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  • lncRNAs
  • Indeed, the finding that only 14% of the well-defined mouse long intergenic ncRNAs (lncRNAs) identified in the FANTOM projects [ 6 , 7 ] have a transcribed ortholog in human (based on analyses of known EST and cDNA data sets) [ 2 ] argues against their functionality. (biomedcentral.com)
  • Quantitatively, lncRNAs demonstrate ~10-fold lower abundance than mRNAs in a population of cells, which is explained by higher cell-to-cell variation of expression levels of lncRNA genes in the individual cells, when compared to protein-coding genes. (wikipedia.org)
  • There have been several attempts to delineate the different categories of selection signatures seen amongst lncRNAs including: lncRNAs with strong sequence conservation across the entire length of the gene, lncRNAs in which only a portion of the transcript (e.g. 5' end, splice sites) is conserved, and lncRNAs that are transcribed from syntenic regions of the genome but have no recognizable sequence similarity. (wikipedia.org)
  • molecules
  • Instead, their preservation across diverse amniotes, their apparent conservation in exon structure, and similarities in their pattern of brain expression during embryonic and early postnatal stages together indicate that these are functional RNA molecules, of which some have roles in vertebrate brain development. (biomedcentral.com)
  • protein-codin
  • At the beginning of this century, many geneticists were predicting that the human genome contained around 100,000 protein-coding genes, partly based on the assumption that more complex organisms would have a greater number of genes. (biomedcentral.com)
  • Ten years later, with far more genomic data from a wide variety of organisms and a much better-quality, well-annotated human genome, this original expectation has been downsized to around 20,000 protein-coding genes. (biomedcentral.com)
  • This means that highly complex organisms like the human have about the same number of protein-coding genes as much simpler life forms such as the roundworm, Caenorhabditis elegans . (biomedcentral.com)
  • When the human genome was initially sequenced and annotated, there was a vast increase in the data available on protein-coding genes. (biomedcentral.com)
  • Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes. (biomedcentral.com)
  • miRNAs regulate expression of protein-coding genes [ 5 , 6 ]. (hindawi.com)
  • How new RNA genes originated and whether this process is controlled by similar evolutionary mechanisms for the origin of protein-coding genes remains unclear. (pnas.org)
  • This molecular process suggests that the mechanism of exon shuffling, which can generate protein-coding genes, also plays a role in the origin of RNA genes. (pnas.org)
  • Indeed, there is ample evidence supporting a common role of exon shuffling in protein-coding genes ( 12 , 13 ). (pnas.org)
  • Does Darwinian selection that shapes new protein-coding genes (e.g., refs. (pnas.org)
  • Phylogenetic comparison of genetic signals has proven to be an efficient method in identifying young protein-coding genes in Drosophila (e.g., refs. (pnas.org)
  • By the time the initial sequence of the Human Genome was published in 2001 [ 2 ], the HGNC database ( http://www.genenames.org ) [ 3 ] contained more than 13,000 approved gene names, mostly for protein-coding genes with only around 200 non-coding RNA (ncRNA) gene names. (biomedcentral.com)
  • It has been suggested that some lncRNAs act in cis to regulate the expression of neighboring protein-coding genes (PCGs) in a mechanism that fine-tunes gene expression. (biomedcentral.com)
  • There are an estimated 19,000-20,000 human protein-coding genes. (wikipedia.org)
  • Computational methods developed for protein coding genes often fail when searching for ncRNAs. (springer.com)
  • Noncoding RNAs play critical roles in regulating protein-coding genes and comprise two major classes: long noncoding RNAs (lncRNAs) and microRNAs (miRNAs). (jcancer.org)
  • Chromosome
  • A cluster of CC chemokine genes exists on chromosome 17q11.2. (genecards.org)
  • C1orf137 (Chromosome 1 Open Reading Frame 137 (Putative)) is an RNA Gene, and is affiliated with the ncRNA class. (genecards.org)
  • This retrosequence, which is located at 102F on the fourth chromosome, recruited a nearby exon and intron, thereby evolving a chimeric gene structure. (pnas.org)
  • The Xist gene, which is polyadenylated and plays a crucial role in inactivating X chromosome, is also only found in mammals ( 9 , 10 ). (pnas.org)
  • Recent results suggest that most of the vast quantities of noncoding DNA within the genome have associated biochemical activities, including regulation of gene expression , organization of chromosome architecture , and signals controlling epigenetic inheritance . (wikipedia.org)
  • HGNC
  • The HUGO Gene Nomenclature Committee (HGNC) is the only organisation authorised to assign standardised nomenclature to human genes. (biomedcentral.com)
  • HGNC is actively engaging with the RNA research community in order to provide unique symbols and names for each sequence that encodes an ncRNA. (biomedcentral.com)
  • Fortunately, the HUGO Gene Nomenclature Committee (HGNC)[ 4 ] was on hand to provide unique names for these genes, thus ensuring that everyone was able to retrieve and discuss relevant information concerning specific loci. (biomedcentral.com)
  • Researchers must contact the HGNC with their suggestions prior to publication, to check whether the proposed gene symbol can be approved. (biomedcentral.com)
  • Working with lncRNA researchers, the HGNC aims to provide unique and, wherever possible, meaningful gene symbols to all lncRNA genes. (biomedcentral.com)
  • Since its inception in the 1970s, the HUGO Gene Nomenclature Committee (HGNC) [ 1 ] has kept apace with the discovery and characterisation of new human genes, providing each gene with a unique symbol and name and thus aiding effective scientific communication. (biomedcentral.com)
  • To ensure their symbol can be approved authors must contact the HGNC prior to publication to agree the nomenclature for each novel lncRNA gene. (biomedcentral.com)
  • sequence
  • We describe a comparative sequence analysis algorithm for detecting novel structural RNA genes. (biomedcentral.com)
  • We formalize this intuition using three probabilistic "pair-grammars": a pair stochastic context free grammar modeling alignments constrained by structural RNA evolution, a pair hidden Markov model modeling alignments constrained by coding sequence evolution, and a pair hidden Markov model modeling a null hypothesis of position-independent evolution. (biomedcentral.com)
  • Given an input pairwise sequence alignment (e.g. from a BLASTN comparison of two related genomes) we classify the alignment into the coding, RNA, or null class according to the posterior probability of each class. (biomedcentral.com)
  • the RNase MRP gene was only detected in the completely sequenced CHH critical region because the RNase MRP sequence was already in the databases. (biomedcentral.com)
  • Maizel and coworkers [ 13 - 15 ] had hypothesized that biologically functional RNA structures may have more stable predicted secondary structures than would be expected for a random sequence of the same base composition. (biomedcentral.com)
  • FAM85A (Family With Sequence Similarity 85 Member A) is an RNA Gene, and is affiliated with the ncRNA class. (genecards.org)
  • spx originated as an insertion of a retroposed sequence of the ATP synthase chain F gene at the cytological region 60DB since the divergence of Drosophila melanogaster from its sibling species 2-3 million years ago. (pnas.org)
  • In contrast, long non-coding RNA (lncRNA) genes represent a disparate set of loci related only by their size, more than 200 bases in length, share no conserved sequence homology, and have variable functions. (biomedcentral.com)
  • The estimate of the number of human genes has been repeatedly revised down from initial predictions of 100,000 or more as genome sequence quality and gene finding methods have improved, and could continue to drop further. (wikipedia.org)
  • Basic information about these molecules and their gene content, based on a reference genome that does not represent the sequence of any specific individual, are provided in the following table. (wikipedia.org)
  • Through a reiterative process of sequence analysis and reannotation, we identified 149 NBS-LRR-encoding genes in the Arabidopsis (ecotype Columbia) genomic sequence. (plantcell.org)
  • mRNAs
  • They are also known to be involved in many other diverse and vital roles within our bodies, including protein biosynthesis and the splicing of messenger RNAs (mRNAs), and have been implicated in many diseases, such as Prader-Willi syndrome and various cancers (for review, see Taft et al . (biomedcentral.com)
  • loci
  • Resistance ( R ) genes have been shown frequently by classic genetics to be single loci that confer resistance against pathogens that express matching avirulence genes in a "gene-for-gene" manner ( Flor, 1956 , 1971 ). (plantcell.org)
  • biological
  • Non-protein-coding RNA genes play an important role in various biological processes. (pnas.org)
  • In extant genomes, there are many RNA genes with important roles in various biological processes ( 2 , 3 ). (pnas.org)
  • However, the biological function of long ncRNA (lncRNA) SNHG20 in ovarian cancer is still unclear. (bioscirep.org)
  • Most (though probably not all) genes have been identified by a combination of high throughput experimental and bioinformatics approaches, yet much work still needs to be done to further elucidate the biological functions of their protein and RNA products. (wikipedia.org)
  • tissues
  • Total RNA was isolated from various tissues (liver, duodenum, jejunum, ileum, colon, brown adipose tissue, white adipose tissue, and skeletal muscle) from adult male conventional and germ-free mice ( n = 3 per group). (biomedcentral.com)
  • functional
  • Indeed, the ENCyclopedia Of DNA Elements (ENCODE) Consortium,[ 2 ] which is aiming to identify all the functional elements in the human genome, suggests that the vast majority of the genome is transcribed as non-protein-coding RNA (ncRNA). (biomedcentral.com)
  • The systematic functional annotation of the potential protein-coding targets enabled us to identify genes with altered expression patterns in the affected brain compartments of SCA1-affected patients. (hindawi.com)
  • pathogenesis
  • In particular, changes in tau gene (MAPT) expression and splicing are directly linked with pathogenesis. (ucl.ac.uk)
  • regulate
  • It has been suggested that ncRNAs can regulate gene expression at transcriptional, post-transcriptional, and epigenetic levels, thereby participating in physiological and pathological processes [ 2 , 4 ]. (jcancer.org)
  • It is a primary mechanism by which ncRNAs regulate gene expression, which is extensively involved in biology, evolution, and pathology [ 5 - 7 ]. (jcancer.org)
  • whereas
  • A conserved coding region tends to show a pattern of synonymous substitutions, whereas a conserved structural RNA tends to show a pattern of compensatory mutations consistent with some base-paired secondary structure. (biomedcentral.com)
  • Molecular
  • A straightforward answer might be obtained by directly examining an RNA gene that originated recently, because the evolutionary characteristics related to the molecular processes of origin and subsequent evolutionary dynamics of new genes may be more easily observed in such a gene. (pnas.org)
  • Transcription
  • Using RNA-FISH we show that the tau-NATs are mostly present in the cytoplasm with some in nuclear spots that could be the sites of active transcription. (ucl.ac.uk)
  • subgroup
  • We extended this approach to search for young genes in the Drosophila melanogaster subgroup, where we identified a young RNA gene that originated in D. melanogaster since it diverged from its sibling species about 2 million years ago. (pnas.org)