MeridianMERIDIAN

RNA Sequence

representation.scientific.rna_sequence

Ribonucleic acid sequence in IUPAC notation (letters: A, U, G, C, and ambiguity codes).

Worked samples

DuckDB 1.5.5 · finetype 0.6.64

ValueAs VARCHARgc_contentlength
AUGCAGCAUGCAGC0.57142857142857147
GCUAGCUAGCUAGGCUAGCUAGCUAG0.538461538461538413
AUGAUGAUGAUGAUGAUG0.33333333333333339

Shape

Pattern
^[AUGCRYSWKMBDHVN]+$
ValueLengthShape
AUGCAGC7matches
GCUAGCUAGCUAG13matches
AUGAUGAUG9matches
augcagc7rejected: lower-cased

Told apart

1 of the 6 other scientific types accept every one of these samples on shape alone.

IUPAC notation: A=Adenine, U=Uracil, G=Guanine, C=Cytosine Plus ambiguity codes.

Background

Origin

An RNA sequence is written as a succession of the letters G, A, C and U, one per nucleotide.[1] In RNA, uracil base-pairs with adenine and replaces thymine during DNA transcription.[2] By convention, nucleic acid sequences are usually presented from the 5' end to the 3' end.[1] Robert W. Holley's alanine transfer RNA structure, completed in 1964, was the first nucleotide sequence of a ribonucleic acid ever determined.[3]

Use

The FASTA format originated from the FASTA software package and has since become a near-universal standard in bioinformatics.[4] A FASTA record begins with a single-line description, followed by lines of sequence data.[5] NCBI BLAST accepts lower-case letters in a FASTA sequence and maps them into upper-case.[5]

In RNA there are many modified bases, including pseudouridine (Ψ), dihydrouridine (D) and inosine (I).[1]

Where you'll meet it

miRBase's entry for hsa-let-7a-5p gives its mature sequence as UGAGGUAGUAGGUUGUAUAGUUU, written with U.[6] RNAcentral's API returns the sequence of a Homo sapiens pre-miRNA, URS000075A685, written with U.[7]

Sources

  1. [1]Nucleic acid sequence - Wikipediasecondary source
  2. [2]Uracil - Wikipediasecondary source
  3. [3]Robert W. Holley - Wikipediasecondary source
  4. [4]FASTA format - Wikipediasecondary source
  5. [5]Query Input and database selection — BlastTopics 0.1.1 documentationdocumentation
  6. [6]miRBase entry: hsa-let-7a-5pdataset
  7. [7]RNAcentral APIdataset

Detection notes

v1 migration: Was science.rna_sequence. Like DNA but uses U instead of T. IUPAC notation: A=Adenine, U=Uracil, G=Guanine, C=Cytosine Plus ambiguity codes. Transform uppercases. Decompose calculates GC content.

Use it

CLI · DuckDB
$ finetype infer -i "AUGCAGC" --mode column
→ representation.scientific.rna_sequence

SELECT ft_infer('AUGCAGC');
-- → 'representation.scientific.rna_sequence'
Cast expression
UPPER(CAST({col} AS VARCHAR))

Schema

https://meridian.online/schemas/representation.scientific.rna_sequence · Frictionless type string

finetype taxonomy representation.scientific.rna_sequence -o json-schema

Aliases

rna

Type Registry