gff3

What is a .gff3 file?

text/x-gff3

GFF3 (General Feature Format version 3) is a tab-delimited format for genome annotations. Each line has nine columns — seqid, source, type, 1-based inclusive start and end, score, strand, phase, and a semicolon-separated attributes column — and parent/child relationships between genes, transcripts, and exons are expressed through ID and Parent attributes. Directives beginning with `##` carry metadata such as the sequence region.

How to use a .gff3 file

Use an example .gff3 file to test annotation parsers and genome-browser importers, checking that the 1-based inclusive coordinates are not treated as BED's half-open ones, that feature hierarchies reconstruct correctly, and that URL-escaped attribute values are decoded.

Download example .gff3 file

GFF3 Gene Annotations — 1-Based Inclusive Coordinates (.gff3)Seven features on a synthetic contig — two genes, an mRNA, two exons and two CDS records — linked by ID and Parent attributes across both strands. GFF3 coordinates are 1-based and inclusive, which is the fact its BED twin exists to contrast.

Convert a .gff3 file to another format

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