RefSeq

Identifier

refseq

License

Public domain

Citation

O'Leary NA, et al. Reference sequence (RefSeq) database at NCBI. Nucleic Acids Res 2016;44(D1):D733-D745. doi:10.1093/nar/gkv1189

Overview

RefSeq is NCBI’s curated collection of reference genome, transcript, and protein sequences.

This namespace contains versioned genome assemblies, their component sequences, and their genome annotations.

assembly_summary identifies current and historical assemblies; version_status distinguishes current records and is_reference identifies NCBI reference genomes.

The versioned assembly_accession (GCF accession) links assembly tables because assembly_name is not globally unique. assembly_sequences lists component sequences, including chromosomes, alternate loci, and scaffolds.

genes, transcripts, cds, and exons describe gene models.

Sequence tables contain one row per sequence position and are queried by accession and interval.

Local GFF identifiers such as gene_id and transcript_id identify features within an assembly; versioned RefSeq accessions and db_xrefs support cross-dataset identity matching.

Tables

• refseq.alignments — RefSeq sequence-to-assembly alignment blocks, one row per block.
• refseq.assembly_regions — Genomic regions with alternate scaffold and patch placements, one row per named region.
• refseq.assembly_sequences — Sequence records in RefSeq genome assemblies, one row per assembly sequence.
• refseq.assembly_statistics — Assembly statistics, one row per assembly unit, molecule, molecule type or location, and sequence type.
• refseq.assembly_summary — Selected current and historical RefSeq genome assemblies, one row per assembly.

assembly_name is NCBI’s human-readable asm_name label and may not be globally unique.

• refseq.cds — RefSeq coding sequence (CDS) intervals.
• refseq.dna_sequences — Individual nucleotide positions in RefSeq genomic FASTA sequences.
• refseq.exons — RefSeq exon intervals.
• refseq.gene_segments — RefSeq immunoglobulin and T-cell receptor gene segment intervals.
• refseq.genes — RefSeq gene and pseudogene annotations.
• refseq.genomic_gaps — Gap intervals in top-level RefSeq genomic sequences.
• refseq.protein_sequences — Individual amino acid positions in accessioned RefSeq protein products.
• refseq.recombination_features — RefSeq recombination intervals, one row per interval, including recombination signal sequences associated with immune gene segments.
• refseq.regulatory_features — RefSeq regulatory element intervals, one row per interval. regulatory_type classifies each element, and the shared schema retains element-specific annotations.
• refseq.repeat_features — RefSeq repeat intervals, one row per interval. repeat_type classifies each interval, while repeat unit and mobile element fields describe repeat subclasses when supplied.
• refseq.replication_features — RefSeq DNA replication intervals, one row per interval. replication_type classifies each interval, and the shared fields retain its evidence and functional annotations.
• refseq.rna_sequences — Individual nucleotide positions in accessioned RefSeq RNA products.
• refseq.sequence_alterations — RefSeq sequence change and assembly artifact intervals, one row per interval.
• refseq.sequence_annotations — RefSeq sequence annotations, one row per interval. annotation_type classifies each annotation, and an annotation ID can label multiple intervals.
• refseq.sequence_regions — RefSeq sequence metadata and rare repeat annotations, one row per interval.
• refseq.structural_features — RefSeq structural sequence element intervals, one row per interval.
• refseq.transcripts — RefSeq RNA and transcript annotations. transcript_type classifies each annotation.