refseq.genes

Python
R

import bedrock_bio as bb

rel = bb.load_table('refseq.genes')
rel = rel.filter("assembly_accession = 'GCF_000001215.4'")

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

	sources	assembly_accession	sequence_accession	start	end	is_forward_strand	is_pseudogene	gene_id	ncbi_gene_id	annotation_method	...	db_xrefs	gene_biotype	gene_locus_tag	pseudogene_type	part	is_partial	is_start_partial	is_end_partial	exception	note
0	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	879	5039	True	False	gene-Dmel_CG45760	5740846	RefSeq	...	[{'db': 'FLYBASE', 'id': 'FBgn0267363'}, {'db'...	protein_coding	Dmel_CG45760	None	<NA>	False	False	False	None	Annotated by Drosophila Heterochromatin Genome...
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	5829	11765	False	True	gene-Dmel_CR32011	3772046	RefSeq	...	[{'db': 'FLYBASE', 'id': 'FBgn0052011'}, {'db'...	pseudogene	Dmel_CR32011	None	<NA>	False	False	False	None	NaN
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	12640	25054	False	True	gene-Dmel_CR32010	3772244	RefSeq	...	[{'db': 'FLYBASE', 'id': 'FBgn0052010'}, {'db'...	pseudogene	Dmel_CR32010	None	<NA>	False	False	False	None	NaN
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	27020	31633	False	True	gene-Dmel_CR32009	3772156	RefSeq	...	[{'db': 'FLYBASE', 'id': 'FBgn0052009'}, {'db'...	pseudogene	Dmel_CR32009	None	<NA>	False	False	False	None	NaN
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	32478	43778	False	False	gene-Dmel_CG17245	43766	RefSeq	...	[{'db': 'FLYBASE', 'id': 'FBgn0025740'}, {'db'...	protein_coding	Dmel_CG17245	None	<NA>	False	False	False	None	NaN

library(bedrockbio)
library(dplyr)

lf <- load_table("refseq.genes")
df <- filter(lf, assembly_accession == "GCF_000001215.4") |> collect()

head(df)

Sample output (5 rows, showing 8 of 23 columns)
   assembly_accession | sequence_accession | start | end   | is_forward_strand | is_pseudogene | gene_id           | ncbi_gene_id
   ------------------ | ------------------ | ----- | ----- | ----------------- | ------------- | ----------------- | ------------
0  GCF_000001215.4    | NC_004353.4        | 879   | 5039  | true              | false         | gene-Dmel_CG45760 | 5740846
1  GCF_000001215.4    | NC_004353.4        | 5829  | 11765 | false             | true          | gene-Dmel_CR32011 | 3772046
2  GCF_000001215.4    | NC_004353.4        | 12640 | 25054 | false             | true          | gene-Dmel_CR32010 | 3772244
3  GCF_000001215.4    | NC_004353.4        | 27020 | 31633 | false             | true          | gene-Dmel_CR32009 | 3772156
4  GCF_000001215.4    | NC_004353.4        | 32478 | 43778 | false             | false         | gene-Dmel_CG17245 | 43766

Description

RefSeq gene and pseudogene annotations.

One row represents one gene feature interval.

A rare multi-part or trans-spliced gene therefore has multiple rows sharing its gene_id.

gene_id is a local feature ID, not an NCBI Gene identifier. ncbi_gene_id extracts the GeneID entry from db_xrefs when supplied. is_pseudogene distinguishes NCBI pseudogene from gene features.

Partitions

assembly_accession
- 'GCF_000001215.4'
- 'GCF_000001405.25'
- 'GCF_000001405.40'
- 'GCF_000001635.20'
- 'GCF_000001635.27'
- 'GCF_000001735.3'
- 'GCF_000001735.4'
- 'GCF_000001895.5'
- 'GCF_000002035.5'
- 'GCF_000002035.6'
- 'GCF_000002285.3'
- 'GCF_000002285.5'
- 'GCF_000002525.2'
- 'GCF_000002655.1'
- 'GCF_000002765.6'
- 'GCF_000002855.4'
- 'GCF_000002945.1'
- 'GCF_000002945.2'
- 'GCF_000002985.6'
- 'GCF_000003025.5'
- 'GCF_000003025.6'
- 'GCF_000003195.3'
- 'GCF_000003625.3'
- 'GCF_000004195.4'
- 'GCF_000004515.5'
- 'GCF_000004515.6'
- 'GCF_000005845.2'
- 'GCF_000006565.2'
- 'GCF_000006665.1'
- 'GCF_000006745.1'
- 'GCF_000006765.1'
- 'GCF_000006845.1'
- 'GCF_000006885.1'
- 'GCF_000006925.2'
- 'GCF_000006945.2'
- 'GCF_000007545.1'
- 'GCF_000007565.2'
- 'GCF_000007785.1'
- 'GCF_000008525.1'
- 'GCF_000008765.1'
- 'GCF_000008805.1'
- 'GCF_000009045.1'
- 'GCF_000009085.1'
- 'GCF_000009205.2'
- 'GCF_000011065.1'
- 'GCF_000011325.1'
- 'GCF_000013425.1'
- 'GCF_000013465.1'
- 'GCF_000015005.1'
- 'GCF_000016305.1'
- 'GCF_000025565.1'
- 'GCF_000025985.1'
- 'GCF_000027005.1'
- 'GCF_000027305.1'
- 'GCF_000146045.2'
- 'GCF_000149245.1'
- 'GCF_000151735.1'
- 'GCF_000167675.1'
- 'GCF_000174395.2'
- 'GCF_000182965.3'
- 'GCF_000188115.5'
- 'GCF_000195715.1'
- 'GCF_000195955.2'
- 'GCF_000195995.1'
- 'GCF_000196035.1'
- 'GCF_000196095.1'
- 'GCF_000203835.1'
- 'GCF_000215625.1'
- 'GCF_000226075.1'
- 'GCF_000237925.1'
- 'GCF_000285655.3'
- 'GCF_000306945.1'
- 'GCF_000349665.1'
- 'GCF_000364345.1'
- 'GCF_000409795.2'
- 'GCF_000767705.1'
- 'GCF_000805365.1'
- 'GCF_001077675.1'
- 'GCF_001433935.1'
- 'GCF_001457595.1'
- 'GCF_001593425.2'
- 'GCF_001704415.1'
- 'GCF_001704415.2'
- 'GCF_001858045.2'
- 'GCF_002263795.3'
- 'GCF_002759435.1'
- 'GCF_002863925.1'
- 'GCF_003339765.1'
- 'GCF_003668045.3'
- 'GCF_007990345.1'
- 'GCF_008728515.1'
- 'GCF_009914755.1'
- 'GCF_011100685.1'
- 'GCF_011764305.1'
- 'GCF_016699485.2'
- 'GCF_016772045.2'
- 'GCF_017654675.1'
- 'GCF_018294505.1'
- 'GCF_020379485.1'
- 'GCF_034190915.1'
- 'GCF_036323735.1'
- 'GCF_037993035.2'
- 'GCF_047675955.1'
- 'GCF_049350105.2'
- 'GCF_049354715.1'
- 'GCF_052040795.1'
- 'GCF_054392235.1'
- 'GCF_902167145.1'
- 'GCF_905237065.1'
- 'GCF_964237555.1'

Schema

Column	Type	Description
`sources`	`STRUCT(url TEXT, filename TEXT, last_modified_at TIMESTAMPTZ, sha256 TEXT)[]`	Source provenance for the row.
`assembly_accession`	`TEXT`	Partition column. Versioned RefSeq assembly accession (GCF accession).
`sequence_accession`	`TEXT`	Versioned RefSeq nucleotide sequence accession on which the interval is annotated; joins `refseq.assembly_sequences.sequence_accession`.
`start`	`INT`	1-based inclusive start coordinate of the feature interval on `sequence_accession`.
`end`	`INT`	1-based inclusive end coordinate of the feature interval on `sequence_accession`.
`is_forward_strand`	`BOOLEAN`	Whether the feature interval is on the forward strand; null when the GFF strand is unspecified.
`is_pseudogene`	`BOOLEAN`	Whether NCBI annotated the feature as a pseudogene.
`gene_id`	`TEXT`	Local GFF3 `ID` of the gene feature; not an NCBI Gene identifier.
`ncbi_gene_id`	`TEXT`	NCBI Gene identifier from the GFF `Dbxref` `GeneID` entry, if supplied.
`annotation_method`	`TEXT`	NCBI GFF column-2 annotation method or source, such as `BestRefSeq`, `Gnomon`, or `GeneMarkS+`, if supplied.
`gene_symbol`	`TEXT`	NCBI primary gene symbol from the GFF `gene` attribute, if supplied.
`gene_symbol_aliases`	`TEXT[]`	Alternative gene symbols from the comma-separated GFF `gene_synonym` attribute.
`gene_name`	`TEXT`	NCBI full gene name from the GFF `description` attribute, if supplied.
`db_xrefs`	`STRUCT(db TEXT, id TEXT)[]`	Database cross-references from GFF `Dbxref`; each item has a database and identifier, which may contain colons.
`gene_biotype`	`TEXT`	Gene biotype calculated by NCBI from the GFF `gene_biotype` attribute, if supplied.
`gene_locus_tag`	`TEXT`	Gene locus tag from the GFF `locus_tag` attribute, if supplied.
`pseudogene_type`	`TEXT`	NCBI pseudogene classification from the GFF `pseudogene` attribute, if supplied.
`part`	`INT`	Ordinal interval number from the GFF `part=N` or `part=N/M` attribute, if supplied.
`is_partial`	`BOOLEAN`	Whether NCBI marks the feature as partial with GFF `partial=true`.
`is_start_partial`	`BOOLEAN`	Whether NCBI marks the column-4 `start` boundary as partial with a GFF `start_range` attribute.
`is_end_partial`	`BOOLEAN`	Whether NCBI marks the column-5 `end` boundary as partial with a GFF `end_range` attribute.
`exception`	`TEXT`	NCBI GFF `exception` annotation describing a transcriptional or biological exception, if supplied.
`note`	`TEXT`	Free text GFF `Note` annotation, if supplied.