transcripts

Identifier

refseq.transcripts

Description

RefSeq RNA and transcript annotations from genomic GFF3 files. transcript_type preserves the source class.

One row represents one GFF transcript-feature interval. transcript_id is the local GFF ID, not the versioned RefSeq transcript accession; use transcript_accession when supplied. gene_ids contains local GFF gene IDs from Parent and can include more than one parent.

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.
transcript_id	TEXT	GFF3 ID of the transcript feature; local to the assembly annotation and not a stable RefSeq transcript identifier.
transcript_type	TEXT	Source SOFA RNA or transcript feature type.
gene_ids	TEXT[]	Local GFF gene IDs from the comma-separated Parent attribute; these are not NCBI GeneID values.
annotation_method	TEXT	NCBI GFF column-2 annotation method or source, such as BestRefSeq, Gnomon, or GeneMarkS+, if supplied.
transcript_accession	TEXT	Versioned RefSeq transcript accession from the GFF transcript_id 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.
product	TEXT	Name of the transcript product from the GFF product attribute, if supplied.
ncrna_class	TEXT	NCBI ncRNA subtype from the GFF ncrna_class attribute, if supplied.
trna_anticodon	TEXT	Anticodon annotation from the GFF anticodon attribute on tRNA features, if supplied.
model_evidence	TEXT	NCBI model-evidence annotation, if supplied.
experiments	TEXT[]	Percent-decoded experimental-evidence entries from the comma-separated GFF experiment attribute.
tags	TEXT[]	Percent-decoded transcript-selection labels from the comma-separated GFF tag attribute, such as MANE Select, MANE Plus Clinical, or RefSeq Select.
inferences	TEXT[]	Percent-decoded non-experimental evidence entries from the comma-separated GFF inference attribute.
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.