Difference between Upstream and Downstream DNA

Upstream DNA

Each DNA strand has both 5’ and 3’ ends. The region that lies towards the 5’ end of the DNA coding strand is termed upstream DNA. The coding strand is formed as complementary to the template strand. The position of the genetic code in the upstream region is marked with negative numbering.

Usually, the promoter of a transcription unit lies here. Both upstream and downstream regions of DNA have a vital role in RNA transcription.

Downstream DNA

The region of the coding strand towards the three prime ends is called the downstream DNA. The position of genetic code in downstream DNA starts with positive numbering. The downstream has the protein-coding region that undergoes transcription. Also, it has a termination site that helps to end the transcription.

Difference between Upstream and Downstream DNA

Upstream DNA

Downstream DNA

It is the region of DNA that is towards the 5’ end.

It is the region of DNA that is towards the 3’ end.

The promoter is seen towards the 5’ end.

The terminator is seen towards the 3’ end.

The nucleotides in the upstream region are negatively numbered.

The nucleotides in the downstream region are positively numbered.

It has regions that help in the initiation and regulation of transcription.

It contains instructions for protein synthesis until termination.

Refer: Difference between Enhancer and Promoter

Frequently Asked Questions


What does 5’ and 3’ ends denote?

The three prime end (3’ end) has a hydroxy group (-OH) attached to the third carbon of the sugar ring structure. The five prime end has a phosphate group attached to the fifth carbon of the sugar ring structure. The 5’ phosphate and the 3’ hydroxyl covalently bind to form a phosphodiester bond.


What is a transcription unit?

The segment or region of DNA that takes part in the process of transcription is called a transcription unit. This unit consists of a promoter, terminator and structural genes. The promoter initiates the protein synthesis, and the structural genes code for any protein or RNA. Finally, the terminator site ends the transcription.

Also Read: Genetic Material

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