transcripts

Identifier

ensembl.transcripts

Description

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

One row per transcript.

Always filter on taxonomy_id (partition column).

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

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

Related tables: ensembl.genes (join on gene_id); ensembl.exons (join on transcript_id); ensembl.cds (join on transcript_id); ensembl.mappings (join on transcript_id).

Partitions

• release
  • '116'
• taxonomy_id
  • '10090'
  • '10116'
  • '7955'
  • '9541'
  • '9544'
  • '9606'
  • '9615'
  • '9823'
  • '9986'

Schema

Column	Type	Description
release	TEXT	Partition column. Ensembl release number the annotation was drawn from.
taxonomy_id	INT	Partition column. NCBI taxonomy ID for the species (partition column).
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.
symbol	TEXT	Gene symbol the transcript belongs to. May be null.
chromosome	TEXT	Chromosome (or scaffold) 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.
strand	TEXT	Strand the transcript is on — forward or reverse.
source	TEXT	Annotation source (e.g. ensembl, havana, ensembl_havana).
biotype	TEXT	Transcript biotype (e.g. protein_coding, retained_intron).
support_level	INT	Transcript Support Level (1 = best, 5 = worst evidence). May be null.
ccds_id	TEXT	Consensus CDS (CCDS) identifier, if assigned. May be null.
in_gencode_basic	BOOLEAN	Transcript is in the GENCODE Basic set.
in_gencode_primary	BOOLEAN	Transcript is in the GENCODE Primary set.
in_mane_select	BOOLEAN	Transcript is the MANE Select representative for its gene (human). May be null.
in_mane_plus_clinical	BOOLEAN	Transcript is in the MANE Plus Clinical set (human). May be null.
is_ensembl_canonical	BOOLEAN	Transcript is the Ensembl canonical transcript for its gene.
has_selenocysteine_edit	BOOLEAN	Transcript has a selenocysteine (U) codon edit.
coding_region_start_confirmed	BOOLEAN	The start of the coding region is experimentally confirmed.
coding_region_end_confirmed	BOOLEAN	The end of the coding region is experimentally confirmed.
mrna_start_confirmed	BOOLEAN	The mRNA start is experimentally confirmed.
mrna_end_confirmed	BOOLEAN	The mRNA end is experimentally confirmed.