genes

Identifier

refseq.genes

Description

RefSeq gene and pseudogene annotations derived from genomic GFF3 files.

One row represents one GFF gene-feature interval.

A rare multi-part or trans-spliced gene therefore has multiple rows sharing its gene_id.

gene_id is the local GFF ID, not an NCBI Gene identifier; use the GeneID entry in db_xrefs for that identifier. is_pseudogene distinguishes NCBI pseudogene from gene features.

Partitions

• assembly_accession
  • 'GCF_000001215.4'
  • 'GCF_000001405.25'
  • 'GCF_000001405.40'
  • 'GCF_000001635.20'
  • 'GCF_000001635.27'
  • 'GCF_000001895.5'
  • 'GCF_000002035.6'
  • 'GCF_000002285.3'
  • 'GCF_000002985.6'
  • 'GCF_000003025.6'
  • 'GCF_000003625.3'
  • 'GCF_000005845.2'
  • 'GCF_000146045.2'
  • 'GCF_003339765.1'
  • 'GCF_012559485.2'
  • 'GCF_015227675.2'
  • 'GCF_036323735.1'
  • 'GCF_037993035.2'
  • 'GCF_049350105.2'
  • 'GCF_052040795.1'
  • 'GCF_054392235.1'
  • 'GCF_964237555.1'

Schema

Column	Type	Description
sources	STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]	Original external inputs used to produce the row. Each item contains its source URL, filename, HTTP Last-Modified timestamp when available, and computed SHA-256 checksum.
assembly_accession	TEXT	Partition column. Versioned RefSeq assembly accession (GCF accession).
sequence_accession	TEXT	Versioned RefSeq nucleotide sequence accession on which the interval is annotated; joins refseq.assembly_sequences.sequence_accession.
start	INT	1-based inclusive start coordinate of the feature interval on sequence_accession.
end	INT	1-based inclusive end coordinate of the feature interval on sequence_accession.
is_forward_strand	BOOLEAN	Whether the feature interval is on the forward strand; null when the GFF strand is unspecified.
is_pseudogene	BOOLEAN	Whether NCBI annotated the feature as a pseudogene.
gene_id	TEXT	Local GFF3 ID of the gene feature; not an NCBI Gene identifier.
annotation_method	TEXT	NCBI GFF column-2 annotation method or source, such as BestRefSeq, Gnomon, or GeneMarkS+, if supplied.
gene_symbol	TEXT	NCBI primary gene symbol from the GFF gene attribute, if supplied.
gene_symbol_aliases	TEXT[]	Alternative gene symbols from the comma-separated GFF gene_synonym attribute.
gene_name	TEXT	NCBI full gene name from the GFF description attribute, if supplied.
db_xrefs	STRUCT(db TEXT, id TEXT)[]	Database cross-references from GFF Dbxref; each item has a database and identifier, which may contain colons.
gene_biotype	TEXT	NCBI-calculated gene biotype from the GFF gene_biotype attribute, if supplied.
gene_locus_tag	TEXT	Gene locus tag from the GFF locus_tag attribute, if supplied.
pseudogene_type	TEXT	NCBI pseudogene classification from the GFF pseudogene attribute, if supplied.
part	INT	Ordinal interval number from the GFF part=N or part=N/M attribute, if supplied.
is_partial	BOOLEAN	Whether NCBI marks the feature as partial with GFF partial=true.
is_start_partial	BOOLEAN	Whether NCBI marks the column-4 start boundary as partial with a GFF start_range attribute.
is_end_partial	BOOLEAN	Whether NCBI marks the column-5 end boundary as partial with a GFF end_range attribute.
exception	TEXT	NCBI GFF exception annotation describing a transcriptional or biological exception, if supplied.
note	TEXT	Free-text GFF Note annotation, if supplied.