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bedrock.bio

ensembl.exons

import bedrock_bio as bb

rel = bb.load_table('ensembl.exons')
rel = rel.filter("genbank_assembly_accession = 'GCA_000001215.4'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources release genbank_assembly_accession transcript_id exon_id exon_version exon_number is_constitutive start_phase end_phase sequence_id start_position end_position is_forward_strand exon_source
0 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0013687_df_pt FBgn0013687_df_pt-E1 <NA> 1 True -1 -1 mitochondrion_genome 14917 19524 True FlyBase
1 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBti0015567-RA FBti0015567-RA-E1 <NA> 1 True -1 -1 2L 20740303 20748120 False FlyBase
2 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBti0018861-RA FBti0018861-RA-E1 <NA> 1 True -1 -1 2R 9726669 9734162 True FlyBase
3 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBti0018862-RA FBti0018862-RA-E1 <NA> 1 True -1 -1 2R 10948083 10955576 True FlyBase
4 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBti0018865-RA FBti0018865-RA-E1 <NA> 1 True -1 -1 2R 10979709 10980121 True FlyBase

Description

Section titled “Description”

Exon annotation (one row per exon within a transcript).

One row per (transcript, exon).

Always filter on genbank_assembly_accession.

Join to transcripts on transcript_id; exon_number gives the exon order within the transcript (5’→3’).

Partitions

Section titled “Partitions”
  • genbank_assembly_accession
    • 'GCA_000001215.4'
    • 'GCA_000001405.29'
    • 'GCA_000001635.9'
    • 'GCA_000001735.1'
    • 'GCA_000002035.4'
    • 'GCA_000002285.4'
    • 'GCA_000002525.1'
    • 'GCA_000002655.1'
    • 'GCA_000002765.3'
    • 'GCA_000002855.2'
    • 'GCA_000002945.2'
    • 'GCA_000002985.3'
    • 'GCA_000003025.6'
    • 'GCA_000003195.3'
    • 'GCA_000003625.1'
    • 'GCA_000004195.4'
    • 'GCA_000004515.4'
    • 'GCA_000005845.2'
    • 'GCA_000006565.2'
    • 'GCA_000006665.1'
    • 'GCA_000006745.1'
    • 'GCA_000006765.1'
    • 'GCA_000006845.1'
    • 'GCA_000006885.1'
    • 'GCA_000006925.2'
    • 'GCA_000006945.2'
    • 'GCA_000007545.1'
    • 'GCA_000007565.2'
    • 'GCA_000007785.1'
    • 'GCA_000008525.1'
    • 'GCA_000008765.1'
    • 'GCA_000008805.1'
    • 'GCA_000009045.1'
    • 'GCA_000009085.1'
    • 'GCA_000009205.2'
    • 'GCA_000011065.1'
    • 'GCA_000011325.1'
    • 'GCA_000013425.1'
    • 'GCA_000013465.1'
    • 'GCA_000015005.1'
    • 'GCA_000016305.1'
    • 'GCA_000025565.1'
    • 'GCA_000025985.1'
    • 'GCA_000027005.1'
    • 'GCA_000027305.1'
    • 'GCA_000146045.2'
    • 'GCA_000149245.3'
    • 'GCA_000151735.1'
    • 'GCA_000167675.2'
    • 'GCA_000174395.2'
    • 'GCA_000182965.3'
    • 'GCA_000196035.1'
    • 'GCA_000196095.1'
    • 'GCA_000215625.1'
    • 'GCA_000226075.1'
    • 'GCA_000237925.3'
    • 'GCA_000285655.3'
    • 'GCA_000306945.1'
    • 'GCA_000349665.1'
    • 'GCA_000409795.2'
    • 'GCA_000805365.1'
    • 'GCA_001433935.1'
    • 'GCA_001457595.1'
    • '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_016699485.1'
    • 'GCA_016772045.2'
    • 'GCA_018294505.1'
    • 'GCA_036323735.1'
    • 'GCA_902167145.1'
    • '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.
transcript_id TEXT Ensembl transcript ID this exon belongs to.
exon_id TEXT Ensembl exon ID (e.g. ENSE00000123456).
exon_version INT Version suffix of the exon ID. May be null.
exon_number INT Ordinal position of the exon within the transcript (5’→3’).
is_constitutive BOOLEAN Whether the exon is present in every transcript of its gene.
start_phase Int8 Coding-frame phase at the exon’s 5’ boundary (-1, 0, 1, or 2). May be null.
end_phase Int8 Coding-frame phase at the exon’s 3’ boundary (-1, 0, 1, or 2). May be null.
sequence_id TEXT GFF3 sequence ID the exon is located on.
start_position INT 1-based start coordinate of the exon.
end_position INT 1-based end coordinate of the exon.
is_forward_strand BOOLEAN Whether the exon is on the forward strand.
exon_source TEXT Annotation source in GFF3 column 2 (e.g. ensembl, havana, ensembl_havana).