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bedrock.bio

ensembl.gene_segments

import bedrock_bio as bb

rel = bb.load_table('ensembl.gene_segments')
rel = rel.filter("genbank_assembly_accession = 'GCA_000001405.29'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources release genbank_assembly_accession gene_id segment_id segment_version segment_name sequence_id start_position end_position is_forward_strand segment_source segment_type biotype segment_support_level is_gencode_basic is_gencode_primary is_ensembl_canonical
0 [{'url': 'https://ftp.ensembl.org/pub/release-... 116 GCA_000001405.29 ENSG00000188403 ENST00000338912 5 IGHV1OR15-9-201 15 19964666 19965101 False havana V_gene_segment IG_V_gene <NA> True True True
1 [{'url': 'https://ftp.ensembl.org/pub/release-... 116 GCA_000001405.29 ENSG00000205274 ENST00000379435 5 TRBV20OR9-2-201 9 33617845 33618508 True havana V_gene_segment TR_V_gene <NA> True True True
2 [{'url': 'https://ftp.ensembl.org/pub/release-... 116 GCA_000001405.29 ENSG00000211592 ENST00000390237 2 IGKC-201 2 88857161 88857683 False havana C_gene_segment IG_C_gene <NA> True True True
3 [{'url': 'https://ftp.ensembl.org/pub/release-... 116 GCA_000001405.29 ENSG00000211593 ENST00000390238 2 IGKJ5-201 2 88860568 88860605 False havana J_gene_segment IG_J_gene <NA> True True True
4 [{'url': 'https://ftp.ensembl.org/pub/release-... 116 GCA_000001405.29 ENSG00000211594 ENST00000390239 2 IGKJ4-201 2 88860886 88860922 False havana J_gene_segment IG_J_gene <NA> True True True

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.

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.
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.