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bedrock.bio

gene_segments

Identifier

Section titled “Identifier”
ensembl.gene_segments

Description

Section titled “Description”

Immunoglobulin and T-cell receptor gene-segment annotation.

One row per Ensembl GFF3 gene-segment feature.

These are not conventional RNA transcript records, even though Ensembl supplies their identifiers through a GFF3 transcript_id attribute.

Join to genes on gene_id; do not join these rows to transcripts.

Related tables: ensembl.genes (join on gene_id).

Partitions

Section titled “Partitions”
  • genbank_assembly_accession
    • 'GCA_000001405.29'
    • 'GCA_000001635.9'
    • 'GCA_000002035.4'
    • 'GCA_000002285.4'
    • 'GCA_000003025.6'
    • 'GCA_000003625.1'
    • 'GCA_000004195.4'
    • 'GCA_001704415.1'
    • 'GCA_001858045.3'
    • 'GCA_002263795.4'
    • 'GCA_002863925.1'
    • 'GCA_003339765.3'
    • 'GCA_003668045.2'
    • 'GCA_008728515.1'
    • 'GCA_011100615.1'
    • 'GCA_016772045.2'
    • 'GCA_036323735.1'
    • 'GCA_905237065.2'

Schema

Section titled “Schema”
Column Type Description
sources STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[] Provenance for the GFF3 feature records.
release TEXT Ensembl release number the annotation was drawn from.
genbank_assembly_accession TEXT Partition column. GenBank assembly accession (partition column).
gene_id TEXT Ensembl gene ID of the parent gene.
segment_id TEXT Ensembl gene-segment identifier, parsed from the GFF3 transcript_id attribute.
segment_version INT Version suffix of the gene-segment identifier. May be null.
segment_name TEXT GFF3 Name for the gene segment.
sequence_id TEXT GFF3 sequence ID the gene segment is located on.
start_position INT 1-based start coordinate of the gene segment.
end_position INT 1-based end coordinate of the gene segment.
is_forward_strand BOOLEAN Whether the gene segment is on the forward strand.
segment_source TEXT Annotation source in GFF3 column 2 (e.g. ensembl, havana, ensembl_havana).
segment_type TEXT Raw GFF3 gene-segment feature type — C_gene_segment, D_gene_segment, J_gene_segment, V_gene_segment, or gene_segment.
biotype TEXT Ensembl gene-segment biotype (e.g. TR_V_gene).
segment_support_level INT Transcript Support Level supplied for the gene segment (1 = best, 5 = worst evidence). May be null.
is_gencode_basic BOOLEAN Gene segment has the GFF3 gencode_basic tag.
is_gencode_primary BOOLEAN Gene segment has the GFF3 gencode_primary tag.
is_ensembl_canonical BOOLEAN Gene segment has the GFF3 Ensembl_canonical tag.