Gramene Acronyms and Abbreviations

 The following is a list of acronyms and abbreviations currently used in Gramene that have been defined for users. In the future, this list will grow to also include definitions of the biological and module-specific terms used in Gramene.

A   B   C   D   E   F   G   H   I   J   K   L   M   N   O   P   Q   R   S   T   U    V    W    X    Y    Z

Select a letter to view terms in that section

Additional Online Biological, Bioinformatic and Biotechnology Glossaries:
A


Abiotic stress
Traits related to stresses from abiotic environment, e.g., water, light, temperature, or chemical.


Abstract
A one-paragraph introduction to the main themes of an article.


Accession number
Identifier assigned to a sequence that is unique to the particular database.


ARS Agricultural Research Service
The U.S. Department of Agriculture's main in-house scientific research agency.


Alias -
Synonym or other name by which a feature may be known.


Allele
Alternate form of the same gene. Two or more different genes occupy the same position (locus) on a chromosome, one of which may have dominance over the other.


Allelic diversity
Polymorphism or variations of different alleles with a locus.


Allelic interaction
The interaction between different alleles within a locus.


Allogamous
Cross-pollinating (plant)


Amino acid
Organic compounds that generally contain an amino (-nh2) and a carboxyl (-cooh) group. Twenty alpha-amino acids are the building blocks of proteins.


Amphibolic
Metabolic pathways that are both catabolic and anabolic.


Amplification
An increase in the number of copies of any particular piece of DNA.


AFLP - Amplified Fragment Length Polymorphism
Marker type used for strain identification.


Anabolic
The synthetic phase of metabolism that yields nucleic acids, proteins, lipids and carbohydrates.


Anatomy
Traits directly measuring plant parts such as root, stem or leaf. Structural makeup.


Anatomy Location
Site of anatomical feature.


Aneuploids
Organisms that possess or that lack 1 extra chromosome in their chromosome set.


Annotate, annotation, annotated
A diagram with a series of explanatory notes.


Arabidopsis
Small flowering plant that is widely used as a model organism in plant biology because of the small gene size and rapid life cycle.


TAIR - Arabidopsis Information Resource, (The)
TAIR Provides a comprehensive resource for the scientific community working with Arabidopsis thaliana.


AGI - Arizona Genomics Institute
AGI


Artificial chromosome
Large fragments of DNA from one species spliced into a host species in order to make many copies of it. Allows large segments of DNA to be cloned.


Artificial selection
Selection imposed by a breeder. Selective Breeding.


Assay
The determination of the amount of a particular constituent of a mixture.


Association
The occurrence together of two or more phenotypic characteristics more often than would be expected by change. To be distinguished from linkage.


Autogamous
Self-pollinating (plant)


ANB - Automated name based

TOP


B
BAC end sequence
Marker type.


Back mutation
A mutation that causes a mutant gene to regain its wild-type sequence.


BAC - Bacterial artificial chromosome
"Large segments of DNA from another species spliced into bacteria and cloned. "


bp - Base pair
Represents a unit of length or the position in a double stranded nucleotide sequence. Two nitrogenous bases (adenine and thymine or guanine and cytosine). Bonds between base pairs forms the double-helix shape of DNA.


BLAST - Basic Local Alignment Search Tool
A very fast search algorithm developed by Altschul et al. (1990) used for sequence similarity searching.


Biochemical assays
Biochemical and physiological traits, e.g., enzyme activity.


Bioinformatics
Describes any use of computers to handle biological information; the use of computers to characterise the molecular components of living things.


Biological process
A phenomenon marked by changes that lead to a particular result, mediated by one or more gene products, such as mitosis or purine metabolism.


Biotic stress
Stresses caused by biological effects such as pests and pathogens.


BLASTN
A BLAST program that compares a nucleotide query sequence against a nucleotide sequence database.


BLASTP
A BLAST program that compares an amino acid query sequence against a protein sequence database


BLASTX
A BLAST program that compares a nucleotide query sequence translated in all reading frames against a protein sequence database


Breakpoint interval
Interval between chromosomal breakpoints


Breeding line
Material obtained by plant breeders as intermediate products.


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C
CAN Library
A collection of cloned DNA fragments.


Candidate gene
A gene, located in a chromosome region suspected of being involved in a disease, whose protein product suggests that it could be the disease gene in question.


Catabase (Please double check whether correct)
A structured file of information or a set of logically related data stored and retrieved using computer-based means.


Catabolic
Metabolic pathway; degradation of large molecules into smaller ones with the release of chemical energy


cDNA - cDNA
DNA synthesized from an RNA template by the enzyme reverse transcriptase; can act as a probe


cDNA library
Represents the structural genes active in a specific cell type at a specific time


Cellular compartment, component ?
The part of a cell of which a gene product is a component; for purpose of GO, includes the extracellular environment of cells; a gene product may be a component of one or more parts of a cell; this term includes gene products that are parts of macromolecular complexes, by the definition that all members of a complex normally copurify under all except extreme conditions.


cM - Centimorgan
A unit of distance between genes on chromosomes, one cM equals about 1 million base pairs.


Centromere
Specialized region of a chromosome. A structure found in chromosomes, the centromere consists of fibres and holds together two chromatids to create the chromosome as a whole, the centromere is difficult to sequence.


Cereal
"Those grasses which yield edible seeds commonly recognised as food grains. "


Chromosome
The self-replicating genetic structures of cells containing the cellular DNA complexed with proteins. Contains genes.


Citation
A specific reference.


Clone
Genetically identical cells or organisms all derived from a single ancestor by asexual or parasexual methods.


Cloning
"Production of large numbers of identical DNA molecules (generally a gene) "


CDS - Coding sequence


Codon
Three bases in a DNA or RNA sequence which specify a single amino acid.


CSHL - Cold Spring Harbor Laboratory;
CSHL The Laboratory has research programs focusing on cancer, neurobiology, plant genetics, genomics and bioinformatics, and a broad educational mission, including the recently established Watson School of Biological Sciences.


Colinearity
Conserved gene order within a chromosomal segment between different species.


CMap - Comparative map viewer
A tool used to compare synteny of of known maps of same or different species.


Complete Linkage
The same genes are linked on the same chromosome; no crossing over.


CVS - Concurrent Versions System
A source code management tool that allows multiple users to edit the same file.


Conjugation
Parasexual process in which the genetic information from one bacterium is transferred to and recombined with that of another bacterium.


Contig -
"Group of clones representing overlapping regions of the genome. Important because they provide the ability to study a complete, and often large segment of the genome. "


Continuous trait
Exhibit a wide range of possible phenotypes that can be expressed with a quantitative distribution. Indicative of complex inheritance and are controlled by many genes with small effects that are influenced by the environment and interaction with other loci.


CSREES - Cooperative State Research, Education and Extension Service
An agency within the U.S. Department of Agriculture


Core collection
Represents, with a minimum number of repetitiveness, the genetic diversity of a crop species and its wild relatives, through a subset of accessions which contains or is believed to contain most of the known genetic diversity.


Correspondence -
Aline that connects features on one map to features on another map.


Correspondence Matrix
Representation of colinearity between different maps and map sets, showing the number of associations between said maps.


Cross over
The exchange of pieces of DNA during the formation of eggs and sperm. Recombination of alleles increases the potential of genetic diversity. Cross over frequency is proportional to the distance separating loci along the chromosome, i.e., the further apart, the more recombination.


Cross reference
Links to another database


Cultivar -
Variety name from which the sequence was derived. Assemblage of cultivated plants which is clearly distinguished by any character (morphological, physiological, cytological, and/or chemical) and which, when reproduced, retains its distinguishing characters


Curated database -
Database providing information collected and compiled from many sources.


Cytochrome
"Any of several intracellular hemoprotein respiratory pigments that are enzymes functioning in electron transport as carriers of electrons. "


Cytogenic Map
"The visual appearance of a chromosome when stained and examined under a microscope. Particularly important are visually distinct regions, called light and dark bands, which give each of the chromosomes a unique appearance. This feature allows a person's chromosomes to be studied in a clinical test known as a karyotype, which allows scientists to look for chromosomal alterations. "

Cytoplasms
Protoplasm of cell minus the nucleus


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D
dd - dd
On the maize FPC map, identifies anonymous EST clusters assembled by DuPont


Deduce
To conclude something based on certain premises.


Deletion map -
Type of low-resolution physical map. It is constructed using a “genome deletion panel” which consists of a series (or collection) of mutant lines containing sub-chromosomal deletions and a reference wild-type line. Markers can be mapped onto the genome using this panel (by Southern hybridization or by PCR) based on the presence or absence of signal when comparing the banding pattern in the mutants lines with the pattern in the wild type. Linked markers (present in the same deleted region) share the same banding pattern (presence or absence) on the deletion panel.


Deletion mutant
Loss of DNA from a Chromosome - all or part of a gene.


DNA - Deoxyribonucleic Acid
Primary carrier of genetic information. A double-stranded molecule held together by weak bonds between base pairs of nucleotides.


Derivation -
Shows every possible path back from the selected term to the root term; depicts a term’s lineage.


Development -
Traits related to plant and plant part development. Also includes maturity related traits.


[d] - Develops from:
Used to describe the relationship between a child term that develops from its parent term. For example in the following image: the root hair develops from trichoblast.


Diploid
Two homologous chromosomes connected by the centromere.


Diploid number - (2n)
The number of chromosomes in most cells (except the gametes) .


Discontinuous trait
The different phenotypes are distinct and each phenotype can be easily separated from all other phenotypes, based on qualitative characteristics


Diversity
Suggest delete as too broad.


DNA Polymerase
Enzyme that catalyzes the synthesis of DNA.


Downstream gene
"Portions of DNA or RNA that are more remote from the initiation sites and that will therefore be translated or transcribed later. "


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E
Emasculation
Genetic male sterility


Ensembl - Ensembl
A joint project between EMBL-EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on metazoan genomes.


Environmental factors -
Description of environmental conditions for a particular study; including temperature, light quality and intensity, moisture, nutrients, etc.


Enzyme
Protein or complex of proteins that catalyses a specific chemical reaction without itself being destroyed


EC - Enzyme Commision
EC Enzyme Commission


Enzyme Commission Number
An accession or an enzyme classification number assigned by the Enzyme Commission.


Eukaryote
Cell with nuclear membrane and organelles.


EMBL - European Molecular Biology Laboratories
Nucleotide sequence database.


EMBL - European Moledular Biology Labs
The EMBL Nucleotide Sequence database is a comprehensive database of DNA and RNA sequences. Produced in collaboration with GenBank and the DNA Database of Japan (DDBJ).

Evidence
Research cited as basis for decisions.


Exon
The sequences of the primary RNA transcript (or the DNA that encodes them) separated by introns. DNA sequence that is retained and expressed.


EST - Expressed sequence tag
Sequence tagged sites (STS)derived from cDNAs.


Expression
see "Gene expression"


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F
FASTA (pronounced FAST-Aye)
FAST-All, FASTA A computer program based on the method of W. Pearson and D. Lipman [Proc. Natl. Acad. Sci. U.S.A. 85, 2444-2448 (1988)] to search simultaneously both protein and DNA sequence databases. This program achieves a high level of sensitivity for similarity searching at high speed.


Feature
a named position on a map


FTP
File transfer protocol


FPC
Finger Print Contigs. See FPC


Flanking
extending on either side of a specific locus


Flat files
text documents that are completely unstructured


Functional genomics
Discovery of how genes function, how their functions combine with those of other genes and for what purpose.


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G
GenBank -
software The public NIH genetic (DNA)sequence database, an annotated collection of all publicly available DNA sequences.


Gene
Unit of inheritance, a set of features on the genome that can produce a functional unit. unit of inheritance that occupies a specific locus on a chromosome, the existence of which can be confirmed by the occurrence of different allelic forms.


Gene expression
"The process by which proteins are made from the instructions encoded in DNA. "


GI - Gene indice
TIGR gene indices


Gene interaction
Occurs when a phenotype is under the influence of more than one gene product.


Gene name
All the gene names by which the molecule is called, as designated by the Commission on Plant Gene Nomenclature.


GO - Gene ontology
Controlled vocabulary for gene products.


GOC - Gene Ontology Consortium
GOC. The goal of the Gene OntologyTM (GO) Consortium is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing.


Gene pair
The two copies of a particular gene present in a diploid cell (one in each chromosome set).


Gene Primer
Marker type.


Gene Product
The polypeptide chain translated from an mRNA molecule transcribed from a gene


GMOD - Generic Model Organism Database
GMOD. A joint effort by the model organism system databases WormBase, FlyBase, MGI, SGD, Gramene, Rat Genome Database, EcoCyc, and TAIR to develop reusable components suitable for creating new community databases of biology.


Genetic conservation
Collection, maintenance and preservation of all segments of a germplasm in a crop species and its wild relatives.


Genetic engineering
see "Recombinant DNA technology"


Genetic map
A representation of a meiotic-recombination map based on analysis of marker segregation in a population of offspring derived from a biparental cross. Marker polymorphism between the parents is required to monitor recombination among loci along a chromosome.


Genetic markers
see "Marker."


Genetic resources
Germplasm that includes the entire array of cultivars in the crop species, related wild species in the genus and hybrids between the wild and cultivated species.


Genetics
"A branch of biology that studies the heredity, variation and evolution of organisms. "


Genome
The complete DNA component of an organism. array of genes carried by an individual, includes both the chromosomes within the nucleus and the DNA in mitochondria.


Genomic sequencing
Deciphering the exact order of base sequences in a genome.


Genomics
Relating to genomes, gene sequencingstudy of patterns of trait inheritance.


Genotype
genetic make-up of an individual.


GRIN - Germplasm Resources Information Network
GRIN


Glyph
Shapes that map features could appear as.


GO Slim
Slim version of the Gene Ontology terms where most of the terms represent broader concepts or a higher order concept.


Grain
Seed of a grass


GrainGenes
GrainGenes Compilation of molecular and phenotypic information on wheat, barley, rye, triticale, and oats.


GR ID - Gramene Accession
Gramene assigned accession identifier.


GRME - Gramene assigned exon ID


GRMG - Gramene assigned gene ID


GRMP - Gramene assigned peptide ID


GRMT - Gramene assigned Transcript ID


Grass
Family of narrow-leaved herbaceous monocot.


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H
Haploid
One homologous chromosome.


Haploid number
The number of chromosomes in a sperm or egg cell, half the diploid number.


Heritability
Proportion of phenotypic variance in a population that is attributable to genetic and not environmental factors.


Heteroduplex
A double-stranded nucleic acid molecule in which each polynucleotide chain has a different origin.


Heterosis
When F1 plants are more vigorous and high yielding than their parents.


Hexamer
A complex or compound containing six subunits or moieties (e.g., a protein complex with six polypeptide chains or an oligopeptide with six amino acid residues).


Homeology
Linear series of markers which map to a similar series of loci in two or more species.


Homologous chromosomes
Identical with respect to their genetic loci and centromere.


Homologous recombination
see "Cross over"

Homologue, homology , homologous
"Chromosomes that are located in different species or in different genomes in polyploid species and that originate from a common ancestral chromosome. Having the same evolutionary origin but serving different functions; ""the wing of a bat and the arm of a man are homologous"". "


Hybrid
An individual produced by crossing two parents of different genotypes.


Hybrid vigor
see "Heterosis"


Hybridisation, hybridization
"Base pairing of two single strands of DNA or RNA. "


HTML - Hypertext Markup Language
The coded format language used for creating hypertext documents on the World Wide Web and controlling how Web pages appear.


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I
Identifier
suggest to delete as too broad.


INS - in silico
Working with information only.


Indica
One of subspecies of cultivated rice (Oryza sativa L.)


IAGP - Inferred by association of genotype from phenotype


IC - Inferred by curator


IDA - Inferred from direct assay


IEA - Inferred from electronic annotation


IEP - Inferred from expression pattern


IGI - Inferred from genetic interaction


IMP - Inferred from mutant phenotype


IPI - Inferred from physical interaction


ISS - Inferred from sequence or structural similarity


Insertion
"Translocation involving three breaks in which a segment is removed from one chromosome and then inserted into a broken region of a nonhomologous chromosome, disrupting the normal structure and function of that gene. "


IS - Insertion sequence element
Mobile DNA segment that is transposable to any of a number of sites in the genome.


TIGR - Institute for Genomic Research
TIGR


ICIS - International Crop Information System
A database system for the management and integration of global information on genetic resources and crop improvement for any crop.


CIMMYT - International Maize and Wheat Improvement Center
CIMMYT CIMMYT has a global mandate to conduct maize and wheat research to benefit developing countries.


IRGSP - International Rice Genome Sequencing Project;
Established in 1997 to obtain a high quality, map-based sequence of the rice genome using the cultivar Nipponbare of Oryza sativa ssp. Japonica. ,


IRRI - International Rice Research Institute;
IRRI A nonprofit agricultural research and training center.


Interpolated phenotype
Phenotypic marker that has been positioned in a separate mapping study and placed on the displayed map relative to other (molecular) markers.


InterPro -
InterPro Database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.;


Introns
Noncoding sequences of DNA within a gene, separated by exons. DNA sequences not present in the final mRNA product


[i] Is a (instance of, type of):
Used to describe the relationship between a child term that represents a specific type of a more general parent term. For example in the following image: a guard cell is a type of cell; a root hair is a cell.


Isozyme
Any of two or more chemically distinct but functionally similar enzymes.


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J
Japonica
One of subspecies of cultivated rice (Oryza sativa L.)


JPEG (jpg) - Joint Photographic Experts Group


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K
Keywords
Words identified as particularly informative about an object. In a sequence, a keyword often relates to the identity of a gene or the function of the gene product.


kb - Kilobase
" equal to 1000 base pairs or nucleotides. A unit of measurement used in genetics to denote 100 bases of DNA or mRNA "


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L
Landmarks


Landraces
Traditional local varieties that have evolved over centuries or milenia; characterized by large diversity, ability to survive unfavorable conditions and low but stable levels of production.


Lap
A linear array of interconnected features.


Library
Set of cloned DNA segments derived from a single individual.


Linkage
"Tendency for two or more non-allelic genes to be inherited together, because they are located more or less closely on the same chromosome. Linked genes and markers tend to be inherited together. "


Linkage group
A set of two or more loci that have been shown by linkage analysis to be physically close in the genome but that have not yet been assigned to specific chromosomes.


Linkage Map
A chromosome map that shows the position of its known genes and/or markers relative to each other, rather than as specific physical points on each chromosome.


Literature
The body of writings and publications on a particular subject.


Loci, locus
The specific site(s) of (a) particular gene(s) on its chromosome.


LOD


LOD score
A statistical estimate of whether two loci are likely to lie near each other on a chromosome and are therefore likely to be inherited together. A LOD score of three or more is generally taken to indicate that the two loci are close.


Low LOD marker
On genetic maps, identifies markers that have been mapped to an interval below the stated LOD threshold.


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M
Maize
Large species of American grass of the genus Zea (Z. Mays), widely cultivated as a forage and food plant.


Maize GDB - Maize Genetics/Genomics Database project;
MaizeGDB A central repository for public maize information.


Maize_est
On the maize FPC map, identifies maize EST singletons that did not cluster with DuPont sequences.


Maize_markers
Used on sequence maps to denote a genomic location that has been specifically probed with a marker from maize.


Map position
The position of a particular feature on the map.


Map Types
Three types of DNA maps can be constructed: physical maps, genetic (linkage) maps, and cytogenetic maps, with the key distinguishing feature among these three types being the landmarks on which they are based.


Map unit
Unit of distance on a map


Mapping
"Determining the relative position of genes on DNA. "


Marker
A segment of DNA with an identifiable physical location on a chromosome for any feature that has been genetically mapped; "marker" is used when the specific marker type (e.g., RFLP, SSR) is unknown. Often used to indirectly track the inheritance pattern of a gene that has not yet been identified, but whose approximate location is known.


Matrix
Shows the number of correspondences between pairs of map sets.


Mb - Megabase
Equal to 1 million nucleotides or 1000 kilobases.


mRNA - Messenger RNA
RNA molecule that is transcribed from DNA and translated into an amino acid sequence.


Microarray
Allows for the display of thousands of genes at once on a “chip,” which then can be used as a sensor to detect genetic messages that are turned on or off when organisms are exposed to stress.


Microsatellite
Repetitive stretches of short sequences of DNA used as genetic markers to track inheritance. They are distributed widely throughout the genome. Using PCR primers to the unique sequences upstream and downstream of a microsatellite their location and polymorphism can be determined and the technique is extensively used in investigating genetic associations with disease.


MMP Unigene - MMP Unigene
On the maize FPC map, identifies maize overgos to Unigenes from the DuPont/MMP/Incyte Genomics partnership


Molecular function
The action characteristic of a gene product.


Monophyletic group
An ancestor plus all of its descendents.


Morphological
Structural


Morphology
Study of the structure of an organism


MPSS - MPSS


Multifactoral
When both multiple genotypes and environmental factors influence phenotype.


Mutagen
Agent that can increase mutation rates.


Mutagenesis method
Method by which a particular agent increases the rate of mutation in a cell or organism.


Mutant
Cell or organism carrying an altered gene.


Mutant genes
Gene with mutated sequence of DNA.


Mutation
A change in a gene.


MYSQL - MYSQL
An open source relational database management system that uses Structured Query Language (SQL).


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N
NB - Name based correspondences


NCBI - National Center for Biotechnology Information;
NCBI NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.


NSF - National Science Foundation;
NSF


Natural selection
Survival based on fitness of a genotype .


NAS - Non-traceable author statement


NR - Not recorded


Nucleotide
Building blocks of nucleic acids; must contain a nitrogenous base, a pentose sugar and a phosphate group.


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O
Obsolete
Map or term that has been replaced by a more up-to-date version, which should be used in place of the old one.


Oligo
Oligonucleotide, short sequence of single-stranded DNA or RNA. Oligos are often used as probes for detecting complementary DNA or RNA because they bind readily to their complements


Ontology
Controlled vocabulary, a glossary of keywords arranged in a structured order/network based on the biological concept that describes the keyword's relationship in an ontology tree.


Operon
Groups of related genes that are under common regulatory control.


Oracle
Oracle is a relational database management system (RDBMS) developed and copyrighted by the Oracle Corporation.


Organelle
Sub-cellular structures that perform a role within each cell. These vary widely from the nucleus, containing all our genetic information, to the golgi apparatus which processes protein and secretes it in vesicles on demand by the cell.


Ortholog
Any gene that can be found in two or more different species that can be traced back to the same common ancestor.


Orthology
Gene loci that arose from a common ancestor and that are conserved in different species.


Oryzabase
Oryzabase Integrated Rice Science Database in Japan.


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P
Paralogous
Gene loci that have arisen from a common ancestor and have evolved side by side within one species.


[p] - Part of
Used to indicate the relationship between a child term that is a part of the parent term. For example in the following image: the root cortex is a part of root.


Pedigree
"A record of the lineage or strain. A simplified diagram that shows family members' relationships to each other and how a particular trait or disease has been inherited. "


Peptide
Compound of two or more amino acids.


Peptide bond
Bond between two amino acids through a dehydration reaction.


Pfam - Pfam
Pfam Database that describes the protein family to which the respective protein entry belongs to


PAC - Phage-derived Artificial Chromosome
One type of vector used to clone DNA fragments in Escherichia coli cells. Based on bacteriophage (a virus) P1 genome.


Phenotype
Physical appearance of a genetic trait.


Physical map
"A chromosome map of a species that shows the specific physical locations of its genes and/or markers on each chromosome. Physical maps are particularly important when searching for disease genes by positional cloning strategies and for DNA sequencing. "


Physical map (as used by CMap in Gramene)
The representation of the collection of cloned DNA fragments that make up a genome, ordered with respect to a reference map (such as genetic map). A genome-sequencing project orders and assembles this collection in its different stages towards obtaining a full genome sequence.


Physio-chemical feature
The physiological and chemical characteristics of a specific molecules.


PO - Plant ontology
Controlled vocabulary for plant anatomy and growth stages.


POC - Plant Ontology Consortium;
POC Aims to develop, curate and share structured controlled vocabularies (ontologies) that describe plant structures and growth/developmental stages.


Plasmid
Extra-chromsomal, circular DNA molecule that replicates independently of the host chromosome; occur naturally in bacteria.


Polygenic traits
Traits that are encoded by many loci; many phenotypes will be present.


PCR Polymerase chain reaction
A fast, inexpensive technique creating many copies of a DNA fragment, occurs in vivo. aka "molecular photocopying." "Amplified" (increase in amount) DNA is used for a variety of tasks, such as the detection of hereditary diseases, the identification of genetic fingerprints, the diagnosis of infectious diseases, the cloning of genes, paternity testing, and DNA computing. "


Polymorphism
Allelic variation. A common variation in the sequence of DNA among individuals.


Polypeptide chain
Ten or more amino acids; precursor of a protein.


Polyploids
Organisms which have a multiple number of chromosomes in relation to the haploid number.


PNG - Portable Network Graphics
A compressed image file format similar to JPEG


Perl - Practical Extraction and Report Language.
A high-level scripting language frequently used for writing CGI scripts.


Predotar
Predotar Prediction service for identifying putative mitochondrial and plastid targeting sequences.


Primer
Marker types, enzyme that can elongate an existing DNA strand. A short artificial nucleotide strand used in a polymerase chain reaction. They adher to the DNA template at starting and ending points, and begin the synthesis of the new DNA strand.


Probe
Radioactive nucleotide that contains a base sequence complimentary to all or part of a gene of interest; allows for selection of a specific clone .


Prokaryote
Simple organism without nuclear membrane and with minimal organelles.


PROSITE
PROSITE Database of protein families and domains.


Protein
Any of a large group of nitrogenous organic compounds that are essential constituents of living cells; consist of polymers of amino acids.


ProtoMap
Automatic hierarchical classification of all SwissProt and TrEMBL proteins.


Protoplasm
The entire contents of a live cell.


PubMed
PubMed Online database of scientific literature.


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Q
QTL map
A type of genetic map which indicates the approximate location of a quantitative trait locus (QTL) within an interval delineated by two or more markers on a genetic map.


QTL map
One type of map in Cmap. The map has been used to detect the QTL in the original QTL study.


Qualitative markers such as phenotypic mutants, isozymes and resistance genes
suggest to delete.


Qualitative Trait
See "discontinuous trait"


Quality
Traits of economic importance that may affect product quality.


Quantitative Trait
See "continuous trait" A characteristic showing quantitative inheritance


QTL - Quantitative trait loci
The loci associated with the quantitave traits.


Query
delete or ask Programmer.


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R
RAPD - Random Amplified Polymorphic DNA
Marker types


Recombinant DNA technology
Creation of a new association between DNA molecules or segments of DNA that are not found together naturally, i.e., from different biological sources used to study the expression of a gene.


Recombinant Gamete
See "Cross over"


Recombination
The creation, by a process of intermolecular exchange, of chromosomes combining genetic information from different sources, typically two genomes of a given species.


References
A publication containing useful facts or information.


Region
suggest to delete.


Relational map
Can only be viewed in relation to some reference map. They have no backbone on their own so they need the coordinate system of the reference map to indicate location.


Residues
"A single unit within a polymer. This term reflects the fact that sugars, nucleotides, and amino acids usually lose a few atoms (usually hydrogen and oxygen) when they are polymerised into a larger molecule. "


Restriction Enzyme
Nuclease that recognizes specific nucleotide sequences in a DNA molecule and cuts the DNA at that site. Often referred to as molecular scissors.


Restriction Enzyme cutting site
Can be used as genetic markers, to reduce the distance between sites for map construction, to increase the accuracy of genetic maps and to provide reference points for the correlation of genetic and physical maps.


RFLP - Restriction fragment length polymorphism
"Markers for gene mapping. A key tool in DNA fingerprinting, and involves cutting DNA with restriction enzymes, creating polymorphisms that can be mapped and used as markers. Also pronounced ""rif"" lip. "


Restriction Map
Compilation of the number and order of and also distance between restriction enzyme cutting sites along a cloned segment of DNA.


Reverse Transcriptase
Enzyme capable of synthesizing DNA on an RNA template; typical of oncogenic viruses.


RNA - Ribonucleic acid
Transfers cell information from DNA to the protein-forming system of the cell.


Ribosomes
Cellular organelles where protein synthesis occurs.


Rice
suggest to delete.


RGN - Rice Genetics Newsletter
RGN A Publication of the Rice Genetics Cooperative, and is a chennel of communication among rice geneticists.


RGP - Rice Genome Research Program
Aims to completely sequence the entire rice genome and subsequently to pursue integrated goals in functional genomics, genome informatics and applied genomics.


Rice Japonica
See Japonica.


Rice marker
Used on sequence maps to denote a genomic location that has been specifically probed with a marker from rice.


TOP

S
SVG - Scalable Vector Graphics
A language for describing two-dimensional graphics in SML.


Schema
Description of the data represented within a database; structure or framework of the data.


Script
A set of instructions for a computer, also called code.


Sequence
The order in which subunits appear in a chain, such as amino acids in a polypeptide or nucleotide bases in a DNA or RNA molecule.


SAS - Sequence Annotated by Structure;
SAS


Sequence datasets
The dataset containing suquence information.


Sequence homology
Refers to the similarity of nucleic acid and protein sequences are similar because they have a common evolutionary origin.


Sequence map
A summarized representation of the contiguous, assembled genomic sequence of an organism in a linear map format.


STS - Sequence tagged site
Marker type. Short tagged tracts of DNA sequence (200 to 500 base pairs) that is operationally unique and has a single occurrence in a genome, and can be used as a landmark in genome mapping.


Sequencing data
suggest to delete.


SSR - Simple sequence repeat
Marker types


SSRIT - Simple Sequence Repeat Identification Tool
Finds all perfect SSRs in a given sequence.


SOG - SOG
Overgos from A. Paterson, derived from probes that have been mapped in maize and other grasses.


Sorghum GSS
Sorghum GSS reads from BACs found in the TAMU FPC Sorghum 2000 physical map


Species
A group of organism that can successfully reproduce and maintain common characteristics.


Splicing
The removal of introns and joining of exons in RNA. With that, introns are spliced out, while exons are spliced together.


Start position
The position on DNA corresonding to the first base incorporated into RNA.


Sterility or fertility:
Traits related to male and female flower sterility or fertility, including incompatibility.


Stop position
The three triplets (UAA, UAG, UGA) which terminate protein synthesis.


Study type
Describes the environment where the study was performed; choices include field, greenhouse, growth chamber, and laboratory.


SwissProt
A curated protein sequence database; http://www.ebi.ac.uk/swissprot/index.html


Symbol
Character used to represent something


Synonym
Alternate name for a term, equivalents that may be interchanged.


Synteny
Gene loci located on the same chromosome. The relationship between two genetic loci (not genes) represented on the same chromosomal pair or (for haploid chromosomes) on the same chromosome; an anatomic rather than a segregational relationship.


TOP

T
Tab-delimited file
Data in this type of file can be saved to and manipulated in a spreadsheet program.


TargetP
Predicts the subcellular location of eukaryotic proteing sequences.


TargetP
Predicts the subcellular location of eukaryotic protein sequences; http://www.cbs.dtu.dk/services/TargetP/


Taxonomy
Study of the general principles of scientific classification.


TBLASTN
Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.


TBLASTX
Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.


tug - Tentative unique gene


Term name
Primary name assigned to this term by either the Gramene curator for the rice TO, or the GO consortium.


Tos17
Marker type


TAS - Traceable author statement


Trait
An inherited qualitative characteristic, an attribute of phenotype


TO - Trait ontology
Controlled vocabulary for phenotypic traits


Transcription
RNA synthesis; occurs in nucleus


Transduction
Phage-mediated transfer of small pieces of DNA from one bacterial cell to another


tRNA - Transfer RNA
Adaptors between codons of mRNA and amino acids


Transformation
Entry and integration of a piece of DNA from one organism into the chromosome of another intact organism.


Transgenic
An organism in which alien genes have been incorporated, usually by injecting the foreign DNA into the nucleus of a fertilized embryo.


Translation
Protein synthesis; a process occurring in ribosomes where mRNA specifies amino acid sequence.


Translocation
"Breakage and removal of a large segment of DNA from one chromosome, followed by the segment's attachment to a different chromosome. "


TMHMM - Transmemberane helices ?
Preditions of transmemberane helices in proteins. Www.cbs.dtu.dk/services/TMHMM


Tn - Transposon element
Can insert into bacterial and viral chromosomes as well as plasmids


TrEMBL
Acomputer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot; http://us.expasy.org/sprot/


TOP

U
Acc ID - Unique accession ID


USDA - United States Department of Agriculture
USDA


Upstream gene,
Refers to nucleotide sequences that precede the codons specifying the mRNA or that precede (are on the 5' side of) the protein coding sequence.


TOP

V
Variant
A group of organisms within a species that differ in trivial ways from similar groups; "a new strain of microorganisms".


Variety
Results from selective breeding. Group of organisms that vary from their parent in minor ways. Subset of subspecies.


Vector
An agent, such as a virus or a small piece of DNA called a plasmid, that carries a modified or foreign gene. Acarrier DNA molecule that is capable of replication in a host organism.


Vigor
Traits related to growth and dormancy


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W
Wild relative
Species that either have shared common ancestors with a crop or are themselves the ancestors of the crop, remaining in the wild under natural selection.


Wildtype
The most commonly observed phenotype or genotype in a population.


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Y
YAC - Yeast Artificial Chromosome
" Large fragments of DNA from another species spliced into yeast DNA to grow large numbers of clones. "


Yield
Standing crop expressed as a rate. Traits contributing directly to yield based on economic value.