A nitrogenous base, one member of the base pair AT (adenine-thymine).
Alternative form of a genetic locus; a single allele for each locus is inherited from each parent (e.g., at a locus for eye color the allele might result in blue or brown eyes).
Variation in alleles among members of the same species.
Different ways of combining a gene's exons to make variants of the complete protein
Any of a class of 20 molecules that are combined to form proteins in living things. The sequence of amino acids in a protein and hence protein function are determined by the genetic code.
An increase in the number of copies of a specific DNA fragment; can be in vivo or in vitro.
Adding pertinent information such as gene coded for, amino acid sequence, or other commentary to the database entry of raw sequence of DNA bases.
Nucleic acid that has a sequence exactly opposite to an mRNA molecule made by the body; binds to the mRNA molecule to prevent a protein from being made.
Individual primary recombinant clones (hosted in phage, cosmid, YAC, or other vector) that are placed in two-dimensional arrays in microtiter dishes. Each primary clone can be identified by the identity of the plate and the clone location (row and column) on that plate. Arrayed libraries of clones can be used for many applications, including screening for a specific gene or genomic region of interest.
Putting sequenced fragments of DNA into their correct chromosomal positions.
A technique that uses X-ray film to visualize radioactively labeled molecules or fragments of molecules; used in analyzing length and number of DNA fragments after they are separated by gel electrophoresis.
A cross between an animal that is heterozygous for alleles obtained from two parental strains and a second animal from one of those parental strains. Also used to describe the breeding protocol of an outcross followed by a backcross.
A vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on naturally occurring F-factor plasmid found in the bacterium E. coli.
One of the molecules that form DNA and RNA molecules.
Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak bonds. Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs.
The order of nucleotide bases in a DNA molecule; determines structure of proteins encoded by that DNA.
A method, sometimes automated, for determining the base sequence.
The science of managing and analyzing biological data using advanced computing techniques. Especially important in analyzing genomic research data.
A set of biological techniques developed through basic research and now applied to research and product development. In particular, biotechnology refers to the use by industry of recombinant DNA, cell fusion, and new bioprocessing techniques.
A computer program that identifies homologous (similar) genes in different organisms, such as rice, arabidopsis, or soybean.
A gene located in a chromosome region suspected of being involved in a disease.
Gel-filled silica capillaries used to separate fragments for DNA sequencing. The small diameter of the capillaries permit the application of higher electric fields, providing high speed, high throughput separations that are significantly faster than traditional slab gels.
A collection of DNA sequences that code for genes. The sequences are generated in the laboratory from mRNA sequences.
A unit of measure of recombination frequency. One centimorgan is equal to a 1% chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation. In rice, one centimorgan is equivalent, on average, to 270 kb.
Circular DNA found in the photosynthesizing organelle (chloroplast) of plants instead of the cell nucleus where most genetic material is located.
The self-replicating genetic structure of cells containing the cellular DNA that bears in its nucleotide sequence the linear array of genes. In prokaryotes, chromosomal DNA is circular, and the entire genome is carried on one chromosome. Eukaryotic genomes consist of a number of chromosomes whose DNA is associated with different kinds of proteins.
An exact copy made of biological material such as a DNA segment (e.g., a gene or other region), a whole cell, or a complete organism.
Using specialized DNA technology to produce multiple, exact copies of a single gene or other segment of DNA to obtain enough material for further study. This process is referred to as cloning DNA. The resulting cloned (copied) collections of DNA molecules are called clone libraries. A second type of cloning exploits the natural process of cell division to make many copies of an entire cell. The genetic makeup of these cloned cells, called a cell line, is identical to the original cell. A third type of cloning produces complete, genetically identical animals such as the famous Scottish sheep, Dolly.
DNA molecule originating from a virus, a plasmid, or the cell of a higher organism into which another DNA fragment of appropriate size can be integrated without loss of the vector's capacity for self-replication; vectors introduce foreign DNA into host cells, where the DNA can be reproduced in large quantities. Examples are plasmids, cosmids, and yeast artificial chromosomes; vectors are often recombinant molecules containing DNA sequences from several sources.
Study of genetics of a newly sequenced genome by comparisons with model organisms such as rice, Arabidopsis etc.
DNA that is synthesized in the laboratory from a messenger RNA template.
Nucleic acid base sequence that can form a double-stranded structure with another DNA fragment by following base-pairing rules (A pairs with T and C with G). The complementary sequence to GTAC for example, is CATG.
Trait that has a genetic component that does not follow strict Mendelian inheritance. May involve the interaction of two or more genes or gene-environment interactions.
In genetics, the expectation that genetic material and the information gained from testing that material will not be available without the donor's consent.
A base sequence in a DNA molecule (or an amino acid sequence in a protein) that has remained essentially unchanged throughout evolution.
Group of cloned (copied) pieces of DNA representing overlapping regions of a particular chromosome.
A map depicting the relative order of a linked library of overlapping clones representing a complete chromosomal segment.
Artificially constructed cloning vector containing the cos gene of phage lambda. Cosmids can be packaged in lambda phage particles for infection into E. coli; this permits cloning of larger DNA fragments (up to 45kb) than can be introduced into bacterial hosts in plasmid vectors.
The breaking during meiosis of one maternal and one paternal chromosome, the exchange of corresponding sections of DNA, and the rejoining of the chromosomes. This process can result in an exchange of alleles between chromosomes.
The study of the physical appearance of chromosomes.
A type of chromosome map whereby genes are located on the basis of cytological findings obtained with the aid of chromosome mutations.
A genetic characteristic in which the genes are found outside the nucleus, in chloroplasts or mitochondria. Results in offspring inheriting genetic material from only one parent.
A nitrogenous base, one member of the base pair GC (guanine and cytosine) in DNA.
A collection of databases, data tables, and mechanisms to access the data on a single subject.
A loss of part of the DNA from a chromosome; can lead to a disease or abnormality.
A description of a specific chromosome that uses defined mutations --specific deleted areas in the genome-- as 'biochemical signposts,' or markers for specific areas.
A full set of genetic material consisting of paired chromosomes, one from each parental set. Most animal cells except the gametes have a diploid set of chromosomes.
Alteration of DNA at a specific site and its reinsertion into an organism to study any effects of the change.
Alleles carrying particular DNA sequences associated with the presence of disease.
The molecule that encodes genetic information. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. The four nucleotides in DNA contain the bases adenine (A), guanine (G), cytosine (C), and thymine (T). In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner.
A facility that stores DNA extracted from various organisms in whole or cloned form.
The use of existing DNA as a template for the synthesis of new DNA strands. In eukaryotes, replication occurs in the cell nucleus.
The relative order of base pairs, whether in a DNA fragment, gene, chromosome, or an entire genome.
A discrete portion of a protein with its own function. The combination of domains in a single protein determines its overall function.
first set of sequences generated by the genome sequencing programme. While
incomplete, it offers a virtual road map to an estimated 95% of all genes.
Draft sequence data are mostly in the form of 10,000 base pair-sized fragments whose
approximate chromosomal locations are known.
A method of separating large molecules (such as DNA fragments or proteins) from a mixture of similar molecules. An electric current is passed through a medium containing the mixture, and each kind of molecule travels through the medium at a different rate, depending on its electrical charge and size. Agarose and acrylamide gels are the media commonly used for electrophoresis of proteins and nucleic acids.
Common bacterium that has been studied intensively by geneticists because of its small genome size, normal lack of pathogenicity, and ease of growth in the laboratory.
DNA originating outside an organism that has been introducted into the organism.
The protein-coding DNA sequence of a gene.
An enzyme that cleaves nucleotides sequentially from free ends of a linear nucleic acid substrate.
A short strand of DNA that is a part of a cDNA molecule and can act as identifier of a gene. Used in locating and mapping genes.
Each generation of offspring in a breeding program, designated F1, F2, etc.
In genetics, the identification of multiple specific alleles on an organism’s DNA to produce a unique identifier for that sample.
High-quality, low error, gap-free DNA sequence of the genome.
A physical mapping approach that uses fluorescein tags to detect hybridization of probes with metaphase chromosomes and with the less-condensed somatic interphase chromatin.
The complete order of bases in a gene. This order determines which protein a gene will produce.
The study of genes, their resulting proteins, and the role played by the proteins the body's biochemical processes.
Mature male or female reproductive cell (sperm or ovum) with a haploid set of chromosomes.
Many DNA sequences carry long stretches of repeated G and C which often indicate a gene-rich region.
The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product (i.e., a protein or RNA molecule).
Repeated copying of a piece of DNA; a characteristic of tumor cells.
Development of cDNA microarrays from a large number of genes. Used to monitor and measure changes in gene expression for each gene represented on the chip.
The process by which a gene's coded information is converted into the structures present and operating in the cell. Expressed genes include those that are transcribed into mRNA and then translated into protein and those that are transcribed into RNA but not translated into protein (e.g., transfer and ribosomal RNAs).
Group of closely related genes that make similar products.
Determination of the relative positions of genes on a DNA molecule (chromosome or plasmid) and of the distance, in linkage units or physical units, between them.
All the variations of genes in a species.
Predictions of possible genes made by a computer program based on how well a stretch of DNA sequence matches known gene sequences
The biochemical material, either RNA or protein, resulting from expression of a gene. The amount of gene product is used to measure how active a gene is; abnormal amounts can be correlated with disease-causing alleles.
The sequence of nucleotides, coded in triplets (codons) along the mRNA, that determines the sequence of amino acids in protein synthesis. A gene's DNA sequence can be used to predict the mRNA sequence, and the genetic code can in turn be used to predict the amino acid sequence.
Altering the genetic material of cells or organisms to enable them to make new substances or perform new functions.
A gene or other identifiable portion of DNA whose inheritance can be followed.
Difference in DNA sequence among individuals, groups, or populations (e.g., genes for red flower versus white flower).
Susceptibility to a genetic disease. May or may not result in actual development of the disease.
Testing a group of plants (especially parental lines) to identify individuals at high risk of having or passing on a specific genetic disorder.
All the genetic material in the chromosomes of a particular organism; its size is generally given as its total number of base pairs.
Research and technology-development effort aimed at mapping and sequencing the genome certain model organisms.
A collection of clones made from a set of randomly generated overlapping DNA fragments that represent the entire genome of an organism.
The study of genes and their function.
The genetic constitution of an organism, as distinguished from its physical appearance (its phenotype).
A nitrogenous base, one member of the base pair GC (guanine and cytosine) in DNA.
A single set of chromosomes (half the full set of genetic material) present in the egg and sperm cells of animals and in the egg and pollen cells of plants.
A way of denoting the collective genotype of a number of closely linked loci on a chromosome.
Having only one copy of a particular gene. For example, in humans, males are hemizygous for genes found on the Y chromosome.
The presence of different alleles at one or more loci on homologous chromosomes.
DNA sequence that is very similar across several different types of organisms.
A fast method of determining the order of bases in DNA.
A member of a chromosome pair in diploid organisms or a gene that has the same origin and functions in two or more species.
Chromosome containing the same linear gene sequences as another, each derived from one parent.
Swapping of DNA fragments between paired chromosomes.
Similarity in DNA or protein sequences between individuals of the same species or among different species.
An organism that has two identical alleles of a gene.
Use of a DNA or RNA probe to detect the presence of the complementary DNA sequence in cloned bacterial or cultured eukaryotic cells.
Studies performed outside a living organism such as in a laboratory.
Studies carried out in living organisms.
During meiosis each of the two copies of a gene is distributed to the germ cells independently of the distribution of other genes.
DNA sequence that interrupts the protein-coding sequence of a gene; an intron is transcribed into RNA but is cut out of the message before it is translated into protein.
An enzyme performing the same function as another enzyme but having a different set of amino acids. The two enzymes may function at different speeds.
Stretches of DNA that do not code for genes; most of the genome consists of so-called junk DNA which may have regulatory and other functions. Also called non-coding DNA.
A photomicrograph of an individual's chromosomes arranged in a standard format showing the number, size, and shape of each chromosome type; used in low-resolution physical mapping to correlate gross chromosomal abnormalities with the characteristics of specific diseases.
Unit of length for DNA fragments equal to 1000 nucleotides.
Deactivation of specific genes; used in laboratory organisms to study gene function.
An unordered collection of clones (i.e., cloned DNA from a particular organism) whose relationship to each other can be established by physical mapping.
The proximity of two or more markers (e.g., genes, RFLP markers) on a chromosome; the closer the markers, the lower the probability that they will be separated during DNA repair or replication processes (binary fission in prokaryotes, mitosis or meiosis in eukaryotes), and hence the greater the probability that they will be inherited together.
Where alleles occur together more often than can be accounted for by chance. Indicates that the two alleles are physically close on the DNA strand.
A map of the relative positions of genetic loci on a chromosome, determined on the basis of how often the loci are inherited together. Distance is measured in centimorgans (cM).
The position on a chromosome of a gene or other chromosome marker; also, the DNA at that position. The use of locus is sometimes restricted to mean expressed DNA regions.
The group of related organisms used in constructing a genetic map.
Unit of length for DNA fragments equal to 1 million nucleotides and roughly equal to 1 cM.
Messenger RNA (mRNA)
Sets of miniaturized chemical reaction areas that may also be used to test DNA fragments, antibodies, or proteins.
The genetic material found in mitochondria, the organelles that generate energy for the cell. Not inherited in the same fashion as nucleic DNA.
The process of nuclear division in cells that produces daughter cells that are genetically identical to each other and to the parent cell.
The use of statistical analysis, computer analysis, or model organisms to predict outcomes of research.
The study of the structure, function, and makeup of biologically important molecules.
The development of transgenics to produce proteins for pharmaceutical and industrial use.
The study of macromolecules important in biological inheritance.
A laboratory approach that performs multiple sets of reactions in parallel (simultaneously); greatly increasing speed and throughput.
Any heritable change in DNA sequence.
A gel-based laboratory procedure that locates mRNA sequences on a gel that are complementary to a piece of DNA used as a probe.
A large molecule composed of nucleotide subunits.
A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA). Thousands of nucleotides are linked to form a DNA or RNA molecule.
The cellular organelle in eukaryotes that contains most of the genetic material.
A molecule usually composed of 25 or fewer nucleotides; used as a DNA synthesis primer.
The sequence of DNA or RNA located between the start-code sequence (initiation codon) and the stop-code sequence (termination codon).
A set of genes transcribed under the control of an operator gene.
One type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on bacteriophage (a virus) P1 genome.
A virus for which the natural host is a bacterial cell.
A trait not caused by inheritance of a gene but appears to be identical to a genetic trait.
A map of the locations of identifiable landmarks on DNA (e.g., restriction-enzyme cutting sites, genes), regardless of inheritance. Distance is measured in base pairs; the highest-resolution map is the complete nucleotide sequence of the chromosomes.
Autonomously replicating extra-chromosomal circular DNA molecules, distinct from the normal bacterial genome and nonessential for cell survival under nonselective conditions. Some plasmids are capable of integrating into the host genome. A number of artificially constructed plasmids are used as cloning vectors.
A method for amplifying a DNA base sequence using a heat-stable polymerase and two 20-base primers, one complementary to the (+) strand at one end of the sequence to be amplified and one complementary to the (-) strand at the other end. Because the newly synthesized DNA strands can subsequently serve as additional templates for the same primer sequences, successive rounds of primer annealing, strand elongation, and dissociation produce rapid and highly specific amplification of the desired sequence. PCR also can be used to detect the existence of the defined sequence in a DNA sample.
Enzyme that catalyzes the synthesis of nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides.
Difference in DNA sequence among individuals that may underlie differences in health. Genetic variations occurring in more than 1% of a population would be considered useful polymorphisms for genetic linkage analysis.
A protein or part of a protein made of a chain of amino acids joined by a peptide bond.
The study of variation in genes among a group/s of individuals.
A technique used to identify genes, usually those that are associated with diseases, based on their location on a chromosome.
Short pre-existing polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase.
Single-stranded DNA or RNA molecules of specific base sequence, labeled either radioactively or immunologically, that are used to detect the complementary base sequence by hybridization.
A DNA site to which RNA polymerase will bind and initiate transcription.
Proteins expressed by a cell or organ at a particular time and under specific conditions.
The study of the full set of proteins encoded by a genome.
A sequence of DNA similar to a gene but nonfunctional; probably the remnant of a once-functional gene that accumulated mutations.
A nitrogen-containing, double-ring, basic compound that occurs in nucleic acids. The purines in DNA and RNA are adenine and guanine.
A nitrogen-containing, single-ring, basic compound that occurs in nucleic acids. The pyrimidines in DNA are cytosine and thymine; in RNA, cytosine and uracil.
Clone containing recombinant DNA molecules.
A combination of DNA molecules of different origin that are joined using recombinant DNA technologies.
Procedure used to join together DNA segments in a cell-free system (an environment outside a cell or organism). Under appropriate conditions, a recombinant DNA molecule can enter a cell and replicate there, either autonomously or after it has become integrated into a cellular chromosome.
The process by which progeny derive a combination of genes different from that of either parent. In higher organisms, this can occur by crossing over.
A DNA base sequence that controls gene expression.
Sequences of varying lengths that occur in multiple copies in the genome.
Degree of molecular detail on a physical map of DNA, ranging from low to high.
A protein that recognizes specific, short nucleotide sequences and cuts DNA at those sites. Bacteria contain over 400 such enzymes that recognize and cut more than 100 different DNA sequences.
Variation between individuals in DNA fragment sizes cut by specific restriction enzymes; polymorphic sequences that result in RFLPs are used as markers on both physical maps and genetic linkage maps. RFLPs usually are caused by mutation at a cutting site.
A specific nucleotide sequence of DNA at which a particular restriction enzyme cuts the DNA. Some sites occur frequently in DNA (e.g., every several hundred base pairs); others much less frequently (rare-cutter; e.g., every 10,000 base pairs).
An enzyme used by retroviruses to form a complementary DNA sequence (cDNA) from their RNA. The resulting DNA is then inserted into the chromosome of the host cell.
A class of RNA found in the ribosomes of cells.
A chemical found in the nucleus and cytoplasm of cells; it plays an important role in protein synthesis and other chemical activities of the cell. The structure of RNA is similar to that of DNA. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different purpose.
A widely used method of determining the order of bases in DNA.
In genomic mapping, a series of contigs that are in the right order but not necessarily connected in one continuous stretch of sequence.
A process whereby the order of multiple sequenced DNA fragments is determined.
Short (200 to 500 base pairs) DNA sequence that has a single occurrence in the genome and whose location and base sequence are known. Detectable by polymerase chain reaction, STSs are useful for localizing and orienting the mapping and sequence data reported from many different laboratories and serve as landmarks on the developing physical map of the genome. Expressed sequence tags (ESTs) are STSs derived from cDNAs.
Determination of the order of nucleotides (base sequences) in a DNA or RNA molecule or the order of amino acids in a protein.
The instrumentation and procedures used to determine the order of nucleotides in DNA.
Sequencing method that involves randomly sequenced cloned pieces of the genome, with no foreknowledge of where the piece originally came from. This can be contrasted with "directed" strategies, in which pieces of DNA from known chromosomal locations are sequenced. Because there are advantages to both strategies, researchers use both random (or shotgun) and directed strategies in combination to sequence the genome.
DNA sequence variations that occur when a single nucleotide (A, T, C, or G) in the genome sequence is altered.
Transfer by absorption of DNA fragments separated in electrophoretic gels to membrane filters for detection of specific base sequences by radio-labeled complementary probes.
The effort to determine the 3D structures of large numbers of proteins using both experimental techniques and computer simulation
Genes occurring in the same order on chromosomes of different species.
Multiple copies of the same base sequence on a chromosome; used as markers in physical mapping.
A nitrogenous base, one member of the base pair AT (adenine-thymine).
The synthesis of an RNA copy from a sequence of DNA (a gene); the first step in gene expression.
A protein that binds to regulatory regions and helps control gene expression.
The full complement of activated genes, mRNAs, or transcripts in a particular tissue at a particular time
A class of RNA having structures with triplet nucleotide sequences that are complementary to the triplet nucleotide coding sequences of mRNA. The role of tRNAs in protein synthesis is to bond with amino acids and transfer them to the ribosomes, where proteins are assembled according to the genetic code carried by mRNA.
A process by which the genetic material carried by an individual cell is altered by incorporation of exogenous DNA into its genome.
An experimentally produced organism in which DNA has been artificially introduced and incorporated into the organism's germ line.
The process in which the genetic code carried by mRNA directs the synthesis of proteins from amino acids.
A class of DNA sequences that can move from one chromosomal site to another.
A nitrogenous base normally found in RNA but not DNA; uracil is capable of forming a base pair with adenine.
A technique used to identify and locate proteins based on their ability to bind to specific antibodies.
The form of an organism that occurs most frequently in nature.
Constructed from yeast DNA, it is a vector used to clone large DNA fragments.