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bedrock.bio

refseq.exons

import bedrock_bio as bb

rel = bb.load_table('refseq.exons')
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 exon_id parent_id annotation_method db_xrefs exon_number 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 1079 True exon-NM_001110622.3-1 rna-NM_001110622.3 RefSeq [{'db': 'FLYBASE', 'id': 'FBtr0346692'}, {'db'... <NA> <NA> 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 1144 1410 True exon-NM_001110622.3-2 rna-NM_001110622.3 RefSeq [{'db': 'FLYBASE', 'id': 'FBtr0346692'}, {'db'... <NA> <NA> False False False None JYalpha-RB%3B Dmel\JYalpha-RB%3B CG45760-RB%3B...
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004353.4 1768 3851 True exon-NM_001110622.3-3 rna-NM_001110622.3 RefSeq [{'db': 'FLYBASE', 'id': 'FBtr0346692'}, {'db'... <NA> <NA> False False False None JYalpha-RB%3B Dmel\JYalpha-RB%3B CG45760-RB%3B...
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004353.4 4353 4527 True exon-NM_001110622.3-4 rna-NM_001110622.3 RefSeq [{'db': 'FLYBASE', 'id': 'FBtr0346692'}, {'db'... <NA> <NA> False False False None JYalpha-RB%3B Dmel\JYalpha-RB%3B CG45760-RB%3B...
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001215.4 NC_004353.4 4592 4824 True exon-NM_001110622.3-5 rna-NM_001110622.3 RefSeq [{'db': 'FLYBASE', 'id': 'FBtr0346692'}, {'db'... <NA> <NA> False False False None JYalpha-RB%3B Dmel\JYalpha-RB%3B CG45760-RB%3B...

Description

Section titled “Description”

RefSeq exon intervals.

One row represents one exon interval; intervals are not inferred from transcripts or CDSs. parent_id is the local ID of the immediate parent feature.

It is usually a transcript ID, but can be a gene ID for non-transcribed pseudogenes and other exceptional annotations.

NCBI generally does not provide exon numbering. exon_number is populated only when the source supplies either exon_number or its legacy number attribute; infer order from genomic coordinates and strand otherwise.

Partitions

Section titled “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

Section titled “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 exon interval is annotated; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the exon interval on sequence_accession.
end INT 1-based inclusive end coordinate of the exon interval on sequence_accession.
is_forward_strand BOOLEAN Whether the exon interval is on the forward strand; null when the GFF strand is unspecified.
exon_id TEXT Local GFF3 ID of the exon interval; not a stable RefSeq identifier.
parent_id TEXT Local GFF3 Parent ID of the immediate parent feature; usually a transcript ID but sometimes a gene ID.
annotation_method TEXT NCBI GFF column-2 annotation method or source, such as BestRefSeq, Gnomon, or GeneMarkS+, 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.
exon_number INT Exon number supplied by the source in exon_number or legacy number, if supplied; do not assume it is present.
part INT Ordinal interval number from the GFF part=N or part=N/M attribute, if supplied.
is_partial BOOLEAN Whether NCBI marks the exon 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.