refseq.transcripts

Python

In [1]:

import bedrock_bio as bb

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

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

Out[1]:

	sources	assembly_accession	sequence_accession	start	end	is_forward_strand	transcript_id	transcript_type	gene_ids	annotation_method	...	is_refseq_select	is_mane_select	is_refseq_plus_clinical	is_mane_plus_clinical	inferences	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	rna-NM_001110622.3	mRNA	[gene-Dmel_CG45760]	RefSeq	...	False	False	False	False	[]	False	False	False	None	JYalpha-RB%3B Dmel\JYalpha-RB%3B CG45760-RB%3B...
1	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	32478	43778	False	rna-NM_001258471.2	mRNA	[gene-Dmel_CG17245]	RefSeq	...	False	False	False	False	[]	False	False	False	None	PlexB-RB%3B Dmel\PlexB-RB%3B CG17245-RB%3B Dme...
2	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	32812	43778	False	rna-NM_079877.4	mRNA	[gene-Dmel_CG17245]	RefSeq	...	False	False	False	False	[]	False	False	False	None	PlexB-RA%3B Dmel\PlexB-RA%3B CG17245-RA%3B Dme...
3	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	42774	43374	True	rna-NR_123741.1	antisense_RNA	[gene-Dmel_CR45124]	RefSeq	...	False	False	False	False	[]	False	False	False	None	asRNA:CR45124-RA%3B Dmel\asRNA:CR45124-RA%3B C...
4	[{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes...	GCF_000001215.4	NC_004353.4	44774	46074	True	rna-NR_123742.1	lnc_RNA	[gene-Dmel_CR44440]	RefSeq	...	False	False	False	False	[]	False	False	False	None	lncRNA:CR44440-RA%3B Dmel\lncRNA:CR44440-RA%3B...

R

In [1]:

library(bedrockbio)
library(dplyr)

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

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 27 columns)
   assembly_accession | sequence_accession | start | end   | is_forward_strand | transcript_id      | transcript_type | annotation_method
   ------------------ | ------------------ | ----- | ----- | ----------------- | ------------------ | --------------- | -----------------
0  GCF_000001215.4    | NC_004353.4        | 879   | 5039  | true              | rna-NM_001110622.3 | mRNA            | RefSeq
1  GCF_000001215.4    | NC_004353.4        | 32478 | 43778 | false             | rna-NM_001258471.2 | mRNA            | RefSeq
2  GCF_000001215.4    | NC_004353.4        | 32812 | 43778 | false             | rna-NM_079877.4    | mRNA            | RefSeq
3  GCF_000001215.4    | NC_004353.4        | 42774 | 43374 | true              | rna-NR_123741.1    | antisense_RNA   | RefSeq
4  GCF_000001215.4    | NC_004353.4        | 44774 | 46074 | true              | rna-NR_123742.1    | lnc_RNA         | RefSeq

Description

RefSeq RNA and transcript annotations. transcript_type classifies each annotation.

One row represents one transcript feature interval. transcript_id is a local feature ID, not the versioned RefSeq transcript accession; use transcript_accession when supplied. gene_ids contains local gene IDs from Parent and can include more than one parent.

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_000002285.5'
  • '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_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.
transcript_id	TEXT	GFF3 ID of the transcript feature; local to the assembly annotation and not a stable RefSeq transcript identifier.
transcript_type	TEXT	Source SOFA RNA or transcript feature type.
gene_ids	TEXT[]	Local GFF gene IDs from the comma-separated Parent attribute; these are not NCBI GeneID values.
annotation_method	TEXT	NCBI GFF column-2 annotation method or source, such as BestRefSeq, Gnomon, or GeneMarkS+, if supplied.
transcript_accession	TEXT	Versioned RefSeq transcript accession from the GFF transcript_id 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.
product	TEXT	Name of the transcript product from the GFF product attribute, if supplied.
ncrna_class	TEXT	NCBI ncRNA subtype from the GFF ncrna_class attribute, if supplied.
trna_anticodon	TEXT	Anticodon annotation from the GFF anticodon attribute on tRNA features, if supplied.
model_evidence	TEXT	NCBI model evidence annotation, if supplied.
experiments	TEXT[]	Percent-decoded experimental evidence entries from the comma-separated GFF experiment attribute.
is_refseq_select	BOOLEAN	Whether the transcript is RefSeq Select, including the MANE Select subset.
is_mane_select	BOOLEAN	Whether the transcript has the GFF MANE Select tag.
is_refseq_plus_clinical	BOOLEAN	Whether the transcript has the GFF RefSeq Plus Clinical tag.
is_mane_plus_clinical	BOOLEAN	Whether the transcript has the GFF MANE Plus Clinical tag.
inferences	TEXT[]	Percent-decoded non-experimental evidence entries from the comma-separated GFF inference attribute.
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.