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79-457: Virions are enveloped and can be spherical or pleomorphic and capable of producing filamentous virions. The diameter is around 150 nm. Genomes are linear, around 15kb in length. Fusion proteins and attachment proteins appear as spikes on the virion surface. Matrix proteins inside the envelope stabilise virus structure. The nucleocapsid core is composed of the genomic RNA, nucleocapsid proteins, phosphoproteins and polymerase proteins. The genome

158-410: A DNA sequence. The presence of an ORF does not necessarily mean that the region is always translated . For example, in a randomly generated DNA sequence with an equal percentage of each nucleotide , a stop-codon would be expected once every 21 codons . A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode

237-571: A stop codon (usually UAA, UAG or UGA in RNA). That start codon (not necessarily the first) indicates where translation may start. The transcription termination site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, an incomplete protein would be made during translation. In eukaryotic genes with multiple exons , introns are removed and exons are then joined together after transcription to yield

316-402: A DNA strand has three distinct reading frames. The double helix of a DNA molecule has two anti-parallel strands; with the two strands having three reading frames each, there are six possible frame translations. The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in

395-430: A big potential to modify the genetic control in a host organism. The movement of TEs is a driving force of genome evolution in eukaryotes because their insertion can disrupt gene functions, homologous recombination between TEs can produce duplications, and TE can shuffle exons and regulatory sequences to new locations. Retrotransposons are found mostly in eukaryotes but not found in prokaryotes. Retrotransposons form

474-506: A defined structure that are able to change their location in the genome. TEs are categorized as either as a mechanism that replicates by copy-and-paste or as a mechanism that can be excised from the genome and inserted at a new location. In the human genome, there are three important classes of TEs that make up more than 45% of the human DNA; these classes are The long interspersed nuclear elements (LINEs), The interspersed nuclear elements (SINEs), and endogenous retroviruses. These elements have

553-518: A hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where

632-531: A large portion of the genomes of many eukaryotes. A retrotransposon is a transposable element that transposes through an RNA intermediate. Retrotransposons are composed of DNA , but are transcribed into RNA for transposition, then the RNA transcript is copied back to DNA formation with the help of a specific enzyme called reverse transcriptase. A retrotransposon that carries reverse transcriptase in its sequence can trigger its own transposition but retrotransposons that lack

711-405: A main driving role to generate genetic novelty and natural genome editing. Works of science fiction illustrate concerns about the availability of genome sequences. Michael Crichton's 1990 novel Jurassic Park and the subsequent film tell the story of a billionaire who creates a theme park of cloned dinosaurs on a remote island, with disastrous outcomes. A geneticist extracts dinosaur DNA from

790-413: A major role in shaping the genome. Duplication may range from extension of short tandem repeats , to duplication of a cluster of genes, and all the way to duplication of entire chromosomes or even entire genomes . Such duplications are probably fundamental to the creation of genetic novelty. Horizontal gene transfer is invoked to explain how there is often an extreme similarity between small portions of

869-467: A major theme of the book. The 1997 film Gattaca is set in a futurist society where genomes of children are engineered to contain the most ideal combination of their parents' traits, and metrics such as risk of heart disease and predicted life expectancy are documented for each person based on their genome. People conceived outside of the eugenics program, known as "In-Valids" suffer discrimination and are relegated to menial occupations. The protagonist of

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948-517: A multiple of six. This is probably due to the advantage of having all RNA bound by N protein (since N binds hexamers of RNA). If RNA is left exposed, the virus does not replicate efficiently. The gene sequence is: Viral replication is cytoplasmic . Entry into the host cell is achieved by viral attachment to host cell. Replication and transcription follow the negative-stranded RNA virus models. Translation takes place by leaky scanning, ribosomal shunting , and RNA termination-reinitiation. The virus exits

1027-474: A new site. This cut-and-paste mechanism typically reinserts transposons near their original location (within 100 kb). DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C. elegans . Genome size is the total number of the DNA base pairs in one copy of a haploid genome. Genome size varies widely across species. Invertebrates have small genomes, this

1106-415: A reference, whereas analyses of coverage depth and mapping topology can provide details regarding structural variations such as chromosomal translocations and segmental duplications. DNA sequences that carry the instructions to make proteins are referred to as coding sequences. The proportion of the genome occupied by coding sequences varies widely. A larger genome does not necessarily contain more genes, and

1185-487: A reverse transcriptase must use reverse transcriptase synthesized by another retrotransposon. Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome. Retrotransposons can be divided into long terminal repeats (LTRs) and non-long terminal repeats (Non-LTRs). Long terminal repeats (LTRs) are derived from ancient retroviral infections, so they encode proteins related to retroviral proteins including gag (structural proteins of

1264-404: A single, linear molecule of DNA, but some are made up of a circular DNA molecule. Prokaryotes and eukaryotes have DNA genomes. Archaea and most bacteria have a single circular chromosome , however, some bacterial species have linear or multiple chromosomes. If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, and if

1343-452: A typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions. Therefore, some authors say that an ORF should have a minimal length, e.g. 100 codons or 150 codons. By itself even a long open reading frame is not conclusive evidence for the presence of a gene . Some short ORFs (sORFs), also named Small open reading frames , usually < 100 codons in length, that lack

1422-424: A vocabulary into which genome fits systematically. It is very difficult to come up with a precise definition of "genome." It usually refers to the DNA (or sometimes RNA) molecules that carry the genetic information in an organism but sometimes it is difficult to decide which molecules to include in the definition; for example, bacteria usually have one or two large DNA molecules ( chromosomes ) that contain all of

1501-504: Is a R-package in Bioconductor for finding open reading frames and using Next generation sequencing technologies for justification of ORFs. orfipy is a tool written in Python / Cython to extract ORFs in an extremely and fast and flexible manner. orfipy can work with plain or gzipped FASTA and FASTQ sequences, and provides several options to fine-tune ORF searches; these include specifying

1580-485: Is a program which not only gives information about the coding and non coding sequences but also can perform pairwise global alignment of different gene/DNA regions sequences. The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their single letter amino acid code, and provides their locations in the sequence. The pairwise global alignment between the sequences makes it convenient to detect

1659-485: Is also correlated to a small number of transposable elements. Fish and Amphibians have intermediate-size genomes, and birds have relatively small genomes but it has been suggested that birds lost a substantial portion of their genomes during the phase of transition to flight.  Before this loss, DNA methylation allows the adequate expansion of the genome. In humans, the nuclear genome comprises approximately 3.1 billion nucleotides of DNA, divided into 24 linear molecules,

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1738-432: Is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes. Long interspersed elements (LINEs) encode genes for reverse transcriptase and endonuclease, making them autonomous transposable elements. The human genome has around 500,000 LINEs, taking around 17% of the genome. Short interspersed elements (SINEs) are usually less than 500 base pairs and are non-autonomous, so they rely on

1817-506: Is associated with bronchiolitis , bronchitis , and pneumonia . HPIV-4 is less common than the other types, and is known to cause mild to severe respiratory tract illnesses. Paramyxoviruses are also responsible for a range of diseases in other animal species, for example canine distemper virus ( dogs ), phocine distemper virus ( seals ), cetacean morbillivirus ( dolphins and porpoises ), Newcastle disease virus ( birds ), and rinderpest virus ( cattle ). Some paramyxoviruses, such as

1896-444: Is carried in plasmids . For this, the word genome should not be used as a synonym of chromosome . Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from Jack jumper ants and an asexual nemotode , which each have only one pair, to a fern species that has 720 pairs. It is surprising the amount of DNA that eukaryotic genomes contain compared to other genomes. The amount

1975-564: Is even more than what is necessary for DNA protein-coding and noncoding genes due to the fact that eukaryotic genomes show as much as 64,000-fold variation in their sizes. However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs). A typical human cell has two copies of each of 22 autosomes , one inherited from each parent, plus two sex chromosomes , making it diploid. Gametes , such as ova, sperm, spores, and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to

2054-492: Is facilitated by active DNA demethylation , a process that entails the DNA base excision repair pathway. This pathway is employed in the erasure of CpG methylation (5mC) in primordial germ cells. The erasure of 5mC occurs via its conversion to 5-hydroxymethylcytosine (5hmC) driven by high levels of the ten-eleven dioxygenase enzymes TET1 and TET2 . Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to

2133-440: Is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice , a mouse , the plant Arabidopsis thaliana , the puffer fish , and the bacteria E. coli . In December 2013, scientists first sequenced the entire genome of a Neanderthal , an extinct species of humans . The genome

2212-431: Is nonsegmented, negative-sense RNA, 15–19 kilobases in length, and contains six to 10 genes. Extracistronic (noncoding) regions include: Each gene contains transcription start/stop signals at the beginning and end, which are transcribed as part of the gene. Gene sequence within the genome is conserved across the family due to a phenomenon known as transcriptional polarity (see Mononegavirales ) in which genes closest to

2291-401: Is rather exceptional, eukaryotes generally have these features in their genes and their genomes contain variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is composed of repetitive DNA. High-throughput technology makes sequencing to assemble new genomes accessible to everyone. Sequence polymorphisms are typically discovered by comparing resequenced isolates to

2370-412: Is that each protein and amino acid has an important function. Thus, any mutation would lead to a decrease or total loss of function, which would in turn cause the new virus to be less efficient. These viruses would not be able to survive as long compared to the more virulent strains, and so would die out. Many paramyxovirus genomes follow the "rule of six" . The total length of the genome is almost always

2449-456: Is the complete list of the nucleotides (A, C, G, and T for DNA genomes) that make up all the chromosomes of an individual or a species. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity. In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish

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2528-421: Is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multi-cellular organisms (see developmental biology ). The work is both in vivo and in silico . There are many enormous differences in size in genomes, specially mentioned before in

2607-582: The Genoscope in Paris. Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity. The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service, to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA.LAND at the New York Genome Center , an example both of

2686-406: The economies of scale and of citizen science . Viral genomes can be composed of either RNA or DNA. The genomes of RNA viruses can be either single-stranded RNA or double-stranded RNA , and may contain one or more separate RNA molecules (segments: monopartit or multipartit genome). DNA viruses can have either single-stranded or double-stranded genomes. Most DNA virus genomes are composed of

2765-455: The henipaviruses , are zoonotic pathogens, occurring naturally in an animal host, but also able to infect humans. Hendra virus and Nipah virus in the genus Henipavirus have emerged in humans and livestock in Australia and Southeast Asia . Both viruses are contagious , highly virulent , and capable of infecting a number of mammalian species and causing potentially fatal disease. Due to

2844-455: The mitochondria . In addition, algae and plants have chloroplast DNA. Most textbooks make a distinction between the nuclear genome and the organelle (mitochondria and chloroplast) genomes so when they speak of, say, the human genome, they are only referring to the genetic material in the nucleus. This is the most common use of 'genome' in the scientific literature. Most eukaryotes are diploid , meaning that there are two of each chromosome in

2923-615: The poly (A) tail at the end of mRNA transcripts by repeatedly moving back one nucleotide at a time at the end of the RNA template. Family: Paramyxoviridae A number of important human diseases are caused by paramyxoviruses. These include mumps , as well as measles , which caused around 136,200 deaths in 2022. The human parainfluenza viruses (HPIV) are the second most common causes of respiratory tract disease in infants and children. There are four types of HPIVs, known as HPIV-1, HPIV-2, HPIV-3 and HPIV-4. HPIV-1 and HPIV-2 may cause cold-like symptoms, along with croup in children. HPIV-3

3002-423: The 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon , Methanococcus jannaschii , was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of complete genome sequences

3081-469: The 3’ end of the genome are transcribed in greater abundance than those towards the 5’ end. This is a result of structure of the genome. After each gene is transcribed, the RNA-dependent RNA polymerase pauses to release the new mRNA when it encounters an intergenic sequence. When the RNA polymerase is paused, a chance exists that it will dissociate from the RNA genome. If it dissociates, it must re-enter

3160-469: The basal group. The respirovirus-henipavirus-morbillivirus clade may be basal to the avulavirus-rubulavirus clade. Genome In the fields of molecular biology and genetics , a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses ). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of

3239-412: The blood of ancient mosquitoes and fills in the gaps with DNA from modern species to create several species of dinosaurs. A chaos theorist is asked to give his expert opinion on the safety of engineering an ecosystem with the dinosaurs, and he repeatedly warns that the outcomes of the project will be unpredictable and ultimately uncontrollable. These warnings about the perils of using genomic information are

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3318-549: The cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and already partially replicated chromosomes. Most prokaryotes have very little repetitive DNA in their genomes. However, some symbiotic bacteria (e.g. Serratia symbiotica ) have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins. Some bacteria have auxiliary genetic material, also part of their genome, which

3397-478: The chromosomes in the nucleus, organelles such as the chloroplasts and mitochondria have their own DNA. Mitochondria are sometimes said to have their own genome often referred to as the " mitochondrial genome ". The DNA found within the chloroplast may be referred to as the " plastome ". Like the bacteria they originated from, mitochondria and chloroplasts have a circular chromosome. Unlike prokaryotes where exon-intron organization of protein coding genes exists but

3476-526: The classical hallmarks of protein-coding genes (both from ncRNAs and mRNAs) can produce functional peptides. 5’-UTR of about 50% of mammal mRNAs are known to contain one or several sORFs, also called upstream ORFs or uORFs . However, less than 10% of the vertebrate mRNAs surveyed in an older study contained AUG codons in front of the major ORF. Interestingly, uORFs were found in two thirds of proto-oncogenes and related proteins. 64–75% of experimentally found translation initiation sites of sORFs are conserved in

3555-455: The co-discoverers of the structure of DNA. Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than a genome sequence and aids in navigating around the genome. The Human Genome Project was organized to map and to sequence the human genome . A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at

3634-447: The coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. ORF Predictor uses a combination of the two different ORF definitions mentioned above. It searches stretches starting with a start codon and ending at a stop codon. As an additional criterion, it searches for a stop codon in the 5' untranslated region (UTR or NTR, nontranslated region ). ORFik

3713-415: The complete nucleotide sequence of a viral RNA-genome ( Bacteriophage MS2 ). The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174 , of 5386 base pairs. The first bacterial genome to be sequenced was that of Haemophilus influenzae , completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of

3792-455: The context of transcriptomics and metagenomics , where a start or stop codon may not be present in the obtained sequences. Such an ORF corresponds to parts of a gene rather than the complete gene. One common use of open reading frames (ORFs) is as one piece of evidence to assist in gene prediction . Long ORFs are often used, along with other evidence, to initially identify candidate protein-coding regions or functional RNA -coding regions in

3871-520: The database. This tool identifies all open reading frames using the standard or alternative genetic codes. The deduced amino acid sequence can be saved in various formats and searched against the sequence database using the basic local alignment search tool (BLAST) server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions. It is also packaged with the Sequin sequence submission software (sequence analyser). ORF Investigator

3950-445: The details of any particular genes and their products. Researchers compare traits such as karyotype (chromosome number), genome size , gene order, codon usage bias , and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown 2002; Saccone and Pesole 2003; Benfey and Protopapas 2004; Gibson and Muse 2004; Reese 2004; Gregory 2005). Duplications play

4029-435: The different mutations, including single nucleotide polymorphism . Needleman–Wunsch algorithms are used for the gene alignment. The ORF Investigator is written in the portable Perl programming language , and is therefore available to users of all common operating systems. OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with

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4108-424: The discovery of new viruses in this group is increasing. The evolution of paramyxoviruses is still debated. Using pneumoviruses (mononegaviral family Pneumoviridae ) as an outgroup, paramyxoviruses can be divided into two clades: one consisting of avulaviruses and rubulaviruses and one consisting of respiroviruses , henipaviruses , and morbilliviruses . Within the second clade the respiroviruses appear to be

4187-441: The essential genetic material but they also contain smaller extrachromosomal plasmid molecules that carry important genetic information. The definition of 'genome' that is commonly used in the scientific literature is usually restricted to the large chromosomal DNA molecules in bacteria. Eukaryotic genomes are even more difficult to define because almost all eukaryotic species contain nuclear chromosomes plus extra DNA molecules in

4266-418: The film is an In-Valid who works to defy the supposed genetic odds and achieve his dream of working as a space navigator. The film warns against a future where genomic information fuels prejudice and extreme class differences between those who can and cannot afford genetically engineered children. Open reading frame In molecular biology , reading frames are defined as spans of DNA sequence between

4345-428: The final mRNA for protein translation. In the context of gene finding , the start-stop definition of an ORF therefore only applies to spliced mRNAs , not genomic DNA, since introns may contain stop codons and/or cause shifts between reading frames. An alternative definition says that an ORF is a sequence that has a length divisible by three and is bounded by stop codons. This more general definition can be useful in

4424-584: The first end-to-end human genome sequence in March 2022. The term genome was created in 1920 by Hans Winkler , professor of botany at the University of Hamburg , Germany. The website Oxford Dictionaries and the Online Etymology Dictionary suggest the name is a blend of the words gene and chromosome . However, see omics for a more thorough discussion. A few related -ome words already existed, such as biome and rhizome , forming

4503-414: The genome at the leader sequence, rather than continuing to transcribe the length of the genome. The result is that the further downstream genes are from the leader sequence, the less they will be transcribed by RNA polymerase. Evidence for a single promoter model was verified when viruses were exposed to UV light. UV radiation can cause dimerization of RNA, which prevents transcription by RNA polymerase. If

4582-458: The genome such as regulatory sequences (see non-coding DNA ), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome . Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics . The genomes of many organisms have been sequenced and various regions have been annotated. The Human Genome Project

4661-413: The genomes of human and mouse and may indicate that these elements have function. However, sORFs can often be found only in the minor forms of mRNAs and avoid selection; the high conservation of initiation sites may be connected with their location inside promoters of the relevant genes. This is characteristic of SLAMF1 gene, for example. Since DNA is interpreted in groups of three nucleotides (codons),

4740-406: The genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes . Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes. Recent empirical data suggest an important role of viruses and sub-viral RNA-networks to represent

4819-472: The greater the chance of RNA dimerization inhibiting RNA polymerase. The virus takes advantage of the single promoter model by having its genes arranged in relative order of protein needed for successful infection. For example, nucleocapsid protein, N, is needed in greater amounts than RNA polymerase, L. Viruses in the Paramyxoviridae family are also antigenically stable, meaning that the glycoproteins on

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4898-471: The host cell by budding. Vertebrates, including humans and birds serve as the natural hosts. Transmission route is airborne particles. The Paramyxoviridae are able to undergo mRNA editing, which produces different proteins from the same mRNA transcript by slipping back one base to read off in a different open reading frame ( ORF ) due to the presence of secondary structures such as pseudoknots. Paramyxoviridae also undergo transcriptional stuttering to produce

4977-455: The human genome All the cells of an organism originate from a single cell, so they are expected to have identical genomes; however, in some cases, differences arise. Both the process of copying DNA during cell division and exposure to environmental mutagens can result in mutations in somatic cells. In some cases, such mutations lead to cancer because they cause cells to divide more quickly and invade surrounding tissues. In certain lymphocytes in

5056-425: The human genome and 9% of the fruit fly genome. Tandem repeats can be functional. For example, telomeres are composed of the tandem repeat TTAGGG in mammals, and they play an important role in protecting the ends of the chromosome. In other cases, expansions in the number of tandem repeats in exons or introns can cause disease . For example, the human gene huntingtin (Htt) typically contains 6–29 tandem repeats of

5135-517: The human immune system, V(D)J recombination generates different genomic sequences such that each cell produces a unique antibody or T cell receptors. During meiosis , diploid cells divide twice to produce haploid germ cells. During this process, recombination results in a reshuffling of the genetic material from homologous chromosomes so each gamete has a unique genome. Genome-wide reprogramming in mouse primordial germ cells involves epigenetic imprint erasure leading to totipotency . Reprogramming

5214-428: The idea of antigenic drift . Since RNA-dependent RNA polymerase does not have an error-checking function, many mutations are made when the RNA is processed. These mutations build up and eventually new strains are created. Due to this concept, one would expect that paramyxoviruses should not be antigenically stable; however, the opposite is seen to be true. The main hypothesis behind why the viruses are antigenically stable

5293-529: The lack of either a licensed human vaccine (a Hendra virus vaccine exists for horses) or antiviral therapies, Hendra virus and Nipah virus are designated as Biosafety level (BSL) 4 agents. The genomic structure of both viruses is that of a typical paramyxovirus. In the past few decades, paramyxoviruses have been discovered from terrestrial, volant , and aquatic animals, demonstrating a vast host range and great viral genetic diversity. As molecular technology advances and viral surveillance programs are implemented,

5372-476: The multicellular eukaryotic genomes. Much of this is due to the differing abundances of transposable elements, which evolve by creating new copies of themselves in the chromosomes. Eukaryote genomes often contain many thousands of copies of these elements, most of which have acquired mutations that make them defective. Here is a table of some significant or representative genomes. See #See also for lists of sequenced genomes. Initial sequencing and analysis of

5451-789: The nucleotides CAG (encoding a polyglutamine tract). An expansion to over 36 repeats results in Huntington's disease , a neurodegenerative disease. Twenty human disorders are known to result from similar tandem repeat expansions in various genes. The mechanism by which proteins with expanded polygulatamine tracts cause death of neurons is not fully understood. One possibility is that the proteins fail to fold properly and avoid degradation, instead accumulating in aggregates that also sequester important transcription factors, thereby altering gene expression. Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion. Transposable elements (TEs) are sequences of DNA with

5530-426: The nucleus but the 'genome' refers to only one copy of each chromosome. Some eukaryotes have distinctive sex chromosomes, such as the X and Y chromosomes of mammals, so the technical definition of the genome must include both copies of the sex chromosomes. For example, the standard reference genome of humans consists of one copy of each of the 22 autosomes plus one X chromosome and one Y chromosome. A genome sequence

5609-590: The proportion of non-repetitive DNA decreases along with increasing genome size in complex eukaryotes. Noncoding sequences include introns , sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences make up 98% of the human genome. There are two categories of repetitive DNA in the genome: tandem repeats and interspersed repeats. Short, non-coding sequences that are repeated head-to-tail are called tandem repeats . Microsatellites consisting of 2–5 basepair repeats, while minisatellite repeats are 30–35 bp. Tandem repeats make up about 4% of

5688-439: The proteins encoded by LINEs for transposition. The Alu element is the most common SINE found in primates. It is about 350 base pairs and occupies about 11% of the human genome with around 1,500,000 copies. DNA transposons encode a transposase enzyme between inverted terminal repeats. When expressed, the transposase recognizes the terminal inverted repeats that flank the transposon and catalyzes its excision and reinsertion in

5767-423: The shortest 45 000 000 nucleotides in length and the longest 248 000 000 nucleotides, each contained in a different chromosome. There is no clear and consistent correlation between morphological complexity and genome size in either prokaryotes or lower eukaryotes . Genome size is largely a function of the expansion and contraction of repetitive DNA elements. Since genomes are very complex, one research strategy

5846-444: The start and stop codons . Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames will be "open" (the "reading", however, refers to the RNA produced by transcription of the DNA and its subsequent interaction with the ribosome in translation ). Such an ORF may contain a start codon (usually AUG in terms of RNA ) and by definition cannot extend beyond

5925-416: The viral genome follows a multiple promoter model, the level inhibition of transcription should correlate with the length of the RNA gene. However, the genome was best described by a single promoter model. When paramyxovirus genome was exposed to UV light, the level of inhibition of transcription was proportional to the distance from the leader sequence. That is, the further the gene is from the leader sequence,

6004-541: The virus), pol (reverse transcriptase and integrase), pro (protease), and in some cases env (envelope) genes. These genes are flanked by long repeats at both 5' and 3' ends. It has been reported that LTRs consist of the largest fraction in most plant genome and might account for the huge variation in genome size. Non-long terminal repeats (Non-LTRs) are classified as long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and Penelope-like elements (PLEs). In Dictyostelium discoideum , there

6083-469: The viruses are consistent between different strains of the same type. Two reasons for this phenomenon are posited: The first is that the genome is nonsegmented, thus cannot undergo genetic reassortment . For this process to occur, segments needed as reassortment happen when segments from different strains are mixed together to create a new strain. With no segments, nothing can be mixed with one another, so no antigenic shift occurs. The second reason relates to

6162-405: Was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave . New sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine . A major step toward that goal was the completion in 2007 of the full genome of James D. Watson , one of

6241-518: Was started in October 1990, and then reported the sequence of the human genome in April 2003, although the initial "finished" sequence was missing 8% of the genome consisting mostly of repetitive sequences. With advancements in technology that could handle sequencing of the many repetitive sequences found in human DNA that were not fully uncovered by the original Human Genome Project study, scientists reported

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