Reverse Complement

Turn a DNA or RNA sequence into its reverse complement, complement or reverse, or write DNA as RNA, from bare letters, a FASTA record or a GenBank record. IUPAC codes are kept and complemented.

Sequence tool

Flip a sequence

Sequence

Bare letters, a FASTA record or a GenBank record. Numbers and spaces from a listing are ignored.

Write out

Reverse complementComplementReverseTo RNA

Paste a DNA or RNA sequence to see its reverse complement.

The formula

Complement

A ↔ T, C ↔ G (A ↔ U in RNA)

Reverse complement

complement, then read it from the other end

5′, 3′: the two ends of a strand; a sequence is always written 5′ to 3′
R, Y, N…: IUPAC codes for more than one base; each has a complement (R ↔ Y, S ↔ S, N ↔ N)

Good to know

The reverse complement is the other strand, written 5′ to 3′ the way every sequence is. A primer that binds the reverse strand is the reverse complement of the stretch it covers, never just the complement.
Reverse alone, the same strand read backwards, is rarely what you want. It is here for checking palindromes and for the odd protocol that asks for it.
IUPAC codes are kept and complemented: R (A or G) becomes Y (C or T), K becomes M, and N stays N.
DNA to RNA only swaps T for U. A real mRNA is also spliced, capped and tailed, which no tool can do from the gene alone.

In the dictionary: DNA, FASTA format and transcription.

Worked example

The pUC19 polylinker, EcoRI to HindIII

015′-GAATTCGAGCTC…GCATGCAAGCTT-3′, 57 bp
02complement: 3′-CTTAAGCTCGAG…CGTACGTTCGAA-5′
03read from the other end: 5′-AAGCTTGCATGC…GAGCTCGAATTC-3′

The reverse complement starts AAGCTT (the HindIII site) and ends GAATTC (EcoRI): the same sites in the other order, as the other strand reads them.

How it works

The reasoning behind it

DNA is two strands held together by base pairs, A with T and C with G, running in opposite directions. Writing the complement of each base gives the other strand, but written 3′ to 5′, backwards from the way sequences are read. Reversing it puts it the right way round: that is the reverse complement.

It comes up constantly: the reverse primer of a PCR pair is the reverse complement of the end of the target; a gene on the minus strand of a genome is read from the reverse complement; and a restriction site that reads the same both ways, like GAATTC, is a palindrome, which is why most enzymes cut both strands.

The tool keeps IUPAC ambiguity codes, so a degenerate primer can be flipped as it is, and reads a FASTA or GenBank record straight from the clipboard. Numbers and spaces from a printed listing are ignored.

Questions

Frequently asked

What is the difference between the complement and the reverse complement?

The complement swaps each base for its partner and keeps the order, so it reads 3′ to 5′. The reverse complement also turns it round, so it reads 5′ to 3′ like any other sequence. For a primer or a strand you will type anywhere else, you want the reverse complement.

How do I get the reverse complement of an RNA sequence?

Paste it with U in place of T. The tool recognises RNA, pairs A with U, and writes the answer with U as well.

Why does my primer not match the sequence it should bind?

A reverse primer binds the forward sequence as its reverse complement. Take the reverse complement of the primer and search for that; or search the reverse complement of the template for the primer as written.

What happens to N and other ambiguity codes?

They are kept and complemented: N stays N, R (A or G) becomes Y (C or T), S (C or G) stays S, and so on. Letters that aren't bases at all are left out and the page says how many.

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