/ensembl/genes/search

POST /api/ensembl/genes/search

Price: 5 credits

List the genes overlapping a genomic region of one species

How to use it

The query is a locus, not a keyword - to go from a gene name to a region, resolve the symbol through ensembl/genes and read `seq_region_name`, `start` and `end`. Chromosome names carry no `chr` prefix here, so the region is `13:32315086-32400268`. A gene is returned when it overlaps the region at all, including one that merely starts before it and runs into it, which is why a gene can come back with `start` below the region you asked for.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• region string required — Genomic region as chromosome:start-end, spanning at most 5,000,000 bases; the bounds are inclusive (examples: "13:32315086-32400268", "X:1-1000000", "17:43044295-43170245"; minLength: 3)
• species string — Ensembl species name the region belongs to (default: "homo_sapiens"; examples: "homo_sapiens", "mus_musculus"; minLength: 1)
• biotype string nullable — Keep only genes of this biotype (examples: "protein_coding", "lncRNA", "processed_pseudogene"; minLength: 1)
• logic_name string nullable — Keep only genes produced by this annotation pipeline (examples: "ensembl_havana_gene_homo_sapiens", "havana_homo_sapiens"; minLength: 1)
• count integer required — Max number of genes to return (min: 1)

Response

• @type string (default: "EnsemblGene")
• id string required
• display_name string (default: "")
• description string (default: "")
• biotype string (default: "")
• object_type string (default: "")
• species string (default: "")
• assembly_name string (default: "")
• seq_region_name string (default: "")
• start integer nullable
• end integer nullable
• strand integer nullable
• version integer nullable
• source string (default: "")
• logic_name string (default: "")
• db_type string (default: "")
• canonical_transcript string (default: "")
• parent_id string (default: "")
• length integer nullable
• is_canonical boolean nullable
• is_gencode_primary boolean nullable
• is_canonical_extended boolean nullable
• transcripts array (default: [])
  • @type string (default: "EnsemblTranscript")
  • id string (default: "")
  • display_name string (default: "")
  • gene_id string (default: "")
  • biotype string (default: "")
  • start integer nullable
  • end integer nullable
  • strand integer nullable
  • length integer nullable
  • version integer nullable
  • source string (default: "")
  • logic_name string (default: "")
  • seq_region_name string (default: "")
  • assembly_name string (default: "")
  • is_canonical boolean nullable
  • is_gencode_primary boolean nullable
  • is_canonical_extended boolean nullable
  • exons array (default: [])
    • @type string (default: "EnsemblExon")
    • id string (default: "")
    • start integer nullable
    • end integer nullable
    • strand integer nullable
    • version integer nullable
    • seq_region_name string (default: "")
  • translation object nullable
    • @type string (default: "EnsemblTranslation")
    • id string (default: "")
    • transcript_id string (default: "")
    • start integer nullable
    • end integer nullable
    • length integer nullable
    • version integer nullable
• url string (default: "")

Errors

• 422 — The request body did not validate Check the fields against this schema. A URN with the wrong prefix is the most common cause.
• 408 — The request ran past its time limit Raise `timeout` in the request body, up to the maximum this endpoint documents. Lowering `count` or turning off the `with_*` flags also helps, because less work finishes sooner.
• 412 — The entity was not found, or a precondition failed Retrying will not help: either the entity does not exist, or the input points at a different one.
• 429 — Too many requests: a rate limit or a usage window is exhausted When the response carries an X-Retry-After header, wait that many seconds and retry: the same number is in the body as `detail.retry_after`, and the limit clears once that window passes. The message in the body names the limit that was hit.
• 500 — Something broke on our side Retrying will not help. If it keeps happening, send us the X-Request-ID from the response headers.
• 529 — Rate limit reached, or the endpoint is overloaded Wait at least 30 seconds, then retry.

Response headers

• X-Error — Error message text (present only on error)
• X-Request-ID — Unique request identifier
• X-Execution-Time — Execution time in seconds
• X-Result-Count — How many records the body carries. 0 means an empty result, which is a normal answer and not by itself an error. A non-zero count can come back together with X-Error when the failure happened partway through — read this header and X-Error independently.
• X-Total-Available-Results — How many records exist for this query, when the endpoint can say. On a `dry_run` request this is the answer and the body is empty. It saturates: the endpoint's documented maximum means 'at least that many', any smaller number is exact.
• X-Warning — Present when the request body carried keys this endpoint does not document. They were ignored, so any filter you meant to apply through them did not apply. Check the spelling against this schema and retry.
• X-Retry-After — Seconds to wait before retrying. Present only on 429.