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bedrock.bio

gene_segments

Identifier

Section titled “Identifier”
refseq.gene_segments

Description

Section titled “Description”

RefSeq immunoglobulin and T-cell-receptor gene-segment intervals from explicit genomic GFF3 rows.

One row represents one segment interval. gene_id is the local GFF ID of the parent gene, allowing a join to refseq.genes.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000001895.5'
    • 'GCF_000002035.6'
    • 'GCF_000002285.3'
    • 'GCF_000003025.6'
    • 'GCF_000003625.3'
    • '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

Section titled “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 gene segment is annotated; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the gene-segment interval on sequence_accession.
end INT 1-based inclusive end coordinate of the gene-segment interval on sequence_accession.
is_forward_strand BOOLEAN Whether the gene-segment interval is on the forward strand; null when the GFF strand is unspecified.
segment_id TEXT Local GFF3 ID of the gene-segment feature; not a stable RefSeq identifier.
gene_id TEXT Local GFF3 Parent ID of the gene containing the segment; joins refseq.genes.gene_id and is not an NCBI GeneID value.
segment_type TEXT Source GFF3 gene-segment type.
annotation_method TEXT NCBI GFF column-2 annotation method or source, such as BestRefSeq or Gnomon, 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.
segment_name TEXT Standard segment name from the GFF standard_name attribute, if supplied.
allele_name TEXT Allele name from the GFF allele attribute, if supplied; this is nomenclature, not a called genomic variant.
model_evidence TEXT NCBI model-evidence annotation for the segment, if supplied.
experiments TEXT[] Percent-decoded experimental-evidence entries from the comma-separated GFF experiment attribute.
inferences TEXT[] Percent-decoded non-experimental evidence entries from the comma-separated GFF inference attribute.
is_partial BOOLEAN Whether NCBI marks the gene segment 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.