ensembl.transposable_elements

Python

In [1]:

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

Out[1]:

	sources	release	genbank_assembly_accession	element_id	element_name	description	analysis_name	sequence_id	start_position	end_position	is_forward_strand	element_source
0	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	GCA_000001215.4	FBti0015567	Tirant{}475	None	flybase	2L	20740303	20748120	False	FlyBase
1	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	GCA_000001215.4	FBti0018861	17.6{}790	None	flybase	2R	9726669	9734162	True	FlyBase
2	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	GCA_000001215.4	FBti0018862	17.6{}804	None	flybase	2R	10948083	10955576	True	FlyBase
3	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	GCA_000001215.4	FBti0018865	297{}805	None	flybase	2R	10979709	10980121	True	FlyBase
4	[{'url': 'https://ftp.ensemblgenomes.ebi.ac.uk...	63	GCA_000001215.4	FBti0018866	297{}832	None	flybase	2R	15085034	15092025	True	FlyBase

R

In [1]:

library(bedrockbio)
library(dplyr)

lf <- load_table("ensembl.transposable_elements")
df <- filter(lf, genbank_assembly_accession == "GCA_000001215.4") |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 12 columns)
   genbank_assembly_accession | release | element_id  | element_name | description | analysis_name | sequence_id | start_position
   -------------------------- | ------- | ----------- | ------------ | ----------- | ------------- | ----------- | --------------
0  GCA_000001215.4            | 63      | FBti0015567 | Tirant{}475  | —           | flybase       | 2L          | 20740303
1  GCA_000001215.4            | 63      | FBti0018861 | 17.6{}790    | —           | flybase       | 2R          | 9726669
2  GCA_000001215.4            | 63      | FBti0018862 | 17.6{}804    | —           | flybase       | 2R          | 10948083
3  GCA_000001215.4            | 63      | FBti0018865 | 297{}805     | —           | flybase       | 2R          | 10979709
4  GCA_000001215.4            | 63      | FBti0018866 | 297{}832     | —           | flybase       | 2R          | 15085034

Description

Annotated transposable-element loci.

One row per verified transposable_element_gene and transposable_element GFF3 parent-child pair with matching sequence and coordinates.

This represents each locus once; it does not describe active transposition in an individual organism.

Partitions

• genbank_assembly_accession
  • 'GCA_000001215.4'
  • 'GCA_000146045.2'

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.
element_id	TEXT	Transposable-element locus identifier from the parent GFF3 gene_id attribute.
element_name	TEXT	Transposable-element name from parent GFF3 Name, if supplied. May be null.
description	TEXT	Parent GFF3 description, if supplied. May be null.
analysis_name	TEXT	Ensembl analysis name from parent GFF3 logic_name.
sequence_id	TEXT	GFF3 sequence ID on which the transposable element is located.
start_position	INT	1-based start coordinate of the transposable-element locus.
end_position	INT	1-based end coordinate of the transposable-element locus.
is_forward_strand	BOOLEAN	Whether the transposable element is on the forward strand.
element_source	TEXT	Annotation source in parent GFF3 column 2.