/ensembl/genes/sequences

POST /api/ensembl/genes/sequences

Price: 10 credits

Get the genomic, cDNA, CDS or protein sequence of an Ensembl feature

How to use it

The level of the id decides which `sequence_type` is meaningful: a transcript id gives cdna, cds or protein directly, while a gene id gives only `genomic` unless `multiple_sequences` is set, in which case one sequence per transcript comes back. `genomic` on a gene id is the whole locus including introns, which is far longer than the coding sequence. `mask`, `expand_5prime` and `expand_3prime` apply to genomic sequence only.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• gene string required — Ensembl stable id of a gene, transcript or translation (examples: "ENSG00000139618", "ENST00000380152", "ENSP00000369497"; minLength: 1)
• sequence_type string — genomic is the locus as it sits on the chromosome; cdna, cds and protein are the transcribed forms and need a transcript id, or `multiple_sequences` on a gene id (default: "genomic"; one of: "genomic", "cds", "cdna", "protein")
• multiple_sequences boolean — Allow a gene id to answer with one sequence per transcript. Without it a non-genomic type on a gene id is refused by the source (default: false)
• mask string nullable — Mask repeats in a genomic sequence, hard as N and soft as lower case (one of: "hard", "soft")
• expand_5prime integer nullable — Extra bases to include before the feature, genomic type only (min: 0)
• expand_3prime integer nullable — Extra bases to include after the feature, genomic type only (min: 0)
• count integer required — Max number of sequences to return (min: 1)

Response

• @type string (default: "EnsemblSequence")
• id string required
• query string (default: "")
• description string (default: "")
• molecule string (default: "")
• version integer nullable
• length integer nullable
• sequence 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 — Sequence not found for this identifier and type 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.