RNAGenIQ (Random RNA sequence generator)
v2.0.0Generate random RNA test sequences with adjustable GC content and optional RNA-like templates and sequence motifs.
Generate random RNA test sequences with adjustable GC content and optional RNA-like templates and sequence motifs.
Choose Random RNA, a sequence length, and a GC target, then generate A/C/G/U sequences in FASTA format. No input file is needed. Each random position independently samples G or C with the chosen GC probability, otherwise A or U. The result can be copied or downloaded as a .fasta file.
For two 12 nt records with a 50% GC target and no added motifs, a verified run returned:
>RNA_random_1 length=12 GC=75% type=random
GUCGGUCCCGCA
>RNA_random_2 length=12 GC=17% type=random
CAAUAUUAACAAThe headers report measured GC percentages rounded to whole numbers. Short sequences can differ substantially from the target. A later run samples different bases.
Select mRNA-like, set the length to 30, leave start and stop codons on, and add a 5 nt poly-A tail. With a 50% GC target and both UTR options off, a verified run produced:
>RNA_mRNA_1 length=35 GC=34% type=mRNA
AUGGUCGGUCCCGCACAAUAUUAACAAUAAAAAAAThe 30 nt before the tail include an initial AUG, 24 random bases, and a terminal stop codon. The tail adds five more A residues. The random middle can contain internal stop codons, so terminal codons alone do not establish an open reading frame.
Counts and lengths must be whole numbers. Counts and sequence lengths start at 1; the poly-A tail length can be 0. GC targets accept decimal values from 0 to 100%.
| Setting | Behavior | Default |
|---|---|---|
Number of sequences | Number of separate FASTA records to generate. | 1 |
RNA template | random, mRNA, tRNA, rRNA, miRNA, lncRNA, piRNA, or circRNA. Choices other than random use illustrative sequence templates described below. | random |
Sequence length (nt) | Requested length including fixed motifs, before a poly-A tail. mRNA without a 3' UTR can be shortened by up to 2 nt to keep its random region in complete triplets. | 100 |
GC content (%) | Sampling probability for random regions. Fixed motifs, stem-loop motifs, and poly-A tails change the final GC percentage. | 50 |
Add start codon (AUG) | Adds AUG after the optional 5' UTR. Visible for mRNA only. | On |
Add stop codon | Adds one randomly selected UAA, UAG, or UGA after the random coding region. Visible for mRNA only. | On |
Add 5' UTR | Adds the fixed Kozak-like prefix GCCACC. AUG is controlled separately by the start-codon option. Visible for mRNA only. | Off |
Add 3' UTR | Adds AAUAAA followed by 15 random bases, plus up to 2 extra bases to fill the requested length around complete coding triplets. Visible for mRNA only. | Off |
Add poly-A tail | Appends A residues after the requested sequence body. Visible for mRNA only. | Off |
Poly-A tail length | Number of appended A residues. Visible for mRNA when the tail is enabled. | 200 |
Add stem-loop structures | Replaces random regions with non-overlapping 16 nt complementary stem-loop motifs, preserving total length. Visible for random, rRNA, and lncRNA. | Off |
Number of stem-loops | Number of inserted motifs. Visible for those templates when stem-loop insertion is enabled. | 1 |
Start and stop codon switches retain their on defaults when hidden, but apply only to the mRNA template. Settings for another template do not modify the selected template.
These templates generate test sequences. They do not validate RNA identity, processing, biological function, or folding. Each non-random template displays a notice to that effect.
| Template | Sequence construction |
|---|---|
Random RNA | Random A/C/G/U bases over the requested length, with optional stem-loop motifs. |
mRNA-like | Optional GCCACC, optional AUG, a random region in complete triplets, optional stop codon, optional 3' UTR, then an optional poly-A tail. The requested body length must fit every selected feature. |
tRNA-like | A fixed illustrative A/C/G/U prefix extended with random bases to the requested length. The length must fit the full prefix. No cloverleaf fold or anticodon function is established. |
rRNA-like | A fixed illustrative prefix followed by random bases. Optional stem-loop motifs occupy the random region and retain the prefix. The length must fit the prefix plus all selected motifs. |
miRNA-like | Begins with UGAGGUAG (truncated if the requested length is shorter than 8 nt), then adds random bases. This does not establish a mature miRNA or target specificity. |
lncRNA-like | Random sequence with optional stem-loop motifs. The label does not establish a non-coding transcript or a biological role. |
piRNA-like | Starts with U and fills the remaining requested length with random bases. |
Circular RNA-like | Starts and ends with AGGU, with random bases between them. Requires at least 8 nt. The exported FASTA remains a linear sequence representation; circularization is not validated. |
A stem-loop motif has six sampled bases, four uniformly sampled loop bases, and the RNA reverse complement of the first six bases. Motifs cannot overlap or extend the requested length. Complementarity allows pairing but does not guarantee the predicted structure of the complete RNA. Assess the sequence with RNAfold when folding matters.
For mRNA without a 3' UTR, any 1 or 2 nt remainder is omitted and reported in a notice. With the 3' UTR on, its random part absorbs that remainder instead. A poly-A tail always adds to the body length, and the FASTA header reports the complete output length.
| Result | Contents |
|---|---|
| FASTA text | One record per sequence, separated by a blank line. |
| Header | RNA_ plus the template and one-based record number, then length=, measured GC=, and type=. |
| Download | The generated A/C/G/U text as a .fasta file. |
| Notices | Template limitations, mRNA triplet rounding, internal-stop limitations, and any unsupported options from saved settings. |
The GC target controls random bases rather than enforcing an exact composition. At 0%, random regions contain only A and U; at 100%, only G and C. Fixed template sequences, four-base stem-loop loops, and poly-A tails can still change the measured GC content.
This generator exports canonical A/C/G/U only and does not annotate modified nucleotides. Saved requests with the retired pseudouridine option display a notice and keep uridines as U. Y is a nucleotide ambiguity symbol, not a pseudouridine annotation; modified bases need a separate annotation convention, as defined by INSDC.
| Goal | Tool |
|---|---|
| Generate new A/C/G/U test sequences | This random RNA generator |
| Generate new A/C/G/T test sequences with optional terminal restriction sites | Random DNA generator |
| Generate new amino acid sequences from selected residue pools | Random protein generator |
| Replace T with U in an existing DNA sequence | DNA to RNA converter |
That depends on the experiment. Matching length and GC content does not preserve dinucleotide frequencies, exclude binding motifs, or rule out biological activity. Validate the generated sequences against the requirements of the comparison.
Random sampling creates variation, especially for short sequences. Fixed template bases and poly-A tails also contribute to the measured percentage.
No. They add terminal sequence motifs. The random middle is not screened for internal stop codons or optimized for expression.
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