Promoter Grabber (PG)

You need promoter sequence when you’re building a luciferase reporter, checking where a ChIP peak sits relative to the TSS, designing PCR to amplify a gene’s promoter, or feeding DNA into our TF binding scanner or cross-species TF scanner.

PG is the “get me the sequence from the database” step. You simply give it a gene name (e.g. TP53, GAPDH or NFYA), pick a species, set how much DNA you want upstream of the TSS and how far into the gene (if at all) you want sequence for, and the page fetches it from NCBI. You also get a genomic context diagram with exons as blocks and your promoter window highlighted, so you’re not working blind from a flat FASTA file.

We built it because we were tired of copying coordinates out of one browser tab and pasting into another. It’s for quick, single-gene work. If you need hundreds of promoters or a specific genome build export, use NCBI or Galaxy properly; PG won’t replace that. After you have sequence, expand the reporter plasmids section below if you’re planning luciferase assays.

1. Find the gene

Your query goes to NCBI (via our small server proxy, with rate limiting so we don’t hammer their API). You can use a common gene name/symbol, a RefSeq mRNA (e.g. NM_…), or a Gene ID (e.g. 7157 for TP53). If NCBI returns several matches, you pick the right one.

2. Choose the TSS

The RefSeq transcripts for that gene are grouped when their TSS (5′ end of the first exon) falls within 10 bp of each other. You must select one group. The promoter TSS for the window is the most common position in the group, or the rounded average if there’s no clear winner. The table shows you what’s in each group so you can make an informed decision.

3. Cut the sequence

From that TSS we apply your bases 5′ of TSS (default 2000 bp upstream) and your 3′ boundary vs TSS (0 = through the TSS; negative = extend further 5′; positive = include into the gene body, e.g. +500 for promoter plus 500 bp downstream).

4. The results display

The sequence is always shown 5′ → 3′ on the transcript. Minus-strand genes are reverse-complemented for you. The map uses a representative transcript from the TSS group for exon structure; zoom/pan on the diagram if the window is wide.

5. Optional extras

Expand Design PCR primers for a suggested pair to amplify the promoter (with basic QC on length/GC/homopolymers; optional restriction sites with a short GAC clamp if you pick enzymes). The reporter plasmids section is our lab note on Promega NanoLuc vectors.

The underlying calls to NCBI use standard E-utilities (search, summary, link, fetch). Details: NCBI E-utilities.

1. Choose species and enter gene (symbol, NM_…, or Gene ID).
2. Set bases 5′ of TSS (1500–2500 bp is a common starting point for mammalian promoters; go shorter if you only care about the core proximal region).
3. Set 3′ boundary vs TSS (0 is usual for “promoter through the start”; use a positive number if you want the first exon in the fetch for context).
4. Click Fetch promoter. Wait a few seconds (NCBI is queried sequentially, ~3 requests/s). A busy gene with many transcripts can take a little longer.
5. If you see multiple genes, pick the one you mean.
6. If you see TSS groups, pick the isoform cluster that matches your biology (often the group with the most RefSeq transcripts).
7. Use the map to confirm exons and where the highlighted window sits. Copy sequence for downstream tools.
8. Optional: open Design PCR primers or read the reporter plasmid notes if you’re heading toward cloning.

Colour legend on the sequence: TSS position, downstream into the gene, and (when primers are shown) the inner amplicon.

• Strand confusion disappears. Antisense-strand genes are handled. The sequence you copy is the one you need to order as oligos or paste into a motif scanner.
• Alternative TSS is visible. Not buried in a table on another site. You choose the group before you download 2 kb of the wrong promoter.
• Context, not just text. The exon map highlights the location of the promoter sequence relative to the first exon.

• RefSeq / NCBI view. Not Ensembl, not GENCODE manual curation. If your field lives on a different annotation, verify the coordinates.
• Genome build. This tool uses whatever NCBI serves for that RefSeq record. For publication, confirm build and TSS against your favourite browser.
• TSS grouping is heuristic. 10 bp buckets are reasonable for mammals but won’t resolve every alternative promoter story.
• Server-mediated NCBI access. Requests go through thebondlab.net to NCBI (not pure client-side). Don’t paste human-identifiable or confidential sequences you wouldn’t send to a third-party API. See privacy policy.
• Primer suggestions are a starting point only. Check Tm, dimers, and internal restriction sites yourself; use the restriction digest analyser on the returned sequence.
• Not batch mode. The tool only handles one gene at a time.

• B.E.E.P. — batch human promoter BED coordinates and ENCODE TF ChIP overlap.
• Cross-species TF scanner — same NCBI promoter logic, two or three species, alignment + conserved motifs.
• TF binding scanner — scan the sequence you just copied for motifs.
• Primer design guide — qPCR/cloning primer workflow.
• Restriction digest analyser — make sure your enzyme sites aren’t already inside the promoter.

Promoter fetches use NCBI E-utilities through our server (rate-limited). Your gene name and chosen coordinates are used to retrieve public RefSeq data; we don’t use your sequence for advertising profiling. Treat unpublished or sensitive loci according to your institute’s rules. Site-wide cookies, analytics, and ads are described in the privacy policy.