DNA to RNA converter
Convert coding-strand DNA to RNA notation by replacing thymine with uracil.
Input
How to convert DNA to RNA
Paste a DNA sequence or upload a sequence file, then select Convert. The DNA to RNA converter changes every thymine (T) to uracil (U), retains the other nucleotide and ambiguity codes, and returns a copyable, downloadable .fasta file. Supply the coding strand in the intended sequence order. The preview reports converted records, sequence characters and replacements.
For a plain sequence, the converter creates a FASTA header and, with the default header setting, adds rna_ before it:
ATGCTTACGAThe default output is:
>rna_Sequence
AUGCUUACGAFASTA input is processed record by record. This example uses Preserve original case and No wrapping (single line) so the case behavior is visible:
>reference_fragment DNA
ATGCTTACGA
>mixed_case
aTgCttNN-.The converted FASTA is:
>rna_reference_fragment DNA
AUGCUUACGA
>rna_mixed_case
aUgCuuNN-.The conversion is a character substitution, not a strand-complement operation. For a template strand written 5′ to 3′, make a reverse complement first, then replace T with U. A template written 3′ to 5′ needs complementation without reversing its order.
Input
| Input | What the converter accepts |
|---|---|
| DNA sequence input | One pasted DNA sequence, multiple FASTA records, or an uploaded .txt, .fasta, .fa, .fas, or .seq file. Text can also be extracted from .docx and text-based .pdf files; scanned PDFs need text recognition first. Uploaded files can be up to 50 MB. Plain sequences receive the default >Sequence header before header formatting is applied. |
| Sequence characters | With validation enabled, A, T, U, C, G, the IUPAC ambiguity codes R, Y, S, W, N, K, M, B, D, H, and V, plus . and -. Whitespace within a sequence is removed. An input U is accepted but reported as an RNA character in DNA input. |
Comment lines beginning with # or ; and blank lines are ignored. Plain sequence lines are joined into one record. For FASTA, put the header on its own line, beginning with >, followed by one or more sequence lines. The complete header, including its description, is retained. Empty records and invalid records are skipped with visible warnings; if every record is skipped, the converter returns an error.
Pasted document text can contain invisible characters or typographic gaps. These are normalized in sequence lines, while FASTA descriptions retain their original text. Matching leading and trailing position numbers, such as 1 ATGC 4, are removed. Embedded digits or inconsistent positions are invalid with validation enabled. Expected cleanup appears in the run log.
Use FASTQ to FASTA for reads with quality scores, GenBank to FASTA for annotated GenBank records, or the FASTA converter for alignment files. For named lists or spreadsheet data, use TXT to FASTA to establish record boundaries before converting DNA to RNA.
Settings
| Setting | Behavior |
|---|---|
Output case | Select UPPERCASE (AUCG) (default), lowercase (aucg), or Preserve original case. Uppercase and lowercase change sequence lines only, not FASTA headers. Preserve original case keeps the capitalization of each input residue while converting T to U. |
Line wrapping | Select 80 characters per line (standard) (default), 60 characters per line, or No wrapping (single line). The setting applies to every output sequence. |
Validate input sequences | Enabled by default. Records containing characters outside the accepted set are skipped and reported in the warnings. DNA input that contains U is still converted, with a warning. When disabled, nonstandard sequence characters are retained and reported. Recognized neighboring formats and unreadable binary text remain rejected. |
Add prefix to headers | Enabled by default. Adds rna_ immediately after > in every FASTA header, such as >sample DNA becoming >rna_sample DNA. Turn it off to retain the original header. Saved settings using the earlier name, Add suffix to headers, keep the same behavior. |
Results
| Result | Contents |
|---|---|
| Preview | The converted sequences in FASTA format. Each record has a header, followed by RNA sequence lines using the selected case and wrapping. |
| Downloadable FASTA file | The same converted FASTA content. Pasted input downloads as converted.fasta; an uploaded file uses its original basename with a .fasta extension. |
| Summary and warnings | Converted and skipped record counts, the number of characters in converted sequences, and the number of T replacements. Character counts include preserved gaps and nonstandard symbols when validation is off. Warnings identify omitted records, retained nonstandard symbols and DNA records containing U. |
run.log | Downloadable conversion counts, selected settings, warning count and cleanup details. It appears in Files and the Logs tab. Headers and sequence contents are excluded. |
What does DNA to RNA conversion represent?
DNA uses thymine, while RNA uses uracil, so a coding-strand DNA sequence ATGC corresponds to RNA AUGC. NCBI's account of transcription describes how RNA is complementary to the template strand. Ambiguity symbols describe uncertain bases and remain unchanged, as do alignment gaps (- and .). This gap support goes beyond NCBI's unaligned nucleotide FASTA submission rules.
In a cell, transcription is performed by an RNA polymerase reading the DNA template strand. This converter does not model promoters, strand orientation, splicing, or RNA processing. It only produces the nucleotide notation change needed when a DNA coding-strand sequence should be represented as RNA. To reverse the notation change, use the RNA to DNA converter.
Which sequence tool should I use?
| Goal | Tool to use | Why |
|---|---|---|
Replace T with U in a coding-strand DNA sequence | DNA to RNA converter | Produces RNA-formatted FASTA while retaining headers, ambiguity codes, and optional wrapping. |
Replace U with T in an RNA sequence | RNA to DNA converter | Reverses this conversion for RNA-formatted input. |
| Obtain the opposite DNA strand before representing it as RNA | Reverse complement | Complements bases and reverses sequence order, which this converter does not do. |
| Translate a coding sequence to amino acids | DNA to protein | Converts codons into a protein sequence rather than changing nucleotide notation. |
| Predict base pairing or secondary structure for RNA | RNAfold | Uses an RNA sequence to predict a secondary-structure ensemble. |
FAQ
Does DNA to RNA conversion complement the DNA sequence?
No. It replaces T with U and leaves the sequence order unchanged. If a template strand is written 5′ to 3′, reverse complement it first. If it is written 3′ to 5′, complement without reversing.
Can I convert multiple DNA sequences to RNA at once?
Yes. Paste or upload multiple FASTA records. The converter processes each valid record independently and returns them together in one FASTA file.
Why does my output header start with rna_?
Add prefix to headers is enabled by default. Disable it when the input headers must remain unchanged. Earlier saved runs use the setting name Add suffix to headers for the same prefix behavior.
Why are there fewer output records than input records?
The converter skips empty records and, with validation enabled, records containing invalid nucleotide characters. The summary reports the skipped count and warnings identify the records to fix. Nothing is downloaded if no records can be converted.
Can DNA input include IUPAC ambiguity codes?
Yes. The converter accepts standard ambiguity codes, including N, R, Y, K, and M, and keeps them unchanged. It only replaces T with U.
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