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| Why we created NONCODE? |
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That
some genes do not encode for proteins (e.g. rRNA genes, tRNA genes), has been known for decades. However, during the last decade an increasing number of genes, tentatively grouped as snoRNA, miRNA, tmRNA, antisense RNA, long mRNA-like RNAs, gRNA etc, have revealed that non protein coding RNAs play important roles in gene regulation and other cellular processes. Even though the function of many ncRNAs has been found, the functions of the majority are still unknown. The classification system is not uniform, as some ncRNA groups are named according to cellular localization, such as snRNAs, snoRNAs or scRNAs, whereas others are classified according to function, like pRNAs (package RNAs), gRNAs (guide RNAs), or tmRNAs (transfer-messenger RNAs), and others again are simply labeled according to their sedimentation coefficients (4.5S RNA, 6S RNA, 5.3 S RNA etc). Furthermore, because of this lack of integration, one type of ncRNA often appears under several names or in more than one category.
On this background, we created a ncRNA database named NONCODE which comprises almost all ncRNAs either confirmed by experimentally or predicted by computationally now publicly available., The data was automatically filtered from reference and GenBank by inhouse software, and were then manually curated. , We also introduce a new classification system, named process function class (pfclass). Based on the cellular process it involves, such as DNA duplication, RNA replication or protein translation etc, each ncRNA is assigned to one or more of 26 pfclasses. In addition to basic information like name, traditional class, alias, and accession number in GenBank, we also annotate each ncRNA with the role that it plays in the cellular process, mechanism by which it works, its cellular location, and whether or not it has undergone splicing. Furthermore, according to the annotation in NCBI, we create figures for all ncRNAs, showing their location in the genome or in a particular DNA fragment, including flanking regulatory elements. For 172,670 entries informationas to whether the ncRNA is disease related, is transcribed from repeats or imprinted domains, induced or repressed by stress, or specific to species, sex, tissue, or developmental stage has been included.
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