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MIPS Fungal Genomes

    

Glossary

Amino Acids

  • The building blocks of proteins. They all have the same carbon backbone structure but differ from one another according to the individual side chain. Only 20 of the naturally occurring amino acids are commonly found in proteins.

Ascospore (Spore)

  • A specialized haploid cell produced during meiosis.

Ascus

  • A sac-like structure containing four spores in S. cerevisiae Plural: asci.

Autonomous Replication Sequence (ARS)

  • A DNA consensus sequence which usually functions as an origin of DNA replication. There are various consensus sequences. We used the conservative 5'-(A/T)TTTAT(A/G)TTT(A/T)-3' consensus for our analysis (Stinchcomb et al. 1981; Broach et al. 1983).

Bases

  • The variable part of DNA. The nitrogenous bases of DNA are divided into two groups: purines [adenine (A) and guanine (G)] and pyrimidines [thymine (T) and cytosine (C)]. In RNA, thymine is replaced by uracil (U). Modified and unusual bases, such as pseudouridine, are found in tRNA molecules.

Base pair (bp)

  • Two bases, linked by noncovalent forces, that pair in double-stranded DNA or RNA molecules.

cDNA (complementary DNA)

  • A DNA molecule usually obtained by a reverse transcription of an mRNA molecule.

cds

  • coding sequence.

Centromere

The attachment site of chromosomes to the mitotic or meiotic spindle.

Chromosomes

  • Discrete physical units carrying genetic information. Each chromosome contains a long duplex DNA molecule and associated proteins. Usually, chromosomes are visible only during cell division. The number of chromosomes varies widely among different species.

Codon

  • A sequence of three nucleotides (in a DNA or mRNA), that encodes a specific amino acid to be incorporated into a protein.

Codon Adaptation Index (CAI)

  • The CAI is used to estimate the expression level of a protein. To calculate the CAI value of a protein, a reference set of highly expressed genes is used. For each codon in this set of reference genes the frequency of usage is calculated. A CAI score for a gene is calculated from the frequency of use of all codons in that gene. [P.M. Sharp and W.H. Li Nucleic Acids Res.15, 1281-1295 (1987)]

Diploid

  • A term used to describe an organism having two sets of identical chromosomes. S. cerevisae is chimeric, in that haploid and diploid forms exist.

DNA (deoxyribonucleic acid)

  • The primary genetic material of all cellular organisms. It is a polymeric macromolecule composed of a repeating backbone of phosphate and sugar subunits to which different bases are attached. DNA is arranged in two opposing strands (the Watson-Crick double helix) in which the complementary bases form hydrogen-bonded basepairs across the two strands. The sugar backbone of DNA is composed of deoxyribose subunits.

DNA-Replication

  • Process of synthesis of a new DNA strand by a mechanism in which a preexisting strand (parental strand) is used as a template. Each new strand is complementary to the parent strand.

EST (Expressed sequence tag)

  • cDNA sequence of a few hundred bases used to identify the corresponding gene.

Eukaryote

  • An organism whose genetic information is, in contrast to prokaryotes (such as bacteria), contained in a separate cellular compartment: the nucleus. Besides algae, fungi and protozoa, all multicellular, cell-differentiating organisms including plants and animals are eukaryotes. In addition to their nuclear genome, all eukaryotic cells contain small additional, extranuclear genomes, which are contained in mitochondria (in all eukaryotes) and in plastids (only in eukaryotes that can perform photosynthesis).

Exons

  • Segments of a eukaryotic gene that encodes mRNA. In DNA, exons are adjacent to non-coding DNA segments, called introns.

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 for similarities between one sequence (the query) and any group of sequences (the database).

Gene

  • A section of DNA coding for a single polypeptide chain; a particular species of tRNA, snRNA or rRNA; or a sequence that is recognized by and interacts with regulator proteins.

Haploid

  • The state of having only one set of chromosomes. See diploid.

Introns

  • Noncoding regions of eukaryotic genes, which are transcribed into mRNA but are then excised by a process called RNA-splicing. See exon.

Long terminal repeats (LTRs)

  • Identical DNA sequences, several hundred nucleotides long, found at both ends of transposons. They are thought to have a role in integrating the transposons into the host DNA. Solo LTRs and remnant LTRs indicate former integration sites of transposable elements.

Meiosis

  • A special process of nuclear division during which spores are produced. Meiosis involves a diminution (by half) in the amount of genetic material; it consists of two successive nuclear divisions with only one round of DNA replication producing four haploid daughter cells (the spores) from an initial diploid cell.

Mitochondria

  • Semi-autonomous, self-reproducing organelles within the cytoplasm of eukaryotic cells that are bounded by two membranes. These organelles are responsible for the energy conversion of most of the cellular energy metabolites into adenosine triphosphate (ATP) by oxidative phosphorylation.

Mitosis

  • The process of nuclear division in eukaryotic cells.

mRNA (messenger RNA)

  • A single-stranded RNA that acts as the template for the amino acid sequence of proteins.

Open reading frames (ORFs)

  • DNA stretches that potentially encode proteins. They always have a start codon (ATG) at one end and a translation-terminating stop codon at the other end.

Proteins

  • Polymers composed of a linear string of amino acids.

Remnant LTR

  • A solitary and degenerated LTR sequence lacking a TY element. As the remaining LTR has no function anymore, and on the other hand its sequence is degenerated, the transposition must have occured long time ago.

RNA (ribonucleic acid)

  • Polymer composed of a repeating backbone of phosphate and sugar subunits to which different bases are attached: adenine (A), cytosine (C), guanine (G), and uracil (U). The sugar backbone of RNA is composed of ribose subunits. RNAs can be distinguished by their different properties:mRNA, tRNA, scRNA, snRNA, and rRNA.

rRNA (ribosomal RNA)

  • A structural and functional component of ribosomes. Ribosomes are the cellular machinery responsible for the translation of the genetic information into proteins. They are composed of rRNA and ribosomal proteins.

scRNA (small cytoplasmic RNA)

  • A set of RNAs that are typically smaller than 300 nucleotides and can be part of signal recognition particles (SRPs).

Signal recognition particles (SRPs)

  • Ribonucleoproteins that are part of the protein-translocating machinery in the ER (endoplasmic reticulum) membrane.

snRNA

  • A set of RNAs that are typically smaller than 300 nucleotides and function in the nucleus in the form of small nuclear ribonucleoprotein particles (snRNPs). The function of snRNPs is to mediate and regulate post-translational RNA processing events.

Solo LTR

  • A solitary LTR sequence lacking a TY element. This indicates that a TY was located in this region. As the remaining LTR has no function anymore, and on the other hand its sequence is well conserved the transposition must have occured in the near past.

Spindle

  • A network of fibrous microtubules and associated molecules formed during mitosis between the opposite poles (centromeres) of eukaryotic cells. It mediates the movement of the duplicated chromosomes to opposite poles.

Spore

  • See ascospore

Sporulation

  • The process of spore development. Sporulation can be induced by external signals, such as absence of nitrogen.

Telomere

  • The terminal part of a eukaryotic chromosome, consisting of a few hundred base pairs with a defined structure. Telomeres are important for maintaining chromosomal structure and stability, as they permit replication of the ends of the linear DNA molecule.

Transcription

  • The process by which DNA is used as a template for the synthesis of an RNA molecule.

Translation

  • The process of protein synthesis from a mRNA template, occurring at the ribosome.

Transposable element (transposon)

  • A mobile DNA sequence that can move from one site in a chromosome to another, or between different chromosomes.

tRNA (transfer RNA)

  • A set of RNAs that act during protein synthesis as adaptor molecules, matching individual amino acids to their corresponding codon on a mRNA. For each amino acid there is at least one tRNA.

TY elements

  • The retro-transposons of yeast. TYs are members of a widely distributed family of eukaryotic elements called LTR- containing retrotransposons. They have the same sequence organization as retroviruses. The complete retrotransposons are 5 to 6 kilobases long. They are bracketed by long terminal repeats (LTR), which are 300 to 400 basepairs long.

Y' element

  • Y' elements normally consist of two ORFs with all splicing signals that are located in the telomeric regions. Their function is unknown.

Zygote

  • The diploid cell resulting from the union of two haploid cells of complementary mating types.

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