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RGD Glossary of Terms

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This glossary provides definitions for some terms found in our help documentation and other terms that are useful in understanding rat genetics and bioinformatics. It is based largely upon that developed by the Mouse Genome Database and is used with their permission. Terms are defined in a general sense as they apply to eukaryotic genetics; some terms are also defined as they are specifically used in the rat or RGD (e.g., gene). This list will grow as time goes on. If there is a term you think should be included in this list, please contact RGD User Support.

Additional Online Glossaries:

If you find an online glossary that you think should be included here, please contact RGD User Support.

3' (3-prime)
A term that identifies one end of a single-stranded nucleic acid molecule. The 3' end is that end of the molecule which terminates in a 3' hydroxyl group. The 3' direction is the direction toward the 3' end. Nucleic acid sequences are written with the 5' end to the left and the 3' end to the right, in reference to the direction of DNA synthesis during replication (from 5' to 3'), RNA synthesis during transcription (from 5' to 3'), and the reading of mRNA sequence (from 5' to 3') during translation. See the Figure at NHGRI, or the Figure at NCBI.
See also 5' (5-prime), Central Dogma.

3' UTR
3' Untranslated Region. That portion of an mRNA from the 3' end to the position of the last codon used in translation.
See also 5' UTR.

5' (5-prime)
A term that identifies one end of a single-stranded nucleic acid molecule. The 5' end is that end of the molecule which terminates in a 5' phosphate group. The 5' direction is the direction toward the 5' end. Nucleic acid sequences are written with the 5' end to the left and the 3' end to the right, in reference to the direction of DNA synthesis during replication (from 5' to 3'), RNA synthesis during transcription (from 5' to 3'), and the reading of mRNA sequence (from 5' to 3') during translation. See the Figure at NHGRI, or the Figure at NCBI.
See also 3' (3-prime), Central Dogma.

5' UTR
5' Untranslated Region. That portion of an mRNA from the 5' end to the position of the first codon used in translation.
See also 3' UTR.

Ab initio
Formulated without experimental data. Latin. From the beginning.

Accession ID
A unique alphanumeric character string that is used to unambiguously identify a particular record in a database. Examples include RGD IDs, GenBank accession IDs, and PubMed IDs.

ACP
See Allele Characterization Project

Adenine (A)
A purine base that is a component of nucleotides and thus a normal component of DNA and RNA. See the Figure at NHGRI.

Agouti
A characteristic of the coat color of wild-type mice and other mammals in which an individual hair has black pigment (eumelanin) at the tip and the base, and a band of yellow pigment (phaeomelanin) in the middle. This coloration has the effect of softening the visual outline of a mammal in the wild, making it harder to see than an animal of solid color.

Algorithm
A detailed sequence of actions to perform to accomplish some task. Technically, an algorithm must reach a result after a finite number of steps, thus ruling out brute force search methods for certain problems, though some might claim that brute force search was also a valid (generic) algorithm. The term is also used loosely for any sequence of actions (which may or may not terminate).

Alias
In RGD, an alternative symbol or name for one of the objects stored in the database. Typically these are names and symbols which were in use in earlier publications but that have since been updated as the result of nomenclature events. They are listed to allow users to related older publications to the current database information.

Allele
One of the variant forms of a gene, differing from other forms in its nucleotide sequence.

Allele Characterization Project (ACP)
A project undertaken in the laboratory of to characterize the microsatellite marker sizes in 48 commonly used rat strains. This data is housed in RGD, is available on the FTP site and is the basis for such tools as Genome Scanner.

Alternative Splicing
The production of two or more distinct mRNAs from RNA transcripts having the same sequence via differences in splicing (by the choice of different exons).

Amino Acid
A molecule of the general formula NH2-CHR-COOH, where "R" is one of a number of different side chains. Amino acids are the building blocks of proteins. The sixty-four codons of the genetic code allow the use of twenty different amino acids (the primary amino acids) in the synthesis of proteins. Other nonprimary amino acids occur in proteins by enzymatic modification of amino acids in mature proteins, and as metabolic intermediates. See the Figure at NHGRI. For Figures showing the structure of each of the twenty primary amino acids, see Figure 1 and Figure 2 from "Molecular Biology of the Cell" by Alberts et al.

Amino Terminus
A term that identifies one end of a protein molecule. The amino terminus is that end of the molecule which terminates in a free amino group. See the Figure at NHGRI.
See also Amino Acid, Central Dogma.

Amorphic Mutation
A type of mutation in which the altered gene product lacks the molecular function of the wild-type gene. Synonyms: Loss-of-function Mutation, Null Mutation.
See also:

Ancestor
In RGD, this term refers to terms in a hierarchical controlled vocabulary like ones containing Gene Ontology (GO) terms. An "ancestor" of a term is a term any number of levels above it in the hierarchy from which it is descended. For example, the GO term enzyme [GO:0003824] is an ancestor to the GO term alcohol dehydrogenase [GO:0004022].
See also: Children, Parent, Sibling.

Aneuploid
Not euploid.

Annotation
Note added to a document to provide additional needed information.
See also Sequence Annotation.

Anonymous DNA segment
A segment of DNA not known to correspond to a named gene that can be used as a marker in the construction of genetic maps.
See also STS.

ANSI
American National Standards Institute. ANSI is a private, non-profit organization that administers and coordinates the U.S. voluntary standardization and conformity assessment system. The Institute's mission is to enhance both the global competitiveness of U.S. business and the U.S. quality of life by promoting and facilitating voluntary consensus standards and conformity assessment systems, and safeguarding their integrity. For further information, see the web site for ANSI.

Antibody
A protein produced by cells of the immune system that binds to an antigen. See the Figure at NHGRI.
See also Monoclonal Antibody.

Antigen
A protein or other molecule that can elicit an immune response; the antibody protein that is produced binds to the antigen.

Antimorphic Mutation
A type of mutation in which the altered gene product possesses an altered molecular function that acts antagonistically to the wild-type allele. Antimorphic mutations are always dominant or semidominant.
See also:

Antisense
1. In molecular biology, that strand of a DNA molecule whose sequence is complementary to the strand represented in mRNA.
2. In molecular biology, an RNA molecule complementary to the strand normally processed into mRNA and translated.

Apoptosis
Programmed cell death, that is, the death of cells by a specific sequence of events triggered in the course of normal development (e.g., cells between digits in the limb bud) or as a means of preserving normal function (e.g., in response to viral infection).

Approved
With respect to a gene symbol, gene name, allele symbol, or allele name within MGI, an "approved" symbol or name is one that has been assigned by the International Nomenclature Committee.

Associated STS
In RGD, with respect to a gene this is a marker (typically a microsatellite) that has been found to be linked to the gene via linkage analysis and hence has been used as a marker for the postition of this gene in genetic mapping experiments.

Associated QTL
In RGD, with respect to a gene this indicates that this gene has been reported in the literature to be a candidate gene for the listed QTL(s).

Assay
In general, the qualitative or quantitative analysis of a substance. Assay types include:

ATCC
American Type Culture Collection. A large collection of microbial stocks, including microbes containing mammalian DNA segments. See the ATCC Home Page for further information.

Autoradiography
The detection of a unstable isotope that emits radiation by a photographic emulsion. In the case of in situ hybridization, this involves dipping microscope slides in liquid emulsion. In the case of Southern blots, Northern blots, or Western blots, the membrane is placed next to a sheet of X-ray film.

Autosome
Any chromosome that is not a sex chromosome.

BAC
Bacterial Artificial Chromosome. A type of cloning vector derived from the naturally-occurring F factor episome. A BAC can carry 100 - 200 kb of foreign DNA.

BAC/YAC End
BAC/YAC end refers to sequences at the end of foreign DNA inserts in a BAC or YAC. These sequences are a source of STSs to determine the extent of overlap between BACs or YACs and to aid in the alignment of sequence contigs.

Backbone species
The species chromosome used as an anchor to which other chromosomes are compared.

Backcross
A type of genetic cross in which a hybrid strain is crossed to one of the two parental strains.
See also:

Bacteriophage
A virus that infects bacteria.

Base
One of a set of nitrogenous compounds attached to the sugar-phosphate backbone in a nucleic acid. In DNA, the purine bases are adenine (A) and guanine (G), while the pyrimidine bases are cytosine (C) and thymine (T). In RNA, the purine bases are adenine (A) and guanine (G), while the pyrimidine bases are cytosine (C) and uracil (U). See the Figure at NHGRI.

Base Pair
In double-stranded nucleic acids, a "base pair" is the structure formed between two complementary nucleotides by hydrogen bonding. In DNA, adenine (A) pairs with thymine (T) and cytosine (C) pairs with guanine (G). In RNA, adenine (A) pairs with uracil (U) and cytosine (C) pairs with guanine (G). See the Figure at NHGRI.

Bioinformatics
The application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research, particularly in genomics.

Biological Process
Refers to a broad category of biological tasks accomplished via one or more ordered assemblies of molecular functions. Usually there is some temporal aspect to it, although a process event may be essentially instantaneous. It often involves transformation, in the sense that something goes into a process and something different comes out of it. Examples of biological processes included in this category are cell growth and maintenance, signal transduction, pyrimidine metabolism, and cAMP biosynthesis. In the GO Project vocabularies, Biological Process is a primary class of terms. See the GO Consortium site for further information.

Bioinformatics Research Center
Housed at the Medical College of Wisconsin, the BRC concentrates on bioinformatics research in both the wet lab and clinical environments using a combination of database, mathematical and scientific approaches. sample projects include the Rat Genome Database, the PhysGen PGA.

Biosynthesis
Synthesis of chemical compounds by enzymatic processes in living organisms.

Biotin
One of the water-soluble B vitamins. It is useful in molecular biology as a chemical tag on nucleic acid probes or antibodies, because the biotin-scavenging proteins avidin and streptavidin bind biotin with high affinity. These biotin-binding proteins can be coupled to fluorescent dyes, enzymes that can be detected using chromogenic reactions, or colloidal gold, allowing detection of biotin-labeled probes or antibodies on Southern blots, Northern blots, Western blots, or cytological preparations.

BLAST
Basic Local Alignment and Searching Tool. A sequence comparison algorithm optimized for speed, which is used to search sequence databases for optimal local alignments to a query sequence. There is a description of the specific algorithm used, and additional information, at NCBI.

Boolean
Refers to an expression that must evaluate to a value of true or false, named for the British mathematician George Boole. In MGI and other databases, Boolean refers to the kind of logical relationship among search terms. Boolean operators include AND, OR, and NOT. For example, searching for all markers of the type "Gene" on Chromosome 2 is equivalent to identifying the union of the two sets: 1) all markers of the type "Gene" (Type Gene? = true) AND 2) all markers on Chromosome 2 (Chromosome 2 = true).

BRC
See Bioinformatics Research Center.
 

cAMP
Cyclic AMP. A form of the nucleotide adenosine monophosphate that serves as a signaling molecule within and between cells.

Candidate Gene
In RGD, a "candidate gene" is the likely causative gene for a particular phenotypic trait localized to a particular region of the genome either by a QTL or a congenic or consomic strain.Typically the author of a paper makes the assertion that gene X is the candidate gene for trait Y based on the fact that gene X lies within a region shown to be associated with trait Y and the known or suspected involvement of gene X in a pathway or function that might cause trait Y.

Carboxyl Terminus
A term that identifies one end of a protein molecule. The carboxyl terminus is that end of the molecule which terminates in a free carboxyl group. See the Figure at NHGRI.
See also Amino Acid, Central Dogma.

Catabolism
Degradation of chemical compounds into compounds having a lower molecular weight by enzymatic processes in living organisms.

cDNA
Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase.

Cellular Component
Refers to subcellular structures, locations, and macromolecular complexes. Some examples are nucleus, telomere and origin recognition complex. In the GO Project vocabularies, Cellular Component is a primary class of terms. See the GO Consortium site for further information.

Centimorgan
A unit of length in a genetic map. Two loci are 1 cM apart if recombination is detected between them in 1% of meioses.

Central Dogma
The principal statement of the molecular basis of inheritance. In its simplest form:

" DNA makes RNA makes protein."

This means that (generally) genetic information is stored in and transmitted as DNA. Genes are expressed by being copied as RNA ( transcription), which is processed into mRNA via splicing and polyadenylation. The information in mRNA is translated into a protein sequence using a genetic code to interpret three-base codons as instructions to add one of twenty amino acids or to stop translation. See the Figure at Access Excellence or the Figure at NHGRI.

Centromere
In mammalian genetics, the primary constriction of a chromosome separating it into the short arm (p) and the long arm (q). The centromere is the chromosomal region over which the kinetochore is organized. See the Figure at NHGRI.Rat chromosomes have centromeres close to one end and many have essentially no short arm. See the idiogram of the rat karyotype at the Ratmap Database.

Chiasma
The cytologically visible consequence of a reciprocal recombination event in meiosis, observable in the later stage of meiotic prophase. Chiasmata hold homologous chromosomes together prior to anaphase of the first meiotic division.

Children
In RGD, this term refers to terms in a hierarchical controlled vocabulary like ones containing Gene Ontology (GO) terms. A "child" of a term is a term any number of levels below it in the hierarchy that is a descendant of the term. For example, the GO term alcohol dehydrogenase [GO:0004022] is a child of the GO term enzyme [GO:0003824].
See also Ancestor, Sibling.

Chimera
1. An animal formed from two different animals, that is from two different embryonic sources. In mouse genetics, targeted mutations produced in embryonic stem cells are recovered by breeding chimeric mice resulting from the mixture of ES cells with a genetically-distinct blastocyst.
2. A clone containing genomic DNA from nonadjacent genomic segments or cDNA from two different mRNAs (see Cloning Artifact).

Chlorambucil
A chemical mutagen, also called nitrogen mustard.

Chromatin
The nuclear material that makes up chromosomes, consisting of DNA and protein.
See also Euchromatin, Heterochromatin.

Chromogenic
Color-generating. A chromogenic substrate is colorless until acted upon by an enzyme; it then becomes an insoluble pigment.

Chromosome
A structural unit within a eukaryotic nucleus that carries genes. A chromosome consists of a long, continuous strand of DNA and associated proteins. See the Figure at NHGRI.

Chromosome Aberration
1. A chromosome rearrangement.
2. Less commonly, a numerical aberration.

Chromosome Rearrangement
A kind of mutation in which there is a change in the arrangement of the genome into chromosomes; this term usually applies to those changes that are visible cytogenetically.
Classes of chromosome rearrangements include:

Clone
1. A segment of DNA contained within a cloning vector.
2. An organism derived from a founding individual by asexual means that is genetically identical to the founding individual.

Cloning Artifact
A DNA clone whose structure does not accurately represent genomic or mRNA sequence, due to errors in the cloning process. For example, two noncontiguous genomic fragments may be joined by ligation prior to being incorporated into the cloning vector.

Cloning Vector
A DNA construct capable of replication within a bacterial or yeast host that can harbor foreign DNA, facilitating experimental manipulation of that DNA segment.

cM
See centimorgan.

Coding Region
That part of a gene whose sequence is read as codons during translation.
See also Central Dogma, Transcription, Translation, Intron, Exon.

Codominant
One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "a" is said to be codominant with respect to the wild-type allele "A" if the A/a heterozygote fully expresses both of the phenotypes associated with the a/a and A/A homozygotes. An example of codominance is the ABO blood type antigens in humans, where AA individuals are type A, BB individuals are type B, and AB individuals are type AB.
See also Dominant, Recessive, Semidominant.

Codon
Three bases in a DNA or RNA sequence that specify an amino acid or a termination signal (stop codon). See the Figure at NHGRI.
See also Central Dogma.

Coisogenic
A strain that differs from a particular inbred strain at only one locus. A coisogenic strain arises when a mutation occurs in an inbred strain. The coisogenic strain can be propagated by intercrossing heterozygotes to produce homozygotes; if these are nonviable the strain can be maintained by backcrossing heterozygotes to the original inbred strain.
See also the Rules for Nomenclature of Mouse and Rat Strains.

Colloidal Gold
Fine particles of gold (on the order of 5-20 nm diameter) that can be coupled to antibodies or other proteins, allowing the detection of the binding of the labeled proteins by electron microscopy.

Complementary Sequence
A single-stranded nucleic acid that would bind to a given single-stranded nucleic acid by base pairing.

Complementation
The appearance of a wild-type phenotype in an individual that is the hybrid offspring of two mutant individuals homozygous for recessive mutations. Complementation shows that the two parental mutant individuals have mutant alleles of different genes, even if they are phenotypically similar.

Congenic
An inbred strain of rat that contains a small genetic region (ideally a single gene)from another strain, but which is otherwise identical to the original inbred strain. Congenic strains are derived by backcrossing to a parental inbred strain for at least ten generations while selecting for heterozygosity at a particular locus.
See also the Rules for Nomenclature of Mouse and Rat Strains.

Conplastic
Conplastic strains are developed by backcrossing the nuclear genome from one inbred strain into the cytoplasm of another, i.e. the mitochondrial parent is always the female parent during the backcrossing program. The strain designation is NUCLEAR GENOME-mtCYTOPLASMIC GENOME. As with congenic strains, a minimum of 10 backcross generations is required, counting the F1 generation as generation 1.
See also the Rules for Nomenclature of Mouse and Rat Strains.

Conserved synteny
The occurrence of synteny of orthologous genes in two different organisms. Conserved synteny between rat and human does not usually extend over entire chromosomes, with the exception of the X chromosome. See the Virtual Comparative Maps

Consomic
An inbred strain of rat that contains a single entire chromosome from another strain.
See also the Rules for Nomenclature of Mouse and Rat Strains.

Contig
1. A physical map of contiguous genomic DNA assembled using overlapping cloned segments (see STS).
2. A contiguous DNA sequence assembled using overlapping DNA sequences.

Controlled Vocabulary
A restricted set of defined terms allowing the representation of complex information in a database. See Gene Ontology.

Cosmid
A type of cloning vector derived from bacteriophage lambda. A cosmid can carry about 40 kb of foreign DNA.

Cre Recombinase
A site-specific recombination enzyme that recognizes the 34 base pair loxP sequence.

Cross
An experimental mating of two genetically distinct sexually reproducing organisms.
See also:

Cross-hybridization
With respect to nucleic acids, "cross-hybridization" refers to the formation of double-stranded DNA, RNA, or DNA/RNA hybrids by complementary base pairing between two molecules that are not identical in sequence. Cross-hybridization may be observed between nucleic acids derived from orthologous or paralogous genes.

Crossover
A reciprocal recombination event.

Curated
With respect to References, "curated" refers to articles from the literature that have been reviewed by the curation staff at RGD who have read the article and extracted the specific information of interest to RGD which was subsequently loaded into the database.

Cy5
A fluorescent dye used to label DNA probes for FISH or antibodies for immunofluorescence or Western blots.

Cytogenetic
Refers to the correlation of genetic and cytological information through the microscopic analysis of stained preparations of chromosomes, including those from individuals carrying mutations.

Cytogenetic Band
One of the subregions of a chromosome visible microscopically after special staining.

Cytogenetic Map
A type of genetic map relating gene positions to chromosomal banding patterns. The maps are built from relating the positions of genes to cytogenetic markers or by in situ hybridization.

Cytogenetic Marker
1. A structure within a chromosome that is visible by microscopic examination, possibly after special staining methods are used.
2. A chromosome rearrangement that is visible by microscopic examination.

Cytoplasm
That part of a eukaryotic cell that is not the nucleus.

Cytosine (C)
A pyrimidine base that is a component of nucleotides and thus a normal component of DNA and RNA. See the Figure at NHGRI.

Database
A data structure that stores metadata, i.e. data about data. More generally, an organized collection of information.

Database Management System (DBMS)
A collection of computer programs that allow storage, modification, and extraction of information from a database. There are many different types of DBMSs, ranging from small systems that run on personal computers to huge systems that run on mainframes. The following are examples of database applications:
  • computerized library systems
  • automated teller machines
  • flight reservation systems
  • computerized parts inventory systems
  • RGD

Data dictionary
In computer science, a table in a database that stores the names, field types, length, and other characteristics of the fields in the database tables.

DBMS
See Database Management System, above.

Default
In RGD and in computer science in general, a setting or action assumed by a computer program when none is specified by the user.

Degenerate
A term describing one of the qualities of the genetic code, specifically, that some amino acids may be specified by more than one codon.

Deletion
A type of mutation caused by loss of one or more nucleotides from a DNA segment. Deletions can be very large, encompassing many genes and megabases of DNA, to the point of producing a visible cytological abnormality in a chromosome. Small deletions within a gene can alter the reading frame, and thus the amino acid sequence of the encoded protein. See the Figure at NHGRI.

Denaturation
1. The separation of the two strands of a double-stranded nucleic acid caused by treatments that overcome hydrogen bonding, e.g., heat.
2. A usually irreversible change in the conformation of a protein caused by treatments that overcome hydrogen bonding, hydrophobic interactions, or other chemical forces that maintain the structure of proteins, e.g., heat.

Dimorphic
Having two forms.

Diploid
Having twice the chromosome number normally found in a gamete. Normal rats are diploid, having a chromosome set from the maternal gamete (the egg) and a chromosome set from the paternal gamete (the sperm).
See also Haploid.

Directed Sequencing
The sequencing of a large DNA segment through the sequencing of subsegments known to be adjacent.
See also Shotgun Sequencing.

DNA
Deoxyribonucleic acid. The nucleic acid of which genes are made. See the Figure at NHGRI.
See also Central Dogma, Nucleic Acid, and RNA.

DNA Construct
An assembly of DNA sequences made in vitro to serve an experimental purpose.

DNA Mapping Panel
A data set obtained by DNA typing of polymorphic markers in backcrosses of hybrid rats.

DNA Methylation
Attachment of methyl groups (-CH3) to DNA, most commonly at the cytosine bases.

DNA Polymerase
An enzyme that carries out replication.

DNA Segment
A length of DNA.

dNTP
Deoxyribonucleotide triphosphate. A generic term referring to the four deoxyribonucleotides: dATP, dCTP, dGTP and dTTP. See the Figure at NHGRI.

Dominant
One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "A" is said to be dominant with respect to the allele "a" if the A/A homozygote and the A/a heterozygote are phenotypically identical and different from the a/a homozygote.
See also Codominant, Recessive, Semidominant.

Draft Genome Sequence
Sequence of genomic DNA having lower accuracy than finished sequence; some segments are missing or in the wrong order or orientation.
See also Finished Sequence.

Duplication
An additional copy of a DNA segment present in the genome. Gene duplication is the source of paralogous genes. See the Figure at NHGRI.

EC Number
A number assigned to a type of enzyme according to a scheme of standardized enzyme nomenclature developed by the Enzyme Commission of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). EC numbers may be found in ENZYME, the Enzyme nomenclature database, maintained at the ExPASy molecular biology server of the Geneva University Hospital and the University of Geneva, Switzerland.

Electroporation
The use of strong, brief pulses of electric current to create temporary holes in cell membranes, allowing the introduction of DNA.

Electrophoresis
The separation of charged molecules ( DNA, RNA or protein) in an electrical field, usually in a supporting medium such as an agarose or polyacrylamide gel.

Embryonic Stem (ES) Cells
Undifferentiated cells derived from blastocyst-stage embryos. ES cells can differentiate in culture to a number of different cell types.

EMS
Ethyl methanesulfonate (methanesulfonic acid ethyl ester). A chemical mutagen.

Endogenous
Contained within. In mouse genetics, endogenous viruses are those that are integrated into the mouse genome and transmitted to progeny as chromosomal elements.

Endonuclease
A protein that cleaves the phosphodiester backbone of a nucleic acid enzymatically, for example a restriction enzyme.

Enhancer
One of the necessary regulatory elements of a gene. An enhancer is a site on DNA to which a complex of transcription factors bind to affect the availability of the promoter to RNA polymerase. A gene may have multiple enhancers.

Enhancer Trap
A type of DNA construct containing a reporter gene sequence downstream of a promoter that is capable of integrating into random chromosomal locations in rat. Integration of the enhancer trap near an enhancer allows the expression of a new mRNA encoding the reporter gene. The reporter gene is therefore expressed in the cells and developmental stages where the enhancer is active.
See also Gene Trap.

ENU
Ethylnitrosourea; N-ethyl-N-nitrosourea. A chemical mutagen.

Enzyme
A protein (or rarely, RNA) that catalyzes a chemical reaction.

Epigenetic
Refers to factors affecting the development or function of an organism other than the primary sequence of the target genes.
See also Imprinting.

Episome
A plasmid able to integrate into bacterial DNA.

Epistasis
Masking of a phenotypic trait through the action of a mutant allele. For example, albinism (absence of pigment) is epistatic to coat color genes that determine black vs. brown fur.

ES Cells
See Embryonic Stem Cells.

EST
Expressed Sequence Tag. A partial sequence of a randomly chosen cDNA, obtained from the results of a single DNA sequencing reaction. ESTs are used both to identify transcribed regions in genomic sequence and to characterize patterns of gene expression in the tissue that was the source of the cDNA.

Ethidium Bromide
A fluorescent dye that intercalates between base pairs in double-stranded nucleic acids or between bases in single-stranded nucleic acids. Ethidium bromide is commonly used to visualize DNA on agarose gels. See one of the Figures in GXD for an example.

Euchromatin
The part of the genome characterized by relatively high gene density and relative absence of highly repetitive sequences.
See also Heterochromatin.

Euploid
Having a chromosome number that is an integral multiple of the haploid number without segmental duplications or deletions.

Evolution
Change of the genes of a population over time, resulting in new species.

Evolutionary Conservation
The presence of similar genes, portions of genes, or chromosome segments in different species, reflecting both the common origin of species and an important functional property of the conserved element.

Exon
Part of a gene whose sequence is present in a mature mRNA after splicing.
See also Intron.

Expressivity
The relative constancy of the phenotype of individuals of a given genotype. Mutations said to have variable expressivity show a relatively large amount of phenotypic variation among individuals having the same genotype.
See also Penetrance.

Field
In a relational database, an item of information, such as a chromosome number, or the centimorgan length on a genetic map. Some fields are numeric, while others are textual; some are long, while others are short. In addition, every field has a name, called the field name. In database management systems, a field can be required, optional, or calculated. A required field is one in which you must enter data, while an optional field is one you may leave blank. A calculated field is one whose value is derived from some formula involving other fields. You do not enter data into a calculated field; the system automatically determines the correct value. A collection of fields is called a record.

Finished sequence
Sequence of genomic DNA in which: a) bases are identified to an accuracy of no more than one error in 10,000 bases, b) there is no ambiguity about the order or orientation of any segment, and c) there are few if any gaps.
See also Draft Genome Sequence.

FISH
Fluorescent in situ hybridization. A method for determining the cytogenetic location of a cloned segment of DNA. The DNA is labeled with a fluorescent dye and hybridized to a cytological preparation of chromosomes that has been denatured to allow nucleic acid hybridization between chromosomal DNA and the probe. The site of hybridization is determined by fluorescent microscopy. See the Figure at NHGRI.
See also In situ Hybridization.

Fluorescence
Emission of secondary light generated by excitation by ultraviolet light, a beta particle or a gamma ray.

Fluorography
The detection of radiation or of a fluorescent compound by secondary light that was generated by the excitation of a "fluor" or a screen by light, a beta particle or a gamma ray.

Floxed
Refers to a DNA construct in which a gene or gene segment is flanked by loxP sites in the same orientation; Cre recombinase excises the segment between the loxP sites.

FTP
File Transfer Protocol. A method for transferring files to and from remote computer systems. See the RGD FTP site for available datasets that can be downloaded.

Frameshift
A type of mutation in which there is an insertion or deletion that changes the reading frame.

Gain-of-function Mutation
A type of mutation in which the altered gene product possesses a new molecular function or a new pattern of gene expression. Gain-of-function mutations are almost always dominant or semidominant.
See also:

Gamete
One of the differentiated cells that is a product of meiosis. In animals, sperm or egg cells.

GDB
Genome Database, a database of human genes. Links to GDB are returned when human genes are displayed, for example in the results of a query using the Mammalian Homology Query Form. See the Central Node at GDB by clicking this link.

GenBank
The database of nucleic acid sequences at NCBI.

Gene
The basic unit of heredity; a portion of DNA that (usually) codes for a protein product.
See also Central Dogma.
In RGD, "gene" may be used to refer to any of the following:

  1. A locus in the cytoplasmic or nuclear genome characterized by an altered phenotype or by an effect on an inserted reporter gene, such as a gene trap or enhancer trap.
  2. A locus in the cytoplasmic or nuclear genome that is necessary and sufficient to express the complete complement of functional products derived from a unit of transcription.
  3. A locus in the cytoplasmic or nuclear genome identified by hybridization to a nucleic acid segment derived from a non-mouse species, where the segment used as probe represents some portion of a functional unit of transcription in the cytoplasmic or nuclear genome of the non-mouse species.
  4. An exon-encoding segment of the germ-line nuclear genome located within a region that undergoes somatic rearrangement.
  5. A locus in the cytoplasmic or nuclear genome that is within an intron of (but not, itself, an exon of) a unit of transcription, which gives rise to a functional product upon transcript processing of the host unit.

Gene Complex
A number of apparently functionally or evolutionarily related loci that are genetically closely linked. Alternative states of complexes are referred to as haplotypes rather than alleles. See H2 for an example.

Gene Conversion
A type of nonreciprocal recombination event in which a recipient strand of DNA receives information from another strand having an allelic difference. The recipient strand has its original allele "converted" to the new allele as a consequence of the event.

Gene Expression
Transcriptional activity of a gene resulting in one or more RNA products and, usually, following translation, one or more protein products.

Gene Family
A group of paralogous genes.

Gene Name
In RGD, a "gene name" is a word or phrase that uniquely identifies a gene. The gene name has an abbreviation that is the gene symbol.
See also Gene Symbol.

Gene Ontology (GO)
A set of controlled vocabularies used to describe biological features within a specified domain of biological knowledge. See the GO Consortium site for further information.

Gene Product
1. A protein molecule that is the product of the expression of a gene, through which the gene influences development or metabolism.
2. An RNA molecule that is the product of the expression of a gene, especially those cases in which the RNA molecule is not translated (see tRNA, rRNA).

Gene Symbol
As used in RGD, a "gene symbol" is a unique abbreviation for the gene name.
See also Gene Name.

Gene Trap
A type of DNA construct containing a reporter gene sequence downstream of a splice acceptor site that is capable of integrating into random chromosomal locations in mouse. Integration of the gene trap into an intron allows the expression of a new mRNA containing one or more upstream exons followed by the reporter gene. The reporter gene is therefore expressed in the same cells and developmental stages as the gene into which the gene trap has inserted.
See also Enhancer Trap.

Genetic Code
The relationship of the sixty-four nucleic acid codons to the twenty primary amino acids. See the Figure for the standard genetic code.
See also Central Dogma.

Genetic Map
A map showing the position of genes or markers on a chromosome. See Physical Map, Linkage Map, and Cytogenetic Map.

Genome
The total genetic information of a cell or organelle. In eukaryotes, "genome" usually refers to nuclear DNA rather than to mitochondrial or chloroplast DNA.

Genomics
The comprehensive study of whole sets of genes and their interactions rather than single genes or proteins.

Genotype
A description of the genetic information carried by an organism. In the simplest case, "genotype" may refer to the information carried at a single locus, as in A/A, A/a, or a/a.

Germ Line
Cells of an animal that give rise to gametes.

Guanine (G)
A purine base that is a component of nucleotides and thus a normal component of DNA and RNA. See the Figure at NHGRI.

Haploid
Having the chromosome number normally found in a gamete.
See also Diploid.

Haploinsufficient
A description applied to a gene that produces a mutant phenotype when present in a diploid individual heterozygous for an amorphic allele.

Haplotype
One of the alternative forms of the genotype of a gene complex. This term is applied to gene complexes rather than the term allele, which refers to one of the forms of a single gene. See H2 for an example.

Hemizygous
The state of a gene present in only one copy in a diploid cell, such as a gene on the X chromosome in a male mammal, or a gene whose homolog has been deleted.

Heterochromatin
1. The part of the genome characterized by relatively low gene density and the presence of highly repetitive sequences. Heterochromatin is more highly condensed than euchromatin.
2. The X chromosome that is highly condensed in a mammalian cell that has undergone X inactivation. The inactive X chromosome resembles heterochromatin as defined above with respect to their state of condensation and genetic inactivity, although there is no change in the DNA sequence as aconsequence of inactivation.
See also Euchromatin.

Heterogametic
Producing two types of euploid gametes with respect to chromosomal content. This term is applied to one of the sexes in species with chromosomal sex determination; in mammals, males are heterogametic.
See also Homogametic, X chromosome, Y chromosome.

Heteropolymer
A polymer composed of different subunits. Some multimeric proteins are normally heteropolymers. Heteropolymers can also be made experimentally, using subunits derived from different species, as a test of homology. Formation of a functional multimeric protein product using subunits from different species is a demonstration of homology.

Heterozygote
An individual that is heterozygous.

Heterozygous
Producing two gamete types with respect to at least one gene (A/a).

Heterozygosity
The state of being heterozygous.

Hierarchical
A description of a structure in which things are organised into a hierarchy.

Hierarchy
An organisation with few things, or one thing, at the top and with several things below each other thing. An inverted tree structure. An example in computing is a directory hierarchy where each directory may contain files or other directories. In RGD, it refers to terms in a controlled vocabulary such as ones containing Gene Ontology (GO) terms.
See also: Ancestor, Child, Parent, Sibling.

Homogametic
Producing a single type of euploid gametes with respect to chromosomal content. This term is applied to one of the sexes in species with chromosomal sex determination; in mammals, females are homogametic.
See also Heterogametic, X chromosome, Y chromosome.

Homolog
1. One of a pair of chromosomes that segregate from one another during the first meiotic division.
2. A gene related to a second gene by descent from a common ancestral DNA sequence. The term, homolog, may apply to the relationship between genes separated by the event of speciation (see ortholog) or to the relationship betwen genes separated by the event of genetic duplication (see paralog).
3. A morphological structure in one species related to that in a second species by descent from a common ancestral structure.

Homologous recombination
1. Reciprocal recombination between DNA sequences that have a high degree of similarity.
2. Reciprocal recombination between DNA sequences that have a high degree of similarity and that are located at corresponding positions on homologous chromosomes.

Homology
1. The relationship of any two characters that have descended from a common ancestor. This term can apply to a morphological structure, a chromosome or an individual gene or DNA segment.
2. In RGD, assertions of homology imply presumed orthology.  See the Figure at NCBI.
See also: Homolog, Orthology, Paralogy.

Homozygote
An individual that is homozygous.

Homozygous
Producing only a single gamete type with respect to one or more genes (A/A).

Homozygosity
The state of being homozygous.

Horseradish Peroxidase
An enzyme for which a chromogenic substrate exists, commonly used as a label for antibodies.

HTML
Hypertext Markup Language. An authoring language for creating and sharing electronic documents over the Internet. This document is written in HTML.
You can view the HTML source code for this document by:
  • selecting Page Source from the View menu in Netscape Navigator
  • selecting Source from the View menu in Microsoft Internet Explorer.

Hybrid
The offspring of two sexually-reproducing homozygous individuals of different genotypes.

Hybridization
With respect to nucleic acids, "hybridization" refers to the formation of double-stranded DNA, RNA, or DNA/RNA hybrids by complementary base pairing.

Hydrophilic
Literally, "water-loving"; polar or charged compounds that are soluble in water.

Hydrophobic
Literally, "water-fearing"; nonpolar compounds that are immiscible with water. The side chains of some amino acids are nonpolar, and hence protein sequences rich in these amino acids tend to locate to the interior of the protein in its native state, away from the solvent.

Hypertext
Text displayed electronically with embedded links to other text or to images, sounds, movies or other multimedia content. This document is an example of hypertext.

Hypermorphic Mutation
A type of mutation in which the altered gene product possesses an increased level of activity, or in which the wild-type gene product is expressed at a increased level.
See also:

Hypomorphic Mutation
A type of mutation in which the altered gene product possesses a reduced level of activity, or in which the wild-type gene product is expressed at a reduced level.
See also:

Identity
In comparison of nucleic acid or protein sequences, the extent to which two sequences have the same nucleotide or amino acid at equivalent positions, usually expressed as a percentage.
See also Similarity.

Idiogram
An idealized drawing. See the idiogram of the rat karyotype at the Ratmap database.

I.M.A.G.E. Consortium
Integrated Molecular Analysis of Genome Expression Consortium. A collection of a large number of partially sequenced cDNAs. See the homepage of the I.M.A.G.E. Consortium for further information.

Immunofluorescence
The detection of an antigen in cytological preparations by using a fluorescent-labeled antibody.

Immunohistochemistry
A method of detecting the presence of specific proteins in cells or tissues. Fixed cells or tissue on a microscope slide, made permeable if necessary with a detergent, are reacted with a primary antibody to the specific protein to be assayed. The preparation is then treated with a secondary antibody that has been coupled to an enzyme and which is directed against the primary antibody (e.g., goat anti-rabbit antibody). The preparation is then treated with a chromogenic substrate. Microscopic examination reveals the presence of staining, and hence of the specific protein to be detected. See one of the Figures from GXD for an example.

Immunological Cross-reaction
The binding of an antibody to a protein that is different from the protein against which the antibody was raised. This result demonstrates sequence or structural similarity between the two proteins and can be evidence of homology.

Imprinting
An epigenetic modification of genes that identifies a given gene as having been inherited from the maternal or paternal parent. In mammals, some genes are expressed primarily from the maternally-inherited or paternally-inherited alleles as a consequence of imprinting.

Inbred Strain
A strain that is essentially homozygous at all loci. In rats and mice, a strain produced from brother-sister matings for at least 20 sequential generations. F344 is a widely-used inbred strain of rat.
See also the Rules for Nomenclature of Mouse and Rat Strains.

Incross
A cross between two identically homozygous individuals (BN/N x BN/N).
See also:

Informatics
The study of the application of computer and statistical techniques to the management of information. In genome projects, informatics includes the development of methods to search databases quickly, to analyze DNA sequence information, and to predict protein sequence and structure from DNA sequence data.

Inhibitor
A chemical compound that has the effect of blocking or slowing an enzymatic reaction.

Insertion
A type of mutation in which one or more nucleotides is inserted into a DNA sequence. Small insertions within a gene can alter the reading frame, and thus the amino acid sequence of the encoded protein.

In silico
Computationally, as opposed to in vitro or in vivo.

Inducible gene targeting
a method of gene targeting that allows the inducible inactivation (or activation) of a targeted gene by experimental manipulation, such as administration of a drug. Example: Cre recombinase is a site-specific recombinase that catalyzes the excision of DNA flanked by lox recognition sequences. Since the promoter for Cre expression is sensitive to the drug interferon, targeted deletion is inducible.

Insertional mutagenesis
insertion of one or more copies of a transgene into the host genome.

Insertional mutation
a mutation caused by the insertion of at least one extra nucleotide base in a DNA sequence.

In situ Hybridization
A method of detecting the presence of specific nucleic acid sequences within a cytological preparation. A DNA or RNA probe is labeled radioactively or chemically and hybridized to a cytological preparation to detect RNA or to a denatured cytological preparation to detect DNA. The hybridization is detected by autoradiography (for radioactive probes) or by chromogenic reactions or fluorescent (for chemically-labeled probes). See one of the Figures from GXD for an example.
See also FISH.

Intercross
A cross between two identically hybrid individuals (A/a X A/a).
See also:

Intergenic
Between genes.

Intron
Part of a gene whose sequence is transcribed but not present in a mature mRNA after splicing.
See also Exon.

In utero
A reaction, process or experiment on an embryo in a living mammal rather than in vitro.

Inversion
A type of mutation in which a length of DNA is broken in two positions and repaired in such a way that the medial segment is now present in reverse order. Inversions range in size from those large enough to be visible cytogenetically to those involving only a few base pairs.

In vitro
Literally, "in glass", meaning a reaction, process or experiment in a metaphorical test tube rather than in a living organism.
See also In vivo, In silico.

In vivo
Literally, "in life", meaning a reaction, process or experiment in a living organism rather than in a metaphorical test tube.
See also In vitro, In silico.

Isogenic
Characterized by essentially identical genes. Identical twins are isogenic.

Karyotype
A description of the condensed chromosomes of a eukaryote as they are seen at metaphase. Additional details are revealed by a variety of staining techniques that produce banded chromosomes. See the idiogram of the rat karyotype at the Ratmap database.

kb
Kilobase. Unit of DNA or RNA sequence equal to 1000 nucleotides.

Kinetochore
A stucture formed adjacent to the centromere of a condensed chromosome that allows the chromosome to attach to microtubules of the meiotic or mitotic spindle.

Knock-in
A casual term for a type of targeted mutation in which an alteration in gene function other than a loss-of-function allele is produced.
See also Knock-out.

Knock-out
A casual term for a type of targeted mutation in which an amorphic ( loss-of-function) allele is produced.
See also Knock-in.

Library
In molecular biology, a "library" is a complex mixture of recombinantDNA molecules in a suitable cloning vector representing either the entire genome of an organism (a genomic library) or the messenger RNA populationof a whole organism, cell type, or tissue type (a cDNA library).

Ligate
In molecular biology, to join two separate DNA or RNA segments to form a single DNA or RNA molecule enzymatically.

Ligand
A molecule that binds to a receptor protein.

Linkage
The property displayed by two genes that do not segregate independently of each other. Genes that are linked are on the same chromosome.

Linkage Analysis
The construction of a linkage map through the analysis of meiotic recombination frequencies between pairs of genes.

Linkage Disequilibrium
The condition in which the frequency of a particular haplotype for two loci is significantly greater or less than that expected from the product of the observed allelic frequencies at each locus. .

Linkage Map
A type of genetic map showing relative gene positions based on meiotic recombination frequencies. The unit of measurement is the centimorgan.

Locus
Literally, "place", plural 'loci'. The location of a gene or set of genes on a chromosome.

LOH
Loss of heterozygosity.

Loss-of-function Mutation
A type of mutation in which the altered gene product lacks the molecular function of the wild-type gene. Synonyms: Amorphic Mutation, Null Mutation.
See also:

Loss of Heterozygosity
A genetic event that can occur in the dividing cells of a diploid organism heterozygous for one or more markers, in which a daughter cell becomes homozygous or hemizygous for one or more alleles through mitotic recombination, deletion, or gene conversion. "Loss of heterozygosity (LOH)" events are often important steps in tumor progression. See the animation of this concept by Robert J. Huskey at the Univeristy of Virginia.

loxP Sequence
A 34 base pair DNA sequence recognized by the site-specific recombination enzyme Cre.

Marker
  1. Any biological feature that can be positioned with respect to other features on a chromosome, by genetic, physical or other mapping methods. For example, a gene, anonymous DNA segment, mutation, or phenotype.
  2. A feature that distinguishes a particular biological state. For example, an expression profile of natural or engineered genes, or a characteristic morphology.

Megabase
Unit of DNA or RNA sequence equal to one million nucleotides.

Meiosis
A pair of nuclear divisions forming gametes wherein the number of chromosomes is reduced from the diploid to the haploid number; resulting cells normally contain one member of each pair of homologous chromosomes.

Membrane
1. A phospholipid bilayer that forms a hydrophobic barrier around and within cells.
2. A sheet of nylon, nitrocellulose, or similar material that is used to create a replica of a gel for Southern blots, Northern blots, or Western blots.

Mendelian
1. That type of inheritance in which a specific trait is affected by a set of alleles of a single gene.
2. That type of inheritance in which genetic information is transmitted by one or more nuclear genes, as opposed to cytoplasmic or epigenetic mechanisms.

Metadata
Data about data. In data processing, metadata is definitional data providing information about or documentation of other data managed within an application or environment, for example, data about a) data elements or attributes (name, size, data type, etc.), b) records or data structures (length, fields, columns, etc.) and c) data (where located, how associated, what ownership, and so on). Metadata may include descriptive information about the context, quality and condition, or characteristics of the data.

MGD
Mouse Genome Database. One of several databases integrated into MGI, containing data on the genes of the mouse.

MGI
Mouse Genome Informatics. The collection of bioinformatics projects at The Jackson Laboratory including MGD, GXD, and MTB.

Microarray
An array of hundreds or thousands of spots containing specific DNA sequences for the analysis of gene expression by hybridization. Microarrays are used to detect changes in gene expression by comparing radioactively- or chemically-labeled cDNA prepared from the total mRNA of an experimental sample to that of a control sample. The relative intensity of the signal corresponding to each spot in the microarray reveals whether the expression of a particular gene is increased, decreased, or unchanged in the experimental mRNA sample compared to the contol mRNA sample.

Microsatellite Marker
A short (up to several hundred base pairs) segment of DNA that consists of multiple tandem repeats of a two or three base-pair sequence. Microsatellites expand and contract (that is, add or remove repeat units) with a frequency much higher than other types of mutations, making them useful as polymorphic markers in closely related mouse strains. Also known as SSLP, STR, SSR.

Microtubule
A cytoskeletal element of eukaryotic cells that is a long, generally straight, hollow tube with an external diameter of 24 nm, consisting of polymerized monomers of tubulin. Microtubules make up the bulk of the spindle.

MIT marker
One of a large series of microsatellite markers in the rat and mouse, developed at the Massachusetts Institute of Technology. These markers have been used to align the physical and linkage maps in both the rat and mouse. It should be noted that there is no relationship between the two sets of markers, D1Mit1 in Rat is a different marker (different sequence, location, primers) to D1Mit1 in Mouse.

Mitochondria
The organelles that generate energy in eukaryotic cells. Mitochondria have their own genome encoding a subset of the proteins found in mitochondria; the mitochondrial genome uses an alternate genetic code.

Mitochondrial gene
A gene contained within the mitochondrial genome of a eukaryote, transmitted independently of the nuclear genome. The mitochondrial genome is transmitted maternally (from the female parent).

Mitosis
The division of the replicated chromosomes of a eukaryotic cell into two daughter nuclei that are genetically identical to that of the original cell. See the Figure at NHGRI.

Mobile Genetic Element
A DNA segment carried within the chromosomes that is capable of moving to new sites in the genome other than by mutation.
See also Retrotransposon.

Molecular Function
Refers to the tasks or activities characteristic of particular gene products. For example, transcription factor refers to one of a number of proteins performing similar tasks. In the GO Project vocabularies, Molecular Function is a primary class of terms. See the GO Consortium site for further information.

Monoclonal Antibody
An antibody produced by cultured cells that have their origin in a single antibody-producing cell, and which is therefore of a single molecular type, in contrast to the polyclonal antibodies normally found in the serum of an immunized animal.

Mutation
a heritable change in DNA sequence resulting from mutagens. Various types of mutations include frame-shift mutations, missense mutations, and nonsense mutations.

Monosomy
The condition of having a single chromosome of a particular type; lacking a homologous chromosome. Normal male mice are monosomic for the X chromosome.
See also Trisomy.

Mosaic
An individual consisting of cells of two or more genotypes. One example is that of a normal female mammal heterozygous for different alleles of X-chromosome genes; because of the process of X-inactivation, such females consist of two cell types, each with a different X chromosome inactivated.This is an unusual example because there is no actual difference in genotype between the two cell types, but rather there is an epigenetic difference.

mRNA
Messenger RNA. An RNA molecule that is the product of transcription of a gene, after that molecule has been spliced and polyadenylated, that can be translated into a protein product. See the Figure at NHGRI.
See also Central Dogma.

Mutagen
An agent that causes mutations.

Mutant
1. A term applied to a gene or phenotype altered by mutation.
2. An individual carrying a mutation.

Mutation
1. The process through which genes undergo a structural change.
2. Any permanent change in DNA, i.e., in its nucleotide sequence. Examples include chromosome rearrangements and point mutations.
See also:

Name
As used in RGD, a "name" is a word or phrase that uniquely identifies an object. The object typically also has an abbreviation that is the symbol. For example: Ace is a gene symbol, Angiotensinogen Converting Enzyme is the corresponding name for that gene. Most other objects have names and symbols

NCBI
National Center for Biotechnology Information.

Neomorphic Mutation
A type of mutation in which the altered gene product possesses a novel molecular function or a novel pattern of gene expression. Antimorphic mutations are usually dominant or semidominant.
See also:

Neonatal
Newborn.

NHGRI
National Human Genome Research Institute.

NIH
National Institutes of Health.

NHLBI
National Heart Lung and Blood Institute.

Nomenclature
The process of reviewing the names and symbols of objects stored in the database to ensure consistency both within a single database and ideally between databases holding information about homologs in a different organism. A change to the nomenclature of an object within RGD is recorded within the database and available at the end of each object's report or by using the nomenclature query form. There are nomenclature guidelines available defining how this process is undertaken in Rat, Mouse and Human.

Nomenclature Event
A change in the status of the nomenclature for an object in RGD. For example, a change in gene symbol from Abc to Abc1 would be a nomenclature event, the old symbol (Abc) would have been withdrawn, the new symbol (Abc1) would have been approved.

Noncoding RNA
An RNA molecule that functions structurally or catalytically (see ribozyme) without being translated. Noncoding RNAs lack conserved