cds

Identifier

refseq.cds

Description

RefSeq coding-sequence (CDS) intervals derived from explicit CDS rows in genomic GFF3 files.

One row represents one CDS interval; a multi-interval CDS repeats its local cds_id across rows.

parent_id is the local GFF ID of the immediate parent feature.

It is usually a transcript ID, but can be a gene ID when no transcript feature is annotated. translation_exceptions retains qualifiers needed to interpret exceptional coding translation.

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 CDS interval is annotated; joins refseq.assembly_sequences.sequence_accession.
start	INT	1-based inclusive start coordinate of the CDS interval on sequence_accession.
end	INT	1-based inclusive end coordinate of the CDS interval on sequence_accession.
is_forward_strand	BOOLEAN	Whether the CDS interval is on the forward strand; null when the GFF strand is unspecified.
phase	Int8	GFF CDS reading-frame offset—the number of bases at the coding-direction start of this interval before the next complete codon (0, 1, or 2).
cds_id	TEXT	Local GFF3 ID of the CDS feature; not a stable RefSeq identifier and shared by its intervals.
parent_id	TEXT	Local GFF3 Parent ID of the immediate parent feature; usually a transcript ID but sometimes a gene ID.
annotation_method	TEXT	NCBI GFF column-2 annotation method or source, such as BestRefSeq, Gnomon, or GeneMarkS+, 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.
product	TEXT	Protein product name from the GFF product attribute, if supplied.
protein_accession	TEXT	Versioned RefSeq or INSDC protein accession from the GFF protein_id attribute, if supplied.
translation_table	Int8	NCBI genetic-code table number from GFF transl_table, if supplied.
translation_exceptions	TEXT[]	Percent-decoded CDS translation-exception expressions from the comma-separated GFF transl_except attribute.
part	INT	Ordinal interval number from the GFF part=N or part=N/M attribute, if supplied.
is_partial	BOOLEAN	Whether NCBI marks the CDS 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 translational exception, if supplied.
note	TEXT	Free-text GFF Note annotation, if supplied.