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bedrock.bio

refseq.recombination_features

import bedrock_bio as bb

rel = bb.load_table('refseq.recombination_features')
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 recombination_feature_id recombination_type annotation_method db_xrefs associated_gene_symbol associated_gene_name is_pseudogene recombination_class experiments is_partial is_start_partial is_end_partial note
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 1222760 1224296 <NA> id-GeneID:110599576-2 meiotic_recombination_region RefSeqFE [{'db': 'GeneID', 'id': '110599576'}] None None False meiotic [EXISTENCE:chromatin immunoprecipitation-seq e... False False False meiotic double-strand break mapped by DNA meio...
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 1224687 1226980 <NA> id-GeneID:110599576-6 meiotic_recombination_region RefSeqFE [{'db': 'GeneID', 'id': '110599576'}] None None False meiotic [EXISTENCE:chromatin immunoprecipitation-seq e... False False False meiotic double-strand break mapped by DNA meio...
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 16350424 16351257 <NA> id-GeneID:106501712-2 non_allelic_homologous_recombination_region RefSeqFE [{'db': 'GeneID', 'id': '106501712'}] None None False non_allelic_homologous [EXISTENCE:nucleotide sequencing assay evidenc... False False False sub-region a%2C recombines with sub-region a' ...
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 16356296 16356459 <NA> id-GeneID:106501712-3 non_allelic_homologous_recombination_region RefSeqFE [{'db': 'GeneID', 'id': '106501712'}] None None False non_allelic_homologous [EXISTENCE:nucleotide sequencing assay evidenc... False False False sub-region b%2C recombines with sub-region b' ...
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 16360546 16362700 <NA> id-GeneID:106501712-4 non_allelic_homologous_recombination_region RefSeqFE [{'db': 'GeneID', 'id': '106501712'}] None None False non_allelic_homologous [EXISTENCE:polymerase chain reaction evidence ... False False False sub-region c%2C recombines with sub-region c' ...

Description

Section titled “Description”

RefSeq recombination intervals, one row per interval, including recombination signal sequences associated with immune gene segments.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_009914755.1'

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 recombination feature is annotated; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the recombination feature interval on sequence_accession.
end INT 1-based inclusive end coordinate of the recombination feature interval on sequence_accession.
is_forward_strand BOOLEAN Whether the recombination feature interval is on the forward strand; null when the GFF strand is unspecified.
recombination_feature_id TEXT Local GFF3 ID of the recombination feature; not a stable RefSeq identifier.
recombination_type TEXT Source GFF3 recombination feature type.
annotation_method TEXT NCBI GFF column-2 annotation method or source, 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.
associated_gene_symbol TEXT Gene symbol from GFF gene, if supplied. This is an annotation rather than a local GFF gene ID join; use db_xrefs for identifier-based matching.
associated_gene_name TEXT Associated gene or segment name from GFF standard_name, if supplied.
is_pseudogene BOOLEAN Whether GFF pseudo=true marks the associated recombination feature as pseudogenic.
recombination_class TEXT NCBI recombination category from GFF recombination_class, if supplied, such as meiotic, mitotic, non-allelic homologous, chromosome breakpoint, or recombination hotspot.
experiments TEXT[] Percent-decoded experimental evidence entries from the comma-separated GFF experiment attribute.
is_partial BOOLEAN Whether NCBI marks the recombination 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.
note TEXT Free text GFF Note annotation, if supplied.