ensembl_feature_overlap
Identify overlapping genomic features (genes, transcripts, regulatory elements) for a specified region or feature ID. Supports species-specific data and assembly formats, enabling precise genomic analysis.
Instructions
Find genomic features (genes, transcripts, regulatory elements) that overlap with a genomic region or specific feature. Automatically handles assembly-specific format variations (GRCh38/hg38, chromosome naming conventions, coordinate systems). Covers /overlap/region and /overlap/id endpoints.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| biotype | No | Filter by biotype (e.g., 'protein_coding', 'lncRNA', 'miRNA', 'pseudogene') | |
| feature_id | No | Feature ID (gene, transcript, etc.) to find overlapping features for (e.g., 'ENSG00000141510', 'ENST00000288602', 'BRCA1'). Use this OR region, not both. | |
| feature_types | No | Types of features to include (e.g., ['gene', 'transcript', 'exon'], ['regulatory', 'enhancer']) | |
| region | No | Genomic region in format 'chromosome:start-end' (e.g., '17:7565096-7590856', 'X:1000000-2000000', '1:100000-200000'). Use this OR feature_id, not both. | |
| species | No | Species name (e.g., 'homo_sapiens', 'mus_musculus', 'danio_rerio') | homo_sapiens |
Input Schema (JSON Schema)
{
"oneOf": [
{
"required": [
"region"
]
},
{
"required": [
"feature_id"
]
}
],
"properties": {
"biotype": {
"description": "Filter by biotype (e.g., 'protein_coding', 'lncRNA', 'miRNA', 'pseudogene')",
"type": "string"
},
"feature_id": {
"description": "Feature ID (gene, transcript, etc.) to find overlapping features for (e.g., 'ENSG00000141510', 'ENST00000288602', 'BRCA1'). Use this OR region, not both.",
"type": "string"
},
"feature_types": {
"description": "Types of features to include (e.g., ['gene', 'transcript', 'exon'], ['regulatory', 'enhancer'])",
"items": {
"type": "string"
},
"type": "array"
},
"region": {
"description": "Genomic region in format 'chromosome:start-end' (e.g., '17:7565096-7590856', 'X:1000000-2000000', '1:100000-200000'). Use this OR feature_id, not both.",
"type": "string"
},
"species": {
"default": "homo_sapiens",
"description": "Species name (e.g., 'homo_sapiens', 'mus_musculus', 'danio_rerio')",
"type": "string"
}
},
"type": "object"
}