MSA can be used to align promoter regions and highlight regions of conservation that may be indicative of transcription factor binding sites.

Quantitative Reverse-Transcription PCR is a modification of PCR in which RNA is first reverse transcribed into cDNA and this is amplified measuring the product (qPCR) in real time. It therefore allows one to analyze transcription by directly measuring the product (RNA) of a gene's transcription. If the gene is transcribed more, the starting product for PCR is larger and the corresponding volume of amplification is also larger.

Rapid Amplification of cDNA Ends is a technique to obtain the full length sequence of an RNA transcript. Most succinctly, the technique exploits the fact that PCR will stop at the ends of a mRNA. Basically, a primer mapping a "center" region of the mRNA is used to perform RT-PCR and terminal deoxynucleotidyl transferase (TdT) is used to add identical nucleotides to the 3' end of the cDNA. Standard PCR using another primer and the TdT-oligomer is performed in the other sense. The technique is frequently used to verify transcription start sites, which are relevant to the function (e.g. repression) of transcription factor binding sites.

Visual inspection of promoter region to identify putative binding sites based on previous knowledge