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bedrock.bio

ensembl.transcripts

import bedrock_bio as bb

rel = bb.load_table('ensembl.transcripts')
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 gene_id transcript_id transcript_version transcript_name note sequence_id start_position ... transcript_type transcript_support_level ccds_id is_gencode_basic is_gencode_primary is_mane_select is_mane_plus_clinical is_ensembl_canonical is_ensembl_canonical_extended is_readthrough_transcript
0 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000003 FBtr0081624 <NA> 7SLRNA:CR32864-RA None 3R 6822500 ... ncRNA <NA> None False False False False True False False
1 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000008 FBtr0071763 <NA> a-RA None 2R 22136968 ... mRNA <NA> None False False False False False False False
2 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000008 FBtr0071764 <NA> a-RB None 2R 22137433 ... mRNA <NA> None False False False False True False False
3 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000008 FBtr0100521 <NA> a-RC None 2R 22136968 ... mRNA <NA> None False False False False False False False
4 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBgn0000008 FBtr0342981 <NA> a-RD None 2R 22136968 ... mRNA <NA> None False False False False False False False

Description

Section titled “Description”

Transcript-level annotation (one row per Ensembl transcript).

One row per transcript.

Always filter on genbank_assembly_accession.

Filter to is_ensembl_canonical = True for the single representative transcript per gene, or is_mane_select = True for the MANE Select transcript (human).

Join to genes on gene_id and to exons / cds / utrs on transcript_id.

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.
gene_id TEXT Ensembl gene ID this transcript belongs to.
transcript_id TEXT Ensembl transcript ID (e.g. ENST00000123456).
transcript_version INT Version suffix of the transcript ID. May be null.
transcript_name TEXT GFF3 Name for the transcript, if supplied. May be null.
note TEXT Transcript sequence-edit note, if supplied. May be null.
sequence_id TEXT GFF3 sequence ID the transcript is located on.
start_position INT 1-based start coordinate of the transcript.
end_position INT 1-based end coordinate of the transcript.
is_forward_strand BOOLEAN Whether the transcript is on the forward strand.
transcript_source TEXT Annotation source in GFF3 column 2 (e.g. ensembl, havana, ensembl_havana).
biotype TEXT Transcript biotype (e.g. protein_coding, retained_intron).
transcript_type TEXT Raw GFF3 transcript feature type, such as mRNA, lnc_RNA, or pseudogenic_transcript.
transcript_support_level INT Transcript Support Level (1 = best, 5 = worst evidence). May be null.
ccds_id TEXT Consensus CDS (CCDS) identifier from GFF3 ccdsid, if assigned. May be null.
is_gencode_basic BOOLEAN Transcript has the GFF3 gencode_basic tag.
is_gencode_primary BOOLEAN Transcript has the GFF3 gencode_primary tag.
is_mane_select BOOLEAN Transcript has the GFF3 MANE_Select tag.
is_mane_plus_clinical BOOLEAN Transcript has the GFF3 MANE_Plus_Clinical tag.
is_ensembl_canonical BOOLEAN Transcript is the Ensembl canonical transcript for its gene.
is_ensembl_canonical_extended BOOLEAN Transcript is in Ensembl’s extended canonical set.
is_readthrough_transcript BOOLEAN Transcript is annotated as a readthrough transcript.