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bedrock.bio

ensembl.utrs

import bedrock_bio as bb

rel = bb.load_table('ensembl.utrs')
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 end sequence_id start_position end_position is_forward_strand utr_source
0 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0005088 five_prime 2L 8366038 8366310 True FlyBase
1 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0005088 three_prime 2L 8369721 8370082 True FlyBase
2 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0006151 five_prime 2L 14615552 14615643 True FlyBase
3 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0006151 five_prime 2L 14616303 14616437 True FlyBase
4 [{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk... 63 GCA_000001215.4 FBtr0006151 five_prime 2L 14616503 14616907 True FlyBase

Description

Section titled “Description”

Untranslated region (UTR) annotation — 5’ and 3’ UTR segments of coding transcripts.

One row per UTR segment.

Always filter on genbank_assembly_accession. end distinguishes the five_prime and three_prime UTR.

Join to transcripts 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_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_000006565.2'
    • 'GCA_000146045.2'
    • 'GCA_000149245.3'
    • 'GCA_000151735.1'
    • 'GCA_000167675.2'
    • 'GCA_000182965.3'
    • 'GCA_000215625.1'
    • 'GCA_000226075.1'
    • 'GCA_000237925.3'
    • 'GCA_000349665.1'
    • 'GCA_000409795.2'
    • 'GCA_001433935.1'
    • '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 UTR belongs to.
end TEXT Which UTR this is — five_prime or three_prime.
sequence_id TEXT GFF3 sequence ID the UTR is located on.
start_position INT 1-based start coordinate of the UTR segment.
end_position INT 1-based end coordinate of the UTR segment.
is_forward_strand BOOLEAN Whether the UTR is on the forward strand.
utr_source TEXT Annotation source in GFF3 column 2 (e.g. ensembl, havana, ensembl_havana).