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bedrock.bio

refseq.gene_segments

import bedrock_bio as bb

rel = bb.load_table('refseq.gene_segments')
rel = rel.filter("assembly_accession = 'GCF_000001405.25'")

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
sources assembly_accession sequence_accession start end is_forward_strand segment_id gene_id segment_type annotation_method ... segment_name allele_name model_evidence experiments inferences is_partial is_start_partial is_end_partial exception note
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000002.11 89156874 89157196 False id-IGKC gene-IGKC C_gene_segment Curated Genomic ... IGKC None None [] [] False False False None None
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000002.11 89160080 89160117 False id-IGKJ5 gene-IGKJ5 J_gene_segment Curated Genomic ... IGKJ5 None None [] [] False False False None None
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000002.11 89160398 89160435 False id-IGKJ4 gene-IGKJ4 J_gene_segment Curated Genomic ... IGKJ4 None None [] [] False False False None None
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000002.11 89160733 89160770 False id-IGKJ3 gene-IGKJ3 J_gene_segment Curated Genomic ... IGKJ3 None None [] [] False False False None None
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000002.11 89161037 89161075 False id-IGKJ2 gene-IGKJ2 J_gene_segment Curated Genomic ... IGKJ2 None None [] [] False False False None None

Description

Section titled “Description”

RefSeq immunoglobulin and T-cell receptor gene segment intervals.

One row represents one segment interval. gene_id is the local ID of the parent gene, allowing a join to refseq.genes.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.20'
    • 'GCF_000001635.27'
    • 'GCF_000001895.5'
    • 'GCF_000002035.5'
    • 'GCF_000002035.6'
    • 'GCF_000002285.3'
    • 'GCF_000002285.5'
    • 'GCF_000003025.5'
    • 'GCF_000003025.6'
    • 'GCF_000003625.3'
    • 'GCF_000004195.4'
    • 'GCF_000151735.1'
    • 'GCF_000215625.1'
    • 'GCF_000349665.1'
    • 'GCF_000364345.1'
    • 'GCF_000409795.2'
    • 'GCF_001704415.1'
    • 'GCF_001704415.2'
    • 'GCF_001858045.2'
    • 'GCF_002263795.3'
    • 'GCF_002863925.1'
    • 'GCF_003339765.1'
    • 'GCF_003668045.3'
    • 'GCF_008728515.1'
    • 'GCF_009914755.1'
    • 'GCF_011100685.1'
    • 'GCF_011764305.1'
    • 'GCF_016699485.2'
    • 'GCF_016772045.2'
    • 'GCF_017654675.1'
    • '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_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 gene segment is annotated; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the gene segment interval on sequence_accession.
end INT 1-based inclusive end coordinate of the gene segment interval on sequence_accession.
is_forward_strand BOOLEAN Whether the gene segment interval is on the forward strand; null when the GFF strand is unspecified.
segment_id TEXT Local GFF3 ID of the gene segment feature; not a stable RefSeq identifier.
gene_id TEXT Local GFF3 Parent ID of the gene containing the segment; joins refseq.genes.gene_id and is not an NCBI GeneID value.
segment_type TEXT Source GFF3 gene segment type.
annotation_method TEXT NCBI GFF column-2 annotation method or source, such as BestRefSeq or Gnomon, 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.
segment_name TEXT Standard segment name from the GFF standard_name attribute, if supplied.
allele_name TEXT Allele name from the GFF allele attribute, if supplied; this is nomenclature, not a called genomic variant.
model_evidence TEXT NCBI model evidence annotation for the segment, if supplied.
experiments TEXT[] Percent-decoded experimental evidence entries from the comma-separated GFF experiment attribute.
inferences TEXT[] Percent-decoded non-experimental evidence entries from the comma-separated GFF inference attribute.
is_partial BOOLEAN Whether NCBI marks the gene segment 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.