were excluded . secondly , the rna was filtered through the coding - non - coding index ( cnci ) ( 23 ) program and only the rnas considered non - coding by cnci were kept.information retrieval . we assigned each transcript a name according to the criterion of noncode v4 and extracted basic information such as location ( 24 ) , exons , length , assembly sequence , source , etc.advanced annotation . advanced annotations included expression profiles , predicted functions , conservation , disease information , etc . human expression profiles were collected from 16 tissues of the human bodymap 2.0 data ( ena archive : erp000546 ) and eight cell lines ( geo accession no . gse30554 ) , while mouse data was collected from six different tissues ( ena archive : erp000591 ) . functions for the lncrna genes were predicted by lnc - gfp ( 25 ) , a coding  non - coding co - expression network ( 26,27 ) based global function predictor.web presence . more annotation information has been added and a more user - friendly interface has been introduced . all of the input data were processed into bed or gtf formats based on one assembly version , for example , hg38 for human and mm10 for mouse . all of the normalized data files were combined together using the cuffcompare program in the cufinks suite ( 22 ) . after eliminating redundancy , firstly , the rna was compared with the coding rna in refseq and ensembl , and the  =  and  c transcripts were excluded . secondly , the rna was filtered through the coding - non - coding index ( cnci ) ( 23 ) program and only the rnas considered non - coding by cnci were kept . we assigned each transcript a name according to the criterion of noncode v4 and extracted basic information such as location ( 24 ) , exons , length , assembly sequence , source , etc . advanced annotations included expression profiles , predicted functions , conservation , disease information , etc . human expression profiles were collected from 16 tissues of the human bodymap 2.0 data ( ena archive : erp000546 ) and eight cell lines ( geo accession no . gse30554 ) , while mouse data was collected from six different tissues ( ena archive : erp000591 ) . functions for the lncrna genes were predicted by lnc - gfp ( 25 ) , a coding  non - coding co - expression network ( 26,27 ) based global function predictor . more annotation information has been added and a more user - friendly interface has been introduced . noncode contains 527,336 lncrna transcripts from 16 species ( human , mouse , cow , rat , chimpanzee , gorilla , orangutan , rhesus macaque , opossum , platypus , chicken , zebrafish , fruitfly , caenorhabditiselegans , yeast and arabidopsis , ) . according to the definition of lncrna genes ( 18 ) , a total of 101,700 and 86,935 genes were generated from 167,150 and 130,558 lncrnas from human and mouse ( shown in table 1 ) , respectively . following the nomenclature of noncode v4 ( 18 ) , both lncrna transcripts and genes were designated systematically : non+ three characters ( representing a species ) + t ( transcript ) or g ( gene ) + six sequential numbers . noncode has annotated expression profiles from all the human and mouse transcripts and genes , and a large number of these genes were annotated with predicted functions . definitive evidence has proven that transcription of the non - coding genome has produced functional rnas ( 1 ) . in particular , lncrnas have been implicated in biological , developmental , and pathological processes , and acted through mechanisms such as chromatin reprogramming , cis regulation at enhancers , and post - transcriptional regulation of mrna processing ( 28 ) . lncrnas are therefore considered to be important regulators of tissue physiology and disease processes including cancer ( 11 ) . although we have collected functional interactions between ncrnas and biomolecules in npinter ( 2931 ) , we think it is also necessary to include disease information into noncode . recent published papers have been explored , and the proven associations between noncode transcripts and diseases has been integrated into the latest version . the noncode assembly also assessed the overlaps of transcripts with the unique disease - associated single - nucleotide polymorphisms ( snps ) from a catalog of gwass ( 32 ) and the snp database ( dbsnp ) ( 33 ) . there were also a lot of relational data between lncrnas and diseases which were analyzed from rna - seq and microarray data . after collecting the basic data , we compared it with the lncrnas in noncode and retained data that overlapped with noncode lncrnas . noncode 2016 contains 1110 lncrnas which were related to 284 diseases . among these associations , disease related data acquisition pipeline in the lncrna gene description pages , users can retrieve the related diseases of the entry , and also get the source of the information , such as the pmid(s ) of the reference paper(s ) . there is also mutational information retrieved from the literature , gwass and the dbsnp database . compared to protein - coding genes and small rnas ( e.g. mirnas and snornas ) , several reports have suggested that lncrnas are modestly conserved ( 11 ) . most lncrnas are less conserved in sequence ( 34 ) , but there are still many lncrnas that are conserved in their genomic loci , exonic sequences and promoter regions ( 35 ) . these are preserved across multiple species , attesting to their important functional potentials ( 36 ) . benefiting from next - generation sequencing technologies , ncrnas are now more easily identied via transcript sequencing . noncode has added six new species , mainly from multi - species rna - seq data ( 37,38 ) . an evolutionary tree from 12 commonly studied species ( human , mouse , cow , rat , chicken , zebrafish , chimpanzee , gorilla , orangutan , rhesus macaque , opossum and platypus ) was constructed using methods introduced in phylononcode ( 39 ) . each human lncrna gene counterpart from the other listed species can be retrieved through browsing the evolutionary tree ( shown in figure 2 ) . the counterpart of each lncrna was computed using the ucsc liftover tool ( 40 ) . in brief , liftover utilized blastz ( 41 ) , an independent implementation of the gapped blast algorithm specifically designed for aligning two long genomic sequences , as a core algorithm to detect homologous regions in other genomes . after mapping to the second species , however , a proper method of in silico transcript reconstruction is an ongoing challenge . according to an assessment by the paul bertone group , < 40% of known transcripts the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current - generation rna - seq data ( 42 ) . furthermore , multiple amplification steps during library preparation complicate the quantification of expression levels . to some extent given sufficient material , amplification - free and fragmentation - free sequencing of full - length cdna molecules provides a more direct view of rna molecules ( 12 ) . noncode contacted the authors of the third - generation single - molecule long - read survey of the human transcriptome paper ( 12 ) . after our analysis , the single - molecule lncrna transcripts were included into noncode . to meet the quality demands of researchers users can choose the subset which is considered high quality . the quality controls include the source of the data , literature support , other database support and long - read sequencing method support . the controls also include selection of exon numbers , the lengths of the transcripts and prediction tools support . the web interface will return the subset according to the conditions users chose and allow users to download the data . noncode 2016 contains 527,336 lncrnas from 16 different species , this compares favorably with other lncrna databases . for example , lncipedia ( human only ) contains 111 685 transcripts ( 43 ) , lncrnator ( human , mouse , fly , zebrafish , worm and yeast ) contains 34 605 transcripts ( 44 ) , while the lncrnawiki ( human only ) contains 105 255 transcripts ( 45 ) . as mentioned above , technical limitations imposed by short - read sequencing lead to a number of computational challenges in transcript reconstruction and quantification . for many transcripts , automated methods failed to identify all of the constituent exons , and in cases in which all exons were reported , the protocols tested often failed to assemble the exons into complete isoforms ( 42 ) . for example , although we have obtained all the data from mitranscriptome ( 11 ) , which contains 384 066 human lncrnas from 7256 rna - seq libraries , the detection of precise refseq splicing patterns from mitranscriptome was only 31% , and the fraction of annotated genes within the entire mitranscriptome was only 46% . although it is reasonable to assume that unannotated transcription is unique to specific lineages , the low refseq detection rate was unusual . we therefore made a decision that noncode would not include mitranscriptome data in the current version . in the future , we will attempt to make clear the real reason(s ) . perhaps a more comprehensive construction tool is required to answer this question . national high technology research and development program (  863 program ) of china [ 2014aa021103 , 2014aa021502 ] ; training program of the major research plan of the national natural science foundation of china ; national natural science foundation of china [ 31371320 , 31401119 ] ; chinese academy of science strategic project of leading science and technology [ xda01020402 ] . funding for open access charge : national high technology research and development program (  863 program ) of china [ 2014aa021103 ] .