Keywords Flashcards
EST
Expressed sequence tags.
ESTs are single-pass reads obtained from either the 5′ or the 3′ end of a cDNA clone. They represent snapshots of the transcriptome in a given set of conditions and therefore are an essential piece of information in order to find all the possible transcripts generated by a given genome. Moreover, although ESTs are sequenced in a given set of cell conditions, they provide a random sampling of the expression, as they are not necessarily constrained to any particular group of gene families. On the other hand, as ESTs represent partial transcripts, they still need to be processed in order to obtain from them a more complete knowledge about the transcriptome.
cDNA
complementary DNA complementary DNA (cDNA) is double-stranded DNA synthesized from a messenger RNA (mRNA) template in a reaction catalysed by the enzyme reverse transcriptase. cDNA is often used to clone eukaryotic genes in prokaryotes.
gene isoform
Gene isoforms are mRNAs that are produced from the same locus but are different in their transcription start sites (TSSs), protein coding DNA sequences (CDSs) and/or untranslated regions (UTRs), potentially altering gene function.
transcriptome
The transcriptome is the set of all messenger RNA molecules in one cell or a population of cells. It differs from the exome in that it includes only those RNA molecules found in a specified cell population, and usually includes the amount or concentration of each RNA molecule in addition to the molecular identities.
exome
The exome is the part of the genome formed by exons, the sequences which when transcribed remain within the mature RNA after introns are removed by RNA splicing. It consists of all DNA that is transcribed into mature RNA in cells of any type as distinct from the transcriptome, which is the RNA that has been transcribed only in a specific cell population
ORF
open reading frame - In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA).[1] An AUG codon within the ORF (not necessarily the first) may indicate where translation starts. The transcription termination site is located after the ORF, beyond the translation stop codon, because if transcription were to cease before the stop codon, an incomplete protein would be made during translation.[2] In eukaryotic genes with multiple exons, ORFs may span exons. These would be spliced into an ORF in the mRNA.
directed acyclic graph
A directed graph (ie with direction arrowheads on the edges) that contains no directed cycles ie That is, it is formed by a collection of vertices and directed edges, each edge connecting one vertex to another, such that there is no way to start at some vertex v and follow a sequence of edges that eventually loops back to v again
snRNA
small nuclear RNA - Small nuclear ribonucleic acid (snRNA), also commonly referred to as U-RNA, is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcribed by either RNA polymerase II or RNA polymerase III, and studies have shown that their primary function is in the processing of pre-messenger RNA (hnRNA) in the nucleus. They have also been shown to aid in the regulation of transcription factors (7SK RNA) or RNA polymerase II (B2 RNA), and maintaining the telomeres
snRNP
snRNA are always associated with a set of specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins (snRNP, often pronounced “snurps”). Each snRNP particle is composed of several Sm proteins, the snRNA component, and snRNP-specific proteins. The most common snRNA components of these complexes are known, respectively, as: U1 spliceosomal RNA, U2 spliceosomal RNA, U4 spliceosomal RNA, U5 spliceosomal RNA, and U6 spliceosomal RNA. Their nomenclature derives from their high uridine content
what is gene annotation
Many organisms have had their entire genome sequenced, however this is not the end of a genome project. Annotation is the process by which pertinent information about these raw DNA sequences is added to the genome databases. This involves describing different regions of the code and identifying which regions can be called genes.
S/MAR
scaffold/matrix attachment region. The term ´S/MAR´ (scaffold/matrix attachment region), otherwise called ´SAR´ (scaffold-attachment region), or ´MAR´ (matrix-associated region), are sequences in the DNA of eukaryotic chromosomes where the nuclear matrix attaches.
What are S/MAR?
are sequences in the DNA of eukaryotic chromosomes where the nuclear matrix attaches. As architectural DNA components that organize the genome of eukaryotes into functional units within the cell nucleus, S/MARs mediate structural organization of the chromatin within the nucleus. These elements constitute anchor points of the DNA for the chromatin scaffold and serve to organize the chromatin into structural domains. Studies on individual genes led to the conclusion that the dynamic and complex organization of the chromatin mediated by S/MAR elements plays an important role in the regulation of gene expression.
5’ UTR
The 5’ untranslated region (5′ UTR) (also known as a Leader Sequence or Leader RNA) is the region of an mRNA that is directly upstream from the initiation codon
3’ UTR
In molecular genetics, the three prime untranslated region (3’-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon.
Termination or stop codon
In the genetic code, a stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.[1] Proteins are based on polypeptides, which are unique sequences of amino acids. Most codons in messenger RNA (from DNA) correspond to the addition of an amino acid to a growing polypeptide chain, which may ultimately become a protein. Stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain. While start codons need nearby sequences or initiation factors to start translation, a stop codon alone is sufficient to initiate termination.
