Chapter 14: Genomes and Genomics Flashcards
Why is cDNA so valuable for identifying codons?
First, cDNA suggest there is mRNA there and if there is mRNA there that means the gene was expressed (so being expressed is the definition of being a gene).
Second, because the cDNA is complementary to the mature mRNA, the introns of the primary transcript have been removed, which greatly facilitates the identification of the exons and introns of a gene
What is the best method to deduce codons in DNA?
Another means of identifying ORFs and exons is through the analysis of mRNA expression. This analysis can be done in two ways. Both methods involve the synthesis of libraries of DNA molecules that are complementary to mRNA sequences, called cDNA.
Full-length cDNA evidence is taken as the gold-standard proof that one has identified the sequence of a transcription unit, including its exons and its location in the genome.
What is cDNA and how is it used to identify genes?
How do we know that the gene is expressed? is there an mRNA coming from it
how do we know if there is mRNA? isolate cDNA and then map them back to the genome
Cells transcribe genes to make mRNA. mRNA is isolated, reverse transcription generates cDNA copies of mRNAs, cDNAs are sequenced by high-throughput sequencing.
Sequences are aligned to the genome sequence to determine where the mRNA came from.
What are ORF’s and how can we use them to identify codons?
Open reading frame: run of sequence with identifiable codons with no stop codon interruption - probably a protein coding region.
Check for “codon bias” as evidence that an ORF is part of a real gene.
Check for conservation of a predicted ORF across species as evidence that it is part of a real gene.
What is a reporter gene?
A gene that researchers attach to a regulatory sequence of another gene of interest in bacteria, cell culture, animals or plants. (GFP, beta-galactosidase)
