The Maize Full Length cDNA Project
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Arizona Genomics Institiute   ~   Arizona Genomics Computational Laboratory   ~   Stanford University 

TERMS GLOSSARY   DEFINITIONS
Amino Acid
An amino acid is a chemical compound that consists of an amino group (NH2) and a carboxyl group (COOH) attached to the same carbon chain. A protein is a string of amino acids folded into a predestined shape. There are 20 different amino acids (differing in their carbon chains) that function as the building blocks of proteins. Messenger RNA provides the code that lets the ribosome build proteins out of these building blocks.
 
Annotation
After sequencing, assembly, and finishing, the process of characterizing expression patterns of representative FLcDNAs and assigning a specific structure and function to each gene.
 
Antisense Strand
DNA consists of two strands. The antisense strand is the one that gets transcribed into “sense” mRNA which in turn is translated into proteins by the ribosome. The DNA “sense” strand - which is complementary to the antisense strand - is typically not transcribed. When the DNA sense strand does get transcribed (which can occur naturally or through transgenic technology), it produces antisense mRNA. Antisense mRNA silences expression of the protein by binding to complementary sense mRNA to create double-stranded mRNA - which the cell degrades. For more information on antisense RNA, visit the Bioteach website
 
BAC
Bacterial
Artificial Chromosome

One of the most common methods for whole genome sequencing employs inserting large segments of DNA from a species into bacteria on a plasmid that is so large it is called a chromosome. BACs typically contain 100-150 kb (100,000 - 150,000 base pairs). Each BAC is sequenced as a separate project, and then these are joined together to form the continuous sequence of an organism's chromosomes.
 
Clone
A clone is a copy of a gene or a group of genetically identical cells or organisms derived from a single cell or individual. As a verb, cloning refers to the process of making an identical copy of a gene or a cell or organism.
 
cDNA
Complementary DNA

Complementary DNA is produced in the laboratory by extracting an organism's single-stranded messenger RNA and transcribing it back into a stable piece of DNA. The cDNA sequence does not include portions of the genomic DNA (introns) that were spliced out of the mRNA while it was still in the cell. cDNAs can be sequenced to identify ESTs and are also plated onto microarrays. Both techniques help identify which genes are turned "on" in a particular tissue. See: How alternative splicing complicates things.
 
ESTs
Expressed
Sequence Tags

Expressed Sequence Tags are pieces of the genetic sequence for genes that are turned "on," i.e., actively being transcribed into messenger RNA in the cell. Learn more at: www.ncbi.nih.gov/About/primer/est.html
 
Exon
An exon is the portion of mRNA that gets translated into protein. www.genome.gov/glossary.cfm?key=exon
 
Finishing
For clones unable to be successfully sequenced in one step, the process of completely sequencing a cDNA clone using a multi-step method such as primer walking and/or transposon tagging.

FLcDNA
Full-length complementary DNA refers to the sequence of an entire messenger RNA. Traditionally, researchers have sequenced only the short segments at the end of cDNAs (ESTs). But FLcDNA sequencing can provide additional information about which segments of the genetic code are spliced out of mRNA before it is translated into protein. For more information, click here for discussion of FLcDNAs
 
Gene
DNA
mRNA

Defining these terms is beyond the purpose of this website.

For a general overview of DNA, see: www.dnaftb.org/
For a general discussion of molecular genetics, see:
Molecular Genetics: Piecing it Together: www.ncbi.nih.gov/About/primer/genetics_molecular.html
What is a Genome: www.ncbi.nih.gov/About/primer/genetics_genome.html
 
Genome
A genome is the complete nucleotide sequence of an organism's DNA.
Learn more at: www.ncbi.nih.gov/About/primer/genetics_genome.html
 
GSS
Genomic Survey Sequence

Genomic Survey Sequence; term for genomic sequence submitted to sequence databases, as opposed to ESTs.
 
High Cot
A method of selecting for low copy number, gene-rich areas of the genome that excludes repetitive DNA by taking advantage of the rate of DNA association hybridization. When DNA is denatured into single strands, repetitive pieces find each other and quickly form hybrids. Rare (gene-like) DNA is slow to hybridize, requiring a long time (high concentration x time = Cot.  See:   maize.danforthcenter.org/high_cot.html
 
Intron
An intron is the portion of mRNA that gets spliced out before the mRNA is translated into protein.
 
Iterative Primer
Walking

In cDNA sequencing projects, the process of designing primers to the 5' and 3' ends in successive, multiple steps across difficult or very long stretches of cDNA sequence.
 
Methyl Filtration
This technique filters out highly methylated regions of the genome before doing sequencing. This leads to greater efficiency in sequencing genes because most maize retrotransposons and repetitive DNA regions are methylated whereas “genic” regions are not.
 
Microarrays
Microarrays are plates or slides dotted with a grid of individual DNAs, cDNAs, or gene-specific, single-stranded sequence (oligonucleotide). When mRNA extracted from a tissue is tagged with a fluorescent dye and "washed" over the surface of the microarray, it binds to its matching complementary sequence on the array. This complementary matching is detected as fluorescent spots on the array. This allows scientists to study gene expression, i.e., which genes are turned "on" in a particular tissue at a particular time and under specific conditions.
Learn more at www.ncbi.nih.gov/About/primer/microarrays.html

qRT-PCR
qRT-PCR stands for quantitative Real-Time Reverse Transcription Polymerase Chain Reaction;
In contrast to regular PCR, qRT-PCR is a quantitative assay that is capable of monitoring the amount of transcript present after every cycle relative to the start of the reaction, giving an accurate reading of how much template is present initially in a particular cell or tissue type.
 
RNA Interference
The suppression of a gene by its corresponding double stranded RNA is called RNA interference (RNAi).
For more information about this process, see www.bioteach.ubc.ca/MolecularBiology/AntisenseRNA/
 
Sense Strand
The DNA sense strand is the one that does NOT usually get transcribed into mRNA. The mRNA sense strand (made from the DNA antisense strand) gets translated into protein. Thus, it's the strand that makes “sense.”
 
Sequencing
The process of determining the sequential order of the building blocks in a linear molecule such as a protein or DNA or RNA. Thus, DNA and RNA sequencing determine the sequence of nucleotides, whereas protein sequencing determines the sequence of amino acids.
 
Splicing
After DNA is transcribed into mRNA in the nucleus, the mRNA is edited: introns are spliced out and the remaining exons are joined together. In some instances, the editorial process produces several alternative versions of the mRNA, which in turn generates various proteins when it is transcribed.
 
Tiling Path
Tiling path is the minimum set of BACS that contain the whole chromosome with the minimum overlap possible.
 
Transcription & Translation
Defining these terms is beyond the purpose of this website. For a general overview see:
What is a Genome: www.ncbi.nih.gov/About/primer/genetics_genome.html
 
Transgenic
An experimentally-produced organism whose DNA includes genetic material that has been introduced by scientists.
 
Transposon
A transposon is a mobile segment of DNA that serves as an agent of genetic change. Some transposons move by being cut and pasted into new locations. Others stay put but insert copies of themselves elsewhere in the genome, a process called replicative transposition. The two ends of a transposon carry a sequence of bases that permit the transposase enzyme to clip and move or copy the DNA segment to new locations in a cell's DNA. In sequencing projects, transposons are useful because they provide precise starting points for sequencing in an otherwise unknown region. In a test tube, transposase can mobilize its transposon and insert it into a target clone. Sequencing reactions from the end of the transposon provide the first step in defining the sequence of that clone. By using transposons inserted at many different sites within the unknown clone, the complete sequence can be obtained.
 

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