Terminology
- Exons
- Coding regions of a protein.
- Used in translation, though parts may be excluded during translation.
- Introns Intervening Sequences
- Non-coding regions of genes.
- These are removed after processing transcription in a process called RNA splicing.
- CDS Coding DNA Sequence
- Coding DNA sequence composed of a gene's open reading frame.
- The portion of a gene's DNA sequence that codes for a protein.
- cDNA Complementary DNA
- DNA that was reverse transcribed (via reverse transcriptase) from an RNA (e.g., messenger RNA or microRNA).
- Note that mRNA may have untranslated regions depending on the open-reading frame.
- Primers
- Depending on goal, these may not surround the entire coding DNA sequence.
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- If they don't, you will only get partial clones of your gene; the open reading frame may be cutoff.
- Although primers may be given both in the 5' to 3' direction, the second primer adheres on the complimentary strand.
- These are included in the cloned DNA sequence.
- ORF Open Reading Frame
- Spans of DNA sequence between the start and stop codons.
- The "reading", however, refers to the RNA produced by transcription of the DNA and its subsequent interaction with the ribosome in translation
- Since DNA is interpreted in groups of three nucleotides (codons), a DNA strand has three distinct reading frames.[15] The double helix of a DNA molecule has two anti-parallel strands; with the two strands having three reading frames each, there are six possible frame translations.
Table 1: Open Reading Frames
| DNA | GTACATGAAGAGGTTTACTGAAGGCCGCGTAGAAGCTTAGGTAC |
|---|---|
| RNA | GUACAUGAAGAGGUUUACUGAAGGCCGCGUAGAAGCUUAGGUAC |
| Reading Frame 1 | GUA CAU GAA GAG GUU UAC UGA AGG CCG CGU AGA AGC UUA GGU AC |
| Reading Frame 2 | GUAC AUG AAG AGG UUU ACU GAA GGC CGC GUA GAA GCU UAG GUA C |
| Reading Frame 3 | GUACA UGA AGA GGU UUA CUG AAG GCC GCG UAG AAG CUU AGG UAC |