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bedrock.bio

refseq.replication_features

import bedrock_bio as bb

rel = bb.load_table('refseq.replication_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 replication_feature_id replication_type annotation_method db_xrefs direction regulatory_class function experiments is_partial is_start_partial is_end_partial note
0 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000002.11 146709700 146710810 <NA> id-GeneID:107228318-2 origin_of_replication RefSeqFE [{'db': 'GeneID', 'id': '107228318'}] NaN None None [EXISTENCE:genetic transformation evidence [EC... False False False 1.1 kb EcoRI fragment%3B promotes replication ...
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000002.11 146709714 146710165 <NA> id-GeneID:107228318-3 origin_of_replication RefSeqFE [{'db': 'GeneID', 'id': '107228318'}] NaN None None [EXISTENCE:fractionation evidence [ECO:0000100... False False False site of nascent strand synthesis determined by...
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000003.11 60461418 60464414 <NA> id-GeneID:107325936-2 origin_of_replication RefSeqFE [{'db': 'GeneID', 'id': '107325936'}] BOTH None None [EXISTENCE:nucleotide analog incorporation evi... False False False Ori 1%3B region of peak nascent strand synthes...
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000003.11 60461713 60461839 <NA> id-GeneID:107325936-3 origin_of_replication RefSeqFE [{'db': 'GeneID', 'id': '107325936'}] BOTH None None [EXISTENCE:nucleotide analog incorporation evi... False False False Ori 1%3B amplicon 3%3B peak of nascent strand ...
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000003.11 60472774 60475730 <NA> id-GeneID:107325936-4 origin_of_replication RefSeqFE [{'db': 'GeneID', 'id': '107325936'}] BOTH None None [EXISTENCE:nucleotide analog incorporation evi... False False False Ori 2%3B region of peak nascent strand synthes...

Description

Section titled “Description”

RefSeq DNA replication intervals, one row per interval. replication_type classifies each interval, and the shared fields retain its evidence and functional annotations.

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_000003625.3'
    • 'GCF_000004195.4'
    • 'GCF_000005845.2'
    • 'GCF_000146045.2'
    • 'GCF_000151735.1'
    • 'GCF_000215625.1'
    • 'GCF_000226075.1'
    • 'GCF_000364345.1'
    • 'GCF_000409795.2'
    • 'GCF_001704415.1'
    • 'GCF_001704415.2'
    • 'GCF_002263795.3'
    • 'GCF_002863925.1'
    • 'GCF_003339765.1'
    • 'GCF_008728515.1'
    • 'GCF_009914755.1'
    • 'GCF_011764305.1'
    • 'GCF_016772045.2'
    • 'GCF_017654675.1'
    • 'GCF_047675955.1'
    • 'GCF_052040795.1'

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 replication feature is annotated; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the replication feature interval on sequence_accession.
end INT 1-based inclusive end coordinate of the replication feature interval on sequence_accession.
is_forward_strand BOOLEAN Whether the replication feature interval is on the forward strand; null when the GFF strand is unspecified.
replication_feature_id TEXT Local GFF3 ID of the replication feature; not a stable RefSeq identifier.
replication_type TEXT Source GFF3 replication 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.
direction TEXT Direction of replication initiation from GFF direction, if supplied.
regulatory_class TEXT NCBI regulatory classification from GFF regulatory_class, if supplied; currently used by replication-regulatory regions.
function TEXT Free text functional description from GFF function, if supplied.
experiments TEXT[] Percent-decoded experimental evidence entries from the comma-separated GFF experiment attribute.
is_partial BOOLEAN Whether NCBI marks the replication 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.