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The Reference Sequence database • • • • • A non-redundant collection of richly annotated DNA, RNA, and protein sequences from diverse taxa The collection includes sequences from plasmids, organelles, viruses, archaea, bacteria, and eukaryotes Each RefSeq represents a single, naturally occurring molecule from one organism. RefSeq biological sequences (also known as RefSeqs) are derived from GenBank records but differ in that each RefSeq is a synthesis of information, not an archived unit of primary research data Similar to a review article in the literature, a RefSeq represents the consolidation of information by a particular group at a particular time. The RefSeq accession number format and molecule types Accession prefix AC_ Molecule type Genomic Comment Complete genomic molecule, alternate assembly NC_ Genomic Complete genomic molecule, reference assembly NG_ Genomic Incomplete genomic region NT_ Genomic Contig or scaffold, clone-based a or WGS NW_ Genomic NS_ Genomic Contig or scaffold, primarily a WGS Environmental sequence b NZ_ NM_ NR_ c XM_ c XR_ AP_ Genomic mRNA RNA mRNA RNA Protein NP_ c YP_ c XP_ c ZP_ Protein Protein Protein Protein a Whole Genome Shotgun sequence data. An ordered collection of WGS for a genome. c Computed. b Unfinished WGS Predicted model Predicted model Annotated on AC_ alternate assembly Predicted model Predicted model, annotated on NZ_ genomic records Flat File Format and Annotated Features RefSeq records appear similar in format to the GenBank records from which they are derived. Features of a RefSeq record RefSeq records may also be displayed in a graphical format RefSeq status codes Code GENOME ANNOTATION Description The RefSeq record is provided via automated processing and is not subject to individual review or revision between builds. INFERRED The RefSeq record has been predicted by genome sequence analysis, but it is not yet supported by experimental evidence. The record may be partially supported by homology data. The RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted. The RefSeq record has not yet been subject to individual review. The initial sequence-to-gene name associations have been established by outside collaborators or NCBI staff. The RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information. The RefSeq record has undergone an initial review to provide the preferred sequence standard. The record has not yet been subject to final review, at which time additional functional information may be provided. The RefSeq record is provided to represent a collection of whole genome shotgun sequences. These records are not subject to individual review or revisions between genome updates. PREDICTED PROVISIONAL REVIEWED VALIDATED WGS Using Entrez Limits to restrict a query to RefSeq http://www.ncbi.nlm.nih.gov/gene Gene maintains information about genes from genomes of interest to the RefSeq group Entrez Gene is accessed like any other Entrez database: Find genes by... free text partial name and multiple species chromosome and symbol Search text human muscular dystrophy transporter[title] AND ("Drosophila melanogaster"[orgn] OR "Mus musculus"[orgn]) (II[chr] OR 2[chr]) AND adh*[sym] associated sequence accession number M11313[accn] gene name (symbol) publication (PubMed ID) Gene Ontology (GO) terms or identifiers Genes with variants of medical interest BRCA1[sym] 11331580[PMID] "cell adhesion"[GO] 10030[GO] gene_snp_clin[filter] chromosome and species Enzyme Commission (EC) numbers Y[CHR] AND human[ORGN] 1.9.3.1[EC]