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SilkSatDb: The First Comprehensive Database on Insect Microsatellites

Silkworm Biology

Transition: A change of one purine or pyrimidine base to a different base under the same class, e

Allele: Any of two or more genes/DNA sequences that have the same relative position on homologous chromosomes and are responsible for alternative characteristics

Base pair: Two complemetary nucleotides which form hydrogen bonds between the two antiparallel DNA strands.

Chromosomes: A structural unit of inheritence; condensed DNA protein complex visible during cell division.

Cloning: The process of making copies of a specific piece of DNA, usually a gene.

Deletion: Loss of a base or more in the repeat track leaving one or more base of the repeat unit intact, e.g. (ATT)3TT(ATT)2.

Dinucleotide repeat/ dimer: Tandem repeat of two nuclotides in the same order, e.g. ATATATATAT.

DNA: Deoxyribonucleic acid. A molecule made out of two strands in antiparallel orientation that are held together by hydrogen bonds, each strand being made up of a sugar (deoxy ribose), a phosphate group and one of four bases (adenine, guanine, cytosine or thymine).

Electrophoresis: The process in which DNA fragments can be separated according to size and electrical charge by applying an electric current to them, generally in a matrix of agarose gel or polyacrylamide gel.

Exon: The region of a gene that encodes amino acids in a protein

Gene: One of the chromosomal units that transmit specific hereditary traits: a segment of the self- reproducing molecule, deoxyribonucleic acid

Genetic code: The set of three nucleotides which transfer the information as a particular amino acid in protein during translation.

Genetic map: A map of chromosomes showing the position of known genes and/or markers relative to each other, rather than as specific physical points on each chromosome

Genetic Markers: Alleles of DNA polymorphisms, used as experimental tags to keep track of an individual, a tissue, a cell, a nucleus, a chromosome, or a gene. Stated another way, any character that acts as a signpost or signal of the presence OR location of a gene OR heredity characteristic in an individual of a population

Genome: The total genetic complement of an organism, i.e. an organism's complete set of DNA sequences.

Genotype: The actual alleles present in an individual; the genetic makeup of an organism

Heterozygous: Having two different alleles at the two corresponding loci on a pair of homologous chromosomes.

Hexanucleotide repeat/ hexamer: Tandem repeat of six nucleotides in the same order, e.g. AATTTC AATTTC AATTTC AATTTC AATTTC.

Homozygous: Having identical alleles at a single locus in the same individual.

Imperfect repeat: A non-continuous repeat track, which is generated by a mutation (insertion/deletion/substitution) interrupting the continuity of the repeat unit., e.g. (ATT)3TT(ATT)2

Insertion: The presence of an odd base(s) disturbing the continuity of the repeat or an additional similar or odd base(s) within the repeat unit e.g. (ATC)3G(ATC)3, (TGA)3TCGA(TGA)2.

Intron: A noncoding sequence of DNA that is initially copied into RNA but is spliced out of the final RNA transcript.

Linkage: The association of genes and/or markers that lie near each other on a chromosome. Linked genes and markers tend to be inherited together

Locus: The position on a chromosome of a gene or a particular segment of DNA (marker).

Microsatellite: Tandem repeats of short simple DNA sequence, gerally of 1-6 bases.

Mononucleotide repeat/ monomer: Tandem repeat of single base, e.g. AAAAAAAAA.

Multiplexing: The process of amplifying a number of different loci in a single polymerase chain reaction and the resolution of these loci either on polyacrylamide gel electrophoresis or agarose gel electrophoresis

Mutation: A disruption in the normal sequence of a DNA strand resulting in a varied sequence at the same position.

Non-coding DNA: The segment of DNA that does not carry the information necessary to make an amino acid sequence.

Nucleotide: One of the structural components, or building blocks, of DNA and RNA. A nucleotide consists of a base (one of five chemicals: adenine, thymine in DNA, uracil in RNA, guanine, and cytosine) plus a molecule of sugar and one of phosphoric acid

Pentanucleotide repeat/ pentamer: Five nucleotides repeating in tandem to each other in the same order, e.g. AATTG AATTG AATTG AATTG.

Phenotype: The visible characteristics of an organism, resultant of genotype and environment.

Point mutation: A change in a single base pair

Polymerase Chain Reaction: (PCR) A method of DNA analysis that exponentially amplifies a specific DNA sequence or region allowing rapid DNA analysis

Polymorphic: The occurrence of more than one form of individual in a single/multiple species within an interbreeding population

Polymorphic locus: A chromosomal region with two or more identifiable alleleic DNA sequences.

Primer: A short oligonucleotide sequence used to amplify DNA sequences in a polymerase chain reaction

SSR: Simple sequence repeats (same as microsatellites). A repeated sequence of 1 to 6 bases.

STR: Short tandem repeats (same as microsatellites). A repeated sequence of 1 to 6 bases.

Substitution: A mutation, where one base is changed for another base.

Tetranucleotide repeat/ tetramer: Tandem repeat of four nucleotides in the same order, e.g. ATAC ATAC ATAC ATAC.

Threshold: A length limit, below which DNA sequence is not considered for the analysis, e.g. Threshold of 6 bases means, 6 base and above is considered but not 5 base.

Transition: A mutation that consists of the replacement of one purine by another purine or one pyrimidine by another pyrimidine, e.g. Adenine to Guanine, Thymine to Cytosine.

Transversion: A mutation that consists of the replacement of a purine by a pyrimidine or vice versa, e.g. Adenine to Thymine.

Trinucleotide repeat/ trimer: Three nucleotides repeating in tandem to each other in the same order, e.g. TAA TAA TAA TAA.

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