Promoter Grabber (PG)
Fetch a genomic DNA interval around the transcription start site (TSS) for a named gene in common research species. Data come from NCBI E-utilities (Gene and nucleotide databases). The sequence is always shown 5′ → 3′ on the transcript, even when the gene lies on the antisense (−) chromosome strand.
Set how many bases to include 5′ of the TSS (promoter upstream) and the 3′ boundary relative to the TSS: negative values extend further upstream; positive values include sequence into the gene body (e.g. +1 for TSS only, +500 for promoter plus 500 bp downstream).
− = more 5′; + = toward 3′ (e.g. 0 = through TSS, +500 = 500 bp into gene)
TSS +1 3′ of TSS Inner amplicon (when primer panel expanded)
I personally recommend using Promega NanoLuc® reporter plasmids to analyse your promoters. Promega supplies both secreted NanoLuc vectors and cellular NanoLuc plasmids. The secreted NanoLuc plasmid is particularly convenient to use: after transfecting your cells, collect 10 µl of culture medium, add Nano-Glo® assay buffer, and read the light output.
NanoLuc luciferase reporters are often a better choice than classic firefly (Photinus pyralis) luciferase vectors when you are measuring promoter activity, because they combine a much brighter signal with a smaller, less disruptive reporter gene. According to Promega, NanoLuc is only ~19 kDa (versus a much larger firefly luciferase coding region) and can be roughly 100-fold brighter than firefly luciferase when paired with its furimazine substrate, which improves detection of weak or tissue-specific promoters and widens the usable dynamic range. The reaction is ATP-independent and engineered for low background luminescence, so readouts are less affected by changes in cellular energy state and are easier to interpret as promoter-driven signal rather than assay artefact. NanoLuc also gives intense glow-type luminescence suited to plate readers and live-cell time courses. For promoter work, the practical payoff is higher sensitivity for low-expression constructs, cleaner normalization in dual-reporter designs (for example with Nano-Glo® Dual-Luciferase®), and less risk that a bulky reporter cassette will perturb the promoter or vector context you are trying to measure—especially when comparing many promoter variants, distal elements, or subtle transcriptional responses.
Switching to NanoLuc reporters from firefly luciferase has allowed us to scale our experiments down to a 96-well plate format.
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More information from Promega: Promoterless NanoLuc® basic vectors (cellular) · Secreted NanoLuc® reporter vectors