# How to Use Ensembl's 'Jump to Region' Feature for Quick Navigation Ensembl's Jump to Region feature lets you type a coordinate such as 17:7668421-7687550, press Enter, and land centered on that exact stretch of the genome. A coordinate is a numbered position on a genome assembly, counted in bases, the individual letters of DNA. By the end of this guide you will know how to use Ensembl to reach a gene, a variant, or a raw coordinate in seconds, confirm you are viewing the right genome assembly, convert BED files into Ensembl links without off-by-one errors, and automate the whole lookup with the Ensembl REST API. You need three things for the walkthrough: a web browser, an internet connection, and the sample coordinates used here, which are real positions for the human TP53 gene on the GRCh38 assembly. For the automation section you also need curl or Python 3. Every command is reproducible as written. ## What 'Jump to Region' Does in Ensembl Ensembl is a free public genome browser and annotation database. A genome browser draws genomic data, such as genes and variants, as layers called tracks along a coordinate ruler. Ensembl covers vertebrates at www.ensembl.org and other branches of life through companion sites such as plants.ensembl.org, where the same controls work the same way. Ensembl organizes each gene or region into tabs. The Location tab draws a stretch of genome. The Gene, Transcript, and Variation tabs describe individual objects. Jump to Region lives inside the Location view. You type a position or a range, press Enter, and the browser redraws centered on that locus. A locus (plural loci) is a specific address on a genome. Three routes reach the same result, and each has a best use: 1. The search bar at the top of every Ensembl page. It accepts gene names, identifiers, variant IDs, and coordinates, and routes you to the most fitting page. 2. The Jump to box inside the Location view. It accepts coordinates and recenters the current view without leaving the page. This is the fastest tool when you are already browsing. 3. The URL itself. Location pages carry the region in an r= parameter, so you can build, bookmark, or share a link that opens the exact view. If you have used older browser software such as GBrowse, which some model organism databases still provide among their tools [1], expect different control names. The underlying action, recentering a view on a coordinate, is the same everywhere. Treat this section and the walkthrough below as a compact Ensembl [genome browser tutorial](/blog/guides/genome-browsers-for-researchers-a-guide-to-inspecting-genomic-evidence) focused on the part that pays off daily. ## Ensembl Among Genome Databases Ensembl does not stand alone. Model organism databases wrap their own curation around the same genomes and link outward. Xenbase, the database for the frog models Xenopus laevis and Xenopus tropicalis, integrates genomic and biological data for Xenopus research and builds gene pages that link to Ensembl, NCBI Entrez, and UniProtKB [1]. It also runs its own BLAST service next to its genome data [1]. The practical consequence for navigation is that you can enter the genome from either side. Search Ensembl directly, or arrive from a curated gene page that has already resolved naming and cross-references for you. Whichever door you use, Jump to Region is the control that moves you around once you are inside. The pattern repeats across the ecosystem of genome databases, which is why the skills in this guide transfer between them. ## Before You Jump: Species, Assemblies, and Coordinate Formats ### Why the genome assembly matters A genome assembly is a reference version of a species' genome sequence. Ensembl layers annotation, the set of genes and other features marked on that sequence, on top of the assembly, and updates both in numbered releases a few times a year. Human coordinates are only meaningful relative to one assembly. Ensembl's current human assembly is GRCh38. The previous assembly, GRCh37, remains in service at grch37.ensembl.org because a large share of published results refer to it. The same gene can sit far apart in the two assemblies. BRCA1, a well-studied breast cancer gene, sits at 17:43044295-43125482 in GRCh38 and at 17:41196312-41277499 in GRCh37, a shift of roughly 1.8 million bases. A jump that ignores the assembly lands you in the wrong place, and nothing on the page will warn you. Other species follow the same pattern. Current mouse annotation sits on GRCm39 and zebrafish on GRCz11. Read the assembly name in the page header every time you land, because the header is the only place Ensembl states which reference you are viewing. ### The coordinate formats Ensembl accepts Ensembl writes coordinates as chromosome:start-end, counted from 1, with both endpoints included. All of these work in the search bar and in the Jump to box: - 17:7668421-7687550, a range - 17:7668421, a single base - 17, a whole chromosome Two formatting habits prevent most failures. First, paste numbers without commas. Ensembl displays coordinates with commas for readability, as in a page title, but the safe input form is the bare number. Second, Ensembl names chromosomes without the chr prefix. If a lookup fails and your source data uses chr17, retry without the prefix. ### Coordinate systems you will meet Genome file formats disagree about where counting starts, and this causes the most common off-by-one error in browser work: | Format | Counting start | End position | Example for the same base | |, - |, - |, - |, - | | Ensembl pages, GFF, GTF, VCF | 1 | included | 17:7668421 | | BED | 0 | excluded | 17 7668420 | A base pair (bp) is one rung of the DNA ladder, and both rows in the table point at the same physical base. To convert BED to Ensembl, add 1 to the BED start and keep the BED end. The worked example later in this guide applies that formula to a real file. ## Ensembl Jump to Region Step by Step This walkthrough uses the human TP53 gene, which encodes the p53 tumor protein, on the GRCh38 assembly. The coordinates are real, so you can follow along and see the same pages. ### Step 1: Open Ensembl and confirm the assembly Point your browser at www.ensembl.org. Before searching, read the header. It names the species (Homo sapiens), the assembly (GRCh38), and the release number. If you arrived through a mirror such as useast.ensembl.org or asia.ensembl.org, the data is identical and only the server differs. ### Step 2: Jump to a coordinate from the search bar Click the search bar at the top of the page and type: ``` 17:7668421-7687550 ``` Press Enter. Ensembl opens a Location page centered on the range. The page title reads like "Chromosome 17: 7,668,421-7,687,550", and the main image, called Region in detail, draws the gene models that overlap your range, TP53 among them. On the main site a bare coordinate normally resolves against human. If Ensembl shows a list of matches instead, choose the Homo sapiens entry. ### Step 3: Read the Location page Four parts of this page matter for navigation: 1. The header, which repeats the species, assembly, and release. Read it on every landing. 2. The coordinate ruler above the image, which shows where you are, and the scale indicator, which shows how wide the view is. 3. The tracks drawn across the image, each labeled on the left, such as the gene model track. 4. The address bar. The URL now carries r=17:7668421-7687550. That r= parameter is the region, and you will use it later for sharing and scripting. For a coarse approach, click the chromosome number in the page path to open the chromosome view with its ideogram, a schematic drawing of the chromosome and its banding. TP53 sits on band 17p13.1. Clicking a band jumps you there, which helps when you know the band but not the coordinate. ### Step 4: Refine the view with the Jump to box Above the region image, next to the chromosome selector, is the Jump to input. Type a narrower window and press Enter or click Go: ``` 17:7676000-7679000 ``` The view recenters without leaving the page. The ruler renumbers, the image redraws, and the r= value in the address bar changes to match. This is the core loop of the feature: search once to arrive, then jump repeatedly to move. The box also rewards strand awareness. A kilobase (kb) is 1,000 bases. TP53 lies on the minus strand, so its transcript starts at the high end of its span, near position 7,687,550, and upstream means higher coordinates. The 2 kb window immediately upstream therefore runs from 17:7687551 to 17:7689550. Check the arithmetic: 7689550 - 7687551 + 1 = 2000 bases. Type that range into the Jump to box and you are looking at the promoter-side window, the stretch where transcription control signals typically sit. ### Step 5: Zoom to the basepair view Drag across part of the image to select a smaller range, or use the zoom controls, until individual bases appear. At high zoom Ensembl draws the sequence itself, base by base, with coding features marked where they overlap transcripts. This view is where you check a codon, a splice site, or a variant base directly. ### Step 6: Verify that you landed correctly Check four things before you trust the view: 1. The header still says Homo sapiens and GRCh38. 2. The coordinate readout matches the range you typed. 3. The gene label you expect, here TP53, sits inside your range. 4. The strand arrow points the right way. TP53 reads right to left across the ruler because it sits on the minus strand. For an independent check, run the REST lookup shown below and compare the coordinates it returns with the ones on screen. ### Step 7: Save, share, and export the view Copy the URL from the address bar. Because the region travels in the r= parameter, the link reopens the same view on any machine. To take the sequence with you, use the Export data link in the left menu, which offers the displayed region as FASTA, or use the REST command in the next section. ## What You Can Type: Query Types and Formats The search bar and the Jump to box accept more than coordinates. An identifier is a stable label for a biological object, and Ensembl indexes several kinds: | Query type | Example | Where you land | |, - |, - |, - | | Coordinate range | 17:7668421-7687550 | Location page centered on the range | | Single base | 17:7668421 | Location page centered on that base | | Gene symbol | TP53 | Gene page, or a match list if the name is shared across species | | Ensembl gene ID | ENSG00000141510 | Gene page for TP53 | | Ensembl transcript ID | ENST00000269305 | Transcript page for a TP53 transcript | | RefSeq transcript ID | NM_000546 | Gene or transcript page through the cross-reference | | UniProt ID | P04637 | Gene page through the cross-reference | | Variant rsID | rs699 | Variation page for that variant | | Species-qualified symbol | mouse Brca1 | Gene page in mouse | Ensembl IDs carry a prefix that names the object type. ENSG marks a gene, ENST a transcript, ENSP a protein, and ENSR a regulatory feature. An rsID is an identifier from dbSNP, the public catalog of genetic variants. A cross-reference is a link between the same object in two databases, which is why NM_000546 and P04637 both resolve to TP53. Symbols are the least reliable input. A symbol such as TP53 exists in many species with different coordinates, so Ensembl shows a disambiguation page, a list of matches for you to choose from. Qualify the species as in the last table row, or search the ID, whenever you need a single unambiguous answer. ## Worked Commands: URLs, REST, and Batch Jumps ### Build a direct URL ``` https://www.ensembl.org/Homo_sapiens/Location/View?r=17:7668421-7687550 ``` The parts of this URL: 1. www.ensembl.org, the server 2. Homo_sapiens, the species path 3. Location/View, the page that draws a region 4. r=17:7668421-7687550, the region parameter Paste the URL into any browser to land directly on the view. For data on the older assembly, keep the same path on the GRCh37 site: ``` https://grch37.ensembl.org/Homo_sapiens/Location/View?r=17:41196312-41277499 ``` Archive pages carry a banner identifying the archive, so you can always tell which reference you are on. ### Look up coordinates with the REST API A REST API is a web service you query with plain URLs and receive [structured data](/blog/data-analysis/what-is-structured-data) from, usually JSON, a text format of labeled values. The lookup endpoint converts an ID into its coordinates: ``` curl "https://rest.ensembl.org/lookup/id/ENSG00000141510?content-type=application/json" ``` Expected output, abbreviated: ```json { "assembly_name": "GRCh38", "biotype": "protein_coding", "end": 7687550, "id": "ENSG00000141510", "seq_region_name": "17", "start": 7668421, "strand": -1 } ``` Read the fields this way. seq_region_name is the chromosome in Ensembl's internal vocabulary. start and end are the 1-based inclusive coordinates. strand of -1 means the gene lies on the minus strand. biotype is the object type Ensembl assigns, here protein_coding. A typo or a retired ID returns HTTP status 404 with a JSON error object, which is your signal to search by symbol instead. The symbol endpoint does the same job from a gene name: ``` curl "https://rest.ensembl.org/lookup/symbol/homo_sapiens/TP53?content-type=application/json" ``` The response has the same shape, with the same coordinates for TP53. ### Pull the sequence for a region ``` curl "https://rest.ensembl.org/sequence/region/human/17:7668421-7687550?content-type=text/plain" ``` The response is FASTA, a plain-text sequence format with a header line that starts with > followed by the sequence in 60-character lines. The header names the region you requested, so you can always trace the sequence back to its coordinates. ### Convert a BED file into Ensembl links ![Worked calculation adding 1 to the BED start 7668420 to get the Ensembl start 7668421, keeping the end 7687550 unchanged.](/article-images/illustrations/ensembl-jump-to-region-bed-conversion.webp) Save this script as bed_to_ensembl.py: ```python # bed_to_ensembl.py # usage: python bed_to_ensembl.py regions.bed # BED columns are tab separated import sys for line in open(sys.argv[1]): line = line.strip() if not line or line.startswith(("#", "track", "browser")): continue fields = line.split() chrom = fields if chrom.startswith("chr"): chrom = chrom[3:] ensembl_start = int(fields[1]) + 1 print(f"https://www.ensembl.org/Homo_sapiens/Location/View?r={chrom}:{ensembl_start}-{fields}") ``` Given this input file, regions.bed: ``` 17 7668420 7687550 TP53 17 43044294 43125482 BRCA1 ``` the script prints: ``` https://www.ensembl.org/Homo_sapiens/Location/View?r=17:7668421-7687550 https://www.ensembl.org/Homo_sapiens/Location/View?r=17:43044295-43125482 ``` The +1 on the start line is the whole trick. BED start 7668420 becomes Ensembl start 7668421, and the end passes through unchanged. The script assumes human and GRCh38. For another species, change the species path. For GRCh37 data, change the host to grch37.ensembl.org. ### Batch a gene list into coordinates Install the requests library once with pip install requests, then run: ```python # genes_to_coords.py import requests symbols = ["TP53", "BRCA1"] for symbol in symbols: url = f"https://rest.ensembl.org/lookup/symbol/homo_sapiens/{symbol}" r = requests.get(url, headers={"Content-Type": "application/json"}) data = r.json() print(f"{symbol}\t{data['seq_region_name']}:{data['start']}-{data['end']}") ``` Expected output: ``` TP53 17:7668421-7687550 BRCA1 17:43044295-43125482 ``` Keep request rates modest when you scale this up. Ensembl's REST documentation asks high-volume users to keep their request rate low and to identify their scripts, and a short pause between requests keeps you comfortably inside that guidance. ## Ensembl Jump to Region Tips ### Qualify the species when a symbol is shared An ortholog is a gene in another species that descends from the same ancestral gene. Symbols survive across species, so Brca1 exists in mouse and rat with different coordinates. Type mouse Brca1, or pick the species first, and you skip the disambiguation page entirely. ### Jump from a model organism database If you work in a non-human species, start at that species' own database and let it hand you to Ensembl. Xenbase gathers curated expression images, ontology terms, and reagent catalogs such as antibodies and morpholinos onto its gene pages [1], so you often arrive knowing more than a bare symbol search would tell you. Follow the Ensembl link from the gene page, then use Jump to Region to center on an exon, a promoter, or a variant. ### Use archive sites for old coordinates Papers often publish coordinates against an assembly that is no longer current. Match the assembly before you match the numbers. GRCh37 human data lives at grch37.ensembl.org, and older Ensembl releases live on month-year archive sites such as dec2021.archive.ensembl.org. Keeping old assemblies reachable is standard practice across genome databases. Xenbase hosts current and archived genomes for both of its frog species so that published analyses stay reproducible [1], and Ensembl's archive sites serve the same purpose. ### Use mirrors when the main site is slow useast.ensembl.org and asia.ensembl.org serve the same data as the main site. If a page hangs during a busy period, switch hosts and continue. Your r= links work on any host. ### Configure tracks before you jump A jump that lands on an empty image tells you little. Open Configure this page from the Location view and turn on the tracks you care about, such as sequence conservation or known variants. The setting persists, so every later jump lands on an informative picture. ### Use BLAST when you only have sequence If your starting point is a sequence rather than an ID, run Ensembl's BLAST service, the Basic Local Alignment Search Tool, which finds genome regions similar to a sequence you supply. It sits under the Tools menu. Map your sequence, then jump to the hit. Genome databases bundle this kind of similarity search next to their browsers, which is exactly how Xenbase pairs BLAST with its genome resources [1]. ### Keep a coordinate notebook Keep a plain text file with one locus per line: the gene, the assembly, and the full r= URL. Paste the URL into the address bar to restore the view in one step. The notebook beats a bookmark folder because it carries the assembly with the position, which is the pairing that actually matters. ## Common Mistakes and Limitations ![Decision path from a wrong landing through assembly, comma and chr prefix checks to the fix for each cause.](/article-images/illustrations/ensembl-jump-to-region-wrong-place-triage.webp) Most Ensembl Jump to Region mistakes trace back to a handful of causes, in the order they tend to strike. 1. Jumping without checking the assembly. Coordinates belong to one assembly, and both GRCh37 and GRCh38 numbers appear throughout the published literature. The BRCA1 example above sits far apart between the two. Read the header on every landing. 2. Pasting formatted numbers. Commas inside coordinates confuse parsers. Strip them before you paste. 3. Carrying a chr prefix into a failed lookup. Ensembl chromosome names carry no prefix. If a lookup fails, retry without chr. 4. Pasting BED starts directly. A BED start is one less than the Ensembl start. If your jump lands one base early and every feature looks shifted, this is why. Use the conversion formula from the table above. 5. Trusting the first match. Shared symbols produce a match list, and the top entry is not always your species. Confirm the species and assembly before you read anything off the page. 6. Ignoring strand. A minus-strand gene reads right to left, so a window you eyeball as upstream may be downstream. The REST lookup reports strand as 1 or -1, and the promoter calculation in Step 4 shows how the direction changes the arithmetic. 7. Reusing a stale ID. Ensembl IDs can change between releases when genes are merged or split. Search by symbol or sequence, or run the old ID through Ensembl's ID history converter. 8. Expecting the jump to validate your biology. Jump to Region recenters a view. It does not check that your coordinates mean what you think, that your file matches the assembly, or that the feature you care about is annotated in this release. A note on limits. Annotation changes between releases, so a view that was correct last year can differ today. Converting coordinates between assemblies is a separate task that needs a dedicated tool, not a manual guess. For clinical or publication work, verify every coordinate against the current release and have a second person check the locus before it leaves your hands. ## Troubleshooting Reference | Symptom | Likely cause | Fix | |, - |, - |, - | | Search returns no usable match | Malformed coordinate, commas or a chr prefix | Strip commas and the prefix, retry | | Page opens, expected gene missing | Assembly mismatch | Read the header, switch to grch37.ensembl.org or back | | View lands one base early | BED start pasted directly | Add 1 to the start | | Match list instead of a page | Symbol shared across species | Pick your species, or qualify the query | | REST lookup returns HTTP 404 | Retired ID or typo | Search by symbol, or use the ID history converter | | Pages hang or time out | Busy server | Switch to useast.ensembl.org or asia.ensembl.org | | Paper coordinates do not match the browser | Paper used an older assembly | Find the assembly in the methods, open the matching archive site | Each row maps to a section above, so the fix usually takes seconds once you can name the symptom. ## Frequently Asked Questions ### What is the difference between the search bar and the Jump to box? The search bar accepts genes, IDs, variants, and coordinates, and routes you to whichever page fits best. The Jump to box lives inside the Location view and recenters the current view on a coordinate without leaving the page. ### Why do my coordinates land in the wrong place? Almost always an assembly mismatch. Coordinates are valid for one assembly only, and the same gene can sit millions of bases apart between GRCh37 and GRCh38. Read the assembly in the header and use the matching archive site for old data. ### Can I jump to a region in a species other than human? Yes. Pick the species first or use a species-qualified query such as mouse Brca1. Model organism databases such as Xenbase also link their gene pages straight to Ensembl [1]. ### How do I convert BED coordinates for Ensembl? Add 1 to the BED start and keep the end. BED counts from 0 and excludes the end base, while Ensembl counts from 1 and includes both endpoints. ### Can I share an Ensembl region view with a colleague? Yes. Copy the URL. The r= parameter carries the region, so the link reopens the same view anywhere. ### Does Ensembl keep old genome assemblies available? Yes. GRCh37 human data sits at grch37.ensembl.org and older releases live on month-year archive sites. Xenbase follows the same practice, keeping archived genomes next to current ones [1]. ### Can I automate region lookups instead of using the browser? Yes. The REST API returns coordinates and sequence for IDs and regions through plain URL queries, which makes batch conversion straightforward. ### What should I do if an Ensembl ID no longer resolves? Search by gene symbol or sequence instead, or run the old ID through Ensembl's ID history converter. IDs can change when a release merges or splits genes. ## Sources 1. [Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.](https://pubmed.ncbi.nlm.nih.gov/29761462/)