Utr Length Ratio
Compare 3-prime and 5-prime UTR lengths.
Description
The untranslated regions at the 5′ and 3′ ends can differ in length.
The untranslated regions at the 5′ and 3′ ends can differ in length. Their ratio describes a transcript's supplied structure without inspecting its sequence.1
Compare 3-prime and 5-prime UTR lengths.
When to use Utr Length Ratio
Use this tool to compare 3-prime and 5-prime UTR lengths.
Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
How to use Utr Length Ratio and understand its results
- Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
- Enter fivePrimeUtrBp, threePrimeUtrBp using the field table and calculation rules, then run the tool.
- Read threeToFiveRatio, totalUtrBp. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| fivePrimeUtrBp | Five prime utr bp | number | Required |
| threePrimeUtrBp | Three prime utr bp | number | Required |
Enter a positive 5′ length and nonnegative 3′ length in base pairs. Return the 3′/5′ ratio and combined UTR length. A zero 3′ UTR gives ratio zero.
threeToFiveRatio=threePrimeBp/fivePrimeBp; total=threePrimeBp+fivePrimeBp Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| threeToFiveRatio | Three to five ratio | number |
| totalUtrBp | Total utr bp | number |
{
"input": {
"fivePrimeUtrBp": 100,
"threePrimeUtrBp": 200
},
"output": {
"threeToFiveRatio": 2,
"totalUtrBp": 300
}
}Limitations and assumptions
Lengths are accepted as finite numbers rather than requiring integer coordinates. Annotation, isoform selection and regulatory effects are not inferred.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Polya Usage Shift: Detect proximal polyadenylation usage shifts between conditions. For a complementary task, use Effective Transcript Length: Union overlapping exon intervals and subtract fragment length to estimate transcript effective length.
References
-
Utr Length Ratio — tool.io
Similar or alternative tools
- Polya Usage Shift
Detect proximal polyadenylation usage shifts between conditions.
- Effective Transcript Length
Union overlapping exon intervals and subtract fragment length to estimate transcript effective length.