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bedrock.bio

refseq.regulatory_features

import bedrock_bio as bb

rel = bb.load_table('refseq.regulatory_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 regulatory_feature_id regulatory_type annotation_method parent_id db_xrefs regulatory_class bound_moiety function 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 20498 21346 <NA> id-GeneID:127898558 enhancer RefSeqFE None [{'db': 'GeneID', 'id': '127898558'}] enhancer None activates a minimal SCP1%2C AML or CMV promote... [EXISTENCE:reporter gene assay evidence [ECO:0... False False False H3K4me1 hESC enhancer chr1:20498-21346 (GRCh37...
1 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 172206 172706 <NA> id-GeneID:127266738 enhancer RefSeqFE None [{'db': 'GeneID', 'id': '127266738'}] enhancer None activates a minimal SCP1%2C AML or CMV promote... [EXISTENCE:reporter gene assay evidence [ECO:0... False False False H3K4me1 hESC enhancer chr1:172206-172706 (GRCh...
2 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 172707 173207 <NA> id-GeneID:127266739 enhancer RefSeqFE None [{'db': 'GeneID', 'id': '127266739'}] enhancer None activates a minimal SCP1%2C AML or CMV promote... [EXISTENCE:reporter gene assay evidence [ECO:0... False False False H3K4me1 hESC enhancer chr1:172707-173207 (GRCh...
3 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 564533 565276 <NA> id-GeneID:127266741 enhancer RefSeqFE None [{'db': 'GeneID', 'id': '127266741'}] enhancer None activates a minimal SCP1%2C AML or CMV promote... [EXISTENCE:reporter gene assay evidence [ECO:0... False False False OCT4-NANOG hESC enhancer chr1:564533-565276 (G...
4 [{'url': 'https://ftp.ncbi.nlm.nih.gov/genomes... GCF_000001405.25 NC_000001.10 565277 566020 <NA> id-GeneID:127266742 enhancer RefSeqFE None [{'db': 'GeneID', 'id': '127266742'}] enhancer None activates a minimal SCP1%2C AML or CMV promote... [EXISTENCE:reporter gene assay evidence [ECO:0... False False False OCT4-NANOG hESC enhancer chr1:565277-566020 (G...

Description

Section titled “Description”

RefSeq regulatory element intervals, one row per interval. regulatory_type classifies each element, and the shared schema retains element-specific annotations.

Partitions

Section titled “Partitions”
  • assembly_accession
    • 'GCF_000001405.25'
    • 'GCF_000001405.40'
    • 'GCF_000001635.27'
    • 'GCF_000001735.3'
    • 'GCF_000002525.2'
    • 'GCF_000006765.1'
    • 'GCF_000006945.2'
    • 'GCF_000146045.2'
    • '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 regulatory feature is annotated; joins refseq.assembly_sequences.sequence_accession.
start INT 1-based inclusive start coordinate of the regulatory feature interval on sequence_accession.
end INT 1-based inclusive end coordinate of the regulatory feature interval on sequence_accession.
is_forward_strand BOOLEAN Whether the regulatory feature interval is on the forward strand; null when the GFF strand is unspecified.
regulatory_feature_id TEXT Local GFF3 ID of the regulatory feature; not a stable RefSeq identifier.
regulatory_type TEXT Source GFF3 regulatory feature type.
annotation_method TEXT NCBI GFF column-2 annotation method or source, if supplied.
parent_id TEXT Local GFF3 Parent ID, if supplied; enhancer rows can use this to reference a parent gene.
db_xrefs STRUCT(db TEXT, id TEXT)[] Database cross-references from GFF Dbxref; each item has a database and identifier, which may contain colons.
regulatory_class TEXT NCBI regulatory classification from GFF regulatory_class, if supplied.
bound_moiety TEXT Bound molecule name from GFF bound_moiety, if supplied; currently used on protein-binding sites.
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 regulatory 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.