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<title>RefSeq</title>

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RefSeq

</h1>

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</style><table class="infobox vevent" style="width:"><caption class="infobox-title summary">Refseq</caption><tbody><tr><td colspan="2" class="infobox-image"></td></tr><tr><th colspan="2" class="infobox-header" style="background-color: lavender; background-color: light-dark(lavender,#353549) !important;">Content</th></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap">Description</th><td class="infobox-data">curated non-redundant sequence database of genomes.</td></tr><tr><th colspan="2" class="infobox-header" style="background-color: lavender; background-color: light-dark(lavender,#353549) !important;">Contact</th></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap"><a href="Research_center" class="mw-redirect" title="Research center">Research center</a></th><td class="infobox-data"><a href="National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">National Center for Biotechnology Information</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap">Primary citation</th><td class="infobox-data"><a href="Kim_D._Pruitt" title="Kim D. Pruitt">Pruitt KD</a> & al. (2005)<a href="#cite_note-pmid15608248-1">[1]</a></td></tr><tr><th colspan="2" class="infobox-header" style="background-color: lavender; background-color: light-dark(lavender,#353549) !important;">Access</th></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap">Website</th><td class="infobox-data"><a rel="nofollow" class="external free" href="https://www.ncbi.nlm.nih.gov/refseq/">https://www.ncbi.nlm.nih.gov/refseq/</a></td></tr></tbody></table>The Reference Sequence (RefSeq) <a href="Sequence_database" title="Sequence database">database</a><a href="#cite_note-pmid15608248-1">[1]</a> is an <a href="Open_access_(publishing)" class="mw-redirect" title="Open access (publishing)">open access</a>, annotated and curated collection of publicly available <a href="Nucleotide" title="Nucleotide">nucleotide</a> sequences (<a href="DNA" title="DNA">DNA</a>, <a href="RNA" title="RNA">RNA</a>) and their <a href="Protein" title="Protein">protein</a> products. RefSeq was introduced in 2000.<a href="#cite_note-2">[2]</a><a href="#cite_note-pmid10637631-3">[3]</a> This database is built by <a href="National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">National Center for Biotechnology Information</a> (NCBI), and, unlike <a href="GenBank" title="GenBank">GenBank</a>, provides only a single record for each natural biological molecule (i.e. DNA, RNA or protein) for major organisms ranging from <a href="Virus" title="Virus">viruses</a> to <a href="Bacteria" title="Bacteria">bacteria</a> to <a href="Eukaryote" title="Eukaryote">eukaryotes</a>.

For each <a href="Model_organism" title="Model organism">model organism</a>, RefSeq aims to provide separate and linked records for the genomic DNA, the gene transcripts, and the proteins arising from those transcripts. RefSeq is limited to major organisms for which sufficient data are available (121,461 distinct "named" <a href="Organism" title="Organism">organisms</a> as of July 2022),<a href="#cite_note-:0-4">[4]</a> while <a href="GenBank" title="GenBank">GenBank</a> includes sequences for any organism submitted (approximately 504,000 formally described <a href="Species" title="Species">species</a>).<a href="#cite_note-5">[5]</a>

<div class="mw-heading mw-heading2"><h2 id="RefSeq_categories">RefSeq categories</h2></div>

RefSeq collection comprises different data types, with different origins, so it is necessary to establish standard categories and identifiers to store each data type. The most important categories are:

<caption>RefSeq accession categories and molecule types

</caption>

<th>Category

</th>

<th>Description

</th></tr>

<tr>

<td>NC

</td>

<td>Complete genomic molecules

</td></tr>

<tr>

<td>NG

</td>

<td>Incomplete genomic region

</td></tr>

<tr>

<td>NM

</td>

</td></tr>

<tr>

<td>NR

</td>

<td><a href="Non-coding_RNA" title="Non-coding RNA">ncRNA</a>

</td></tr>

<tr>

<td>NP

</td>

<td><a href="Protein" title="Protein">Protein</a>

</td></tr>

<tr>

<td>XM

</td>

<td>predicted <a href="Messenger_RNA" title="Messenger RNA">mRNA</a> model

</td></tr>

<tr>

<td>XR

</td>

<td>predicted <a href="Non-coding_RNA" title="Non-coding RNA">ncRNA</a> model

</td></tr>

<tr>

<td>XP

</td>

<td>predicted <a href="Protein" title="Protein">Protein</a> model (eukaryotic sequences)

</td></tr>

<tr>

<td>WP

</td>

<td>predicted <a href="Protein" title="Protein">Protein</a> model (prokaryotic sequences)

</td></tr></tbody></table>

For more details and more categories, see <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.entrez_queries_to_retrieve_sets_o/">Table 1</a> in <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/books/NBK21091/">Chapter 18 of the book The Reference Sequence (RefSeq) Database</a>.

<div class="mw-heading mw-heading2"><h2 id="RefSeq_Projects">RefSeq Projects</h2></div>

Several projects to improve RefSeq services are currently in development by the NCBI, often in collaboration with research centers such as EMBL-EBI:

<ul><li><a href="Consensus_CDS_Project" title="Consensus CDS Project">Consensus CDS</a> (CCDS): This project aims to identify a core set of human and mouse <a href="Coding_region" title="Coding region">protein-coding regions</a> and standardize sets of genes with high and consistent levels of genomic annotation quality. This project was announced in 2009 and is still in development.<a href="#cite_note-6">[6]</a><a href="#cite_note-7">[7]</a></li></ul>

<ul><li>RefSeq Functional Elements (RefSeqFE): It is focused on describing non-genic functional elements which are gene regulatory regions such as: <a href="Enhancer_(genetics)" title="Enhancer (genetics)">enhancers</a>, <a href="Silencer_(genetics)" title="Silencer (genetics)">silencers</a>, <a href="DNase_I_hypersensitive_site" title="DNase I hypersensitive site">DNase I hypersensitive regions</a>, <a href="Origin_of_replication" title="Origin of replication">DNA replication origins</a> etc.). The current scope of this project is restricted to the human and mouse genomes.<a href="#cite_note-8">[8]</a></li>

<li>RefSeqGene: Its main goal is to define genomic sequences to be used as reference standards for well-characterized genes. Previously described <a href="Messenger_RNA" title="Messenger RNA">mRNA</a>, protein and chromosome sequences have the weaknesses of not providing explicit genomic coordinates of gene flanking and intronic regions as well as showing awkwardly large coordinates that change with every new genome assembly. The RefSeqGene project is designed to eliminate these errors.<a href="#cite_note-9">[9]</a></li>

<li>Targeted Loci: This project records molecular markers, specially protein-coding and <a href="Ribosomal_RNA" title="Ribosomal RNA">ribosomal RNA</a> loci that are used for <a href="Phylogenetics" title="Phylogenetics">phylogenetic</a> and <a href="DNA_barcoding" title="DNA barcoding">barcoding analysis</a>. The scope of this project includes sequences for <a href="Archaea" title="Archaea">Archaea</a>, <a href="Bacteria" title="Bacteria">Bacteria</a> and <a href="Fungus" title="Fungus">Fungi</a> organisms, accessible via <a href="Entrez" title="Entrez">Entrez</a> and <a href="BLAST_(biotechnology)" title="BLAST (biotechnology)">BLAST</a> queries. It also includes <a href="GenBank" title="GenBank">GenBank</a> sequences for <a href="Animal" title="Animal">Animals</a>, <a href="Plant" title="Plant">Plants</a> and <a href="Protist" title="Protist">Protists</a>, accessible via BLAST queries.<a href="#cite_note-10">[10]</a></li>

<li>Virus Variation (ViV): It is a specific resource of sequence data processing pipelines and analysis tools for display and retrieval of sequences from several viral groups such as <a href="Orthomyxoviridae" title="Orthomyxoviridae">influenza virus</a>, <a href="Ebolavirus" title="Ebolavirus">ebolavirus</a>, <a href="MERS-CoV" class="mw-redirect" title="MERS-CoV">MERS coronavirus</a> or <a href="Zika_virus" title="Zika virus">Zika virus</a>. New viruses, processing pipelines, tools and other features are included regularly.<a href="#cite_note-11">[11]</a></li>

<li>RefSeq Select: This project aims to select datasets of RefSeq Select transcripts, as the most representative for every protein-coding gene, based on multiple criteria: prior use in clinical databases, transcript expression, <a href="Conserved_sequence" title="Conserved sequence">evolutionary conservation</a> of the coding region etc. Since many genes are represented by multiple RefSeq transcripts/proteins due to the biological process of <a href="Alternative_splicing" title="Alternative splicing">alternative splicing</a>, this complexity is problematic for studies such as <a href="Comparative_genomics" title="Comparative genomics">comparative genomics</a> or exchange of clinical variant data.<a href="#cite_note-12">[12]</a></li>

<li>MANE (Matched Annotation from the NCBI and EMBL-EBI): It is a collaborative project between <a href="National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">NCBI</a> and <a href="European_Molecular_Biology_Laboratory" title="European Molecular Biology Laboratory">EMBL</a>-<a href="European_Bioinformatics_Institute" title="European Bioinformatics Institute">EBI</a> whose main goal is to define a set of transcripts and their proteins for all the protein-coding genes in the human genome. By doing that, the differences in transcripts annotation between RefSeq and <a href="Ensembl_genome_database_project" title="Ensembl genome database project">Ensembl</a>/<a href="GENCODE" title="GENCODE">GENCODE</a> annotation systems are reduced. A MANE Select transcripts set are created as a useful universal standard for clinical reporting and comparative or evolutionary genomics. A second MANE Plus Clinical set are also created with additional transcripts to report all Pathogenic (P) or Likely Pathogenic (LP) clinical variants available in public resources.<a href="#cite_note-13">[13]</a> This project was announced in 2018 and is expected to finish in 2022.</li></ul>

<div class="mw-heading mw-heading2"><h2 id="Statistics">Statistics</h2></div>

According to the RefSeq release 213 (July 2022), the number of species represented in the database by counting distinct taxonomic IDs are as follows:<a href="#cite_note-:0-4">[4]</a>

</caption>

<th>Taxonomic ID

</th>

<th>Species

</th></tr>

<tr>

<td><a href="Archaea" title="Archaea">Archaea</a>

</td>

<td align="right">1443

</td></tr>

<tr>

<td><a href="Bacteria" title="Bacteria">Bacteria</a>

</td>

<td align="right">69122

</td></tr>

<tr>

<td><a href="Fungus" title="Fungus">Fungi</a>

</td>

<td align="right">16869

</td></tr>

<tr>

<td><a href="Invertebrate" title="Invertebrate">Invertebrate</a>

</td>

<td align="right">5715

</td></tr>

<tr>

<td><a href="Mitochondrion" title="Mitochondrion">Mitochondrion</a>

</td>

<td align="right">13648

</td></tr>

<tr>

<td><a href="Plant" title="Plant">Plant</a>

</td>

<td align="right">9177

</td></tr>

<tr>

<td><a href="Plasmid" title="Plasmid">Plasmid</a>

</td>

<td align="right">6073

</td></tr>

<tr>

<td><a href="Plastid" title="Plastid">Plastid</a>

</td>

<td align="right">9430

</td></tr>

<tr>

<td><a href="Protozoa" title="Protozoa">Protozoa</a>

</td>

<td align="right">746

</td></tr>

<tr>

<td>Vertebrate (<a href="Mammal" title="Mammal">mammalian</a>)

</td>

<td align="right">1509

</td></tr>

<tr>

<td><a href="Virus" title="Virus">Viral</a>

</td>

<td align="right">11620

</td></tr>

<tr>

<td>Vertebrate (other)

</td>

<td align="right">5237

</td></tr>

<tr>

<td>Other

</td>

<td align="right">4

</td></tr>

<tr>

<td>Complete

</td>

<td align="right">121461

</td></tr></tbody></table>

The counts of accession and basepairs per molecule type are:<a href="#cite_note-:0-4">[4]</a>

</caption>

<th>Molecule type

</th>

<th>Accessions

</th>

<th>Basepairs/residues

</th></tr>

<tr>

<td>Genomics

</td>

<td align="middle">40,758,769

</td>

<td align="middle">2.923212393984×10<s style="display:none">^</s>12

</td></tr>

<tr>

<td>RNA

</td>

<td align="middle">45,781,716

</td>

<td align="middle">1.22253022047×10<s style="display:none">^</s>11

</td></tr>

<tr>

<td>Protein

</td>

<td align="middle">234,520,053

</td>

<td align="middle">9.129062394×10<s style="display:none">^</s>10

</td></tr></tbody></table>

<ul><li><a href="GenBank" title="GenBank">GenBank</a></li>

<li><a href="Sequence_analysis" title="Sequence analysis">Sequence analysis</a></li>

<li><a href="Sequence_profiling_tool" title="Sequence profiling tool">Sequence profiling tool</a></li>

<li><a href="Sequence_motif" title="Sequence motif">Sequence motif</a></li>

<li><a href="UniProt" title="UniProt">UniProt</a></li>

<li><a href="List_of_sequenced_eukaryotic_genomes" title="List of sequenced eukaryotic genomes">List of sequenced eukaryotic genomes</a></li>

<li><a href="List_of_sequenced_archaeal_genomes" title="List of sequenced archaeal genomes">List of sequenced archaeal genomes</a></li></ul>

<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

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</style><cite id="CITEREFPruittTatusovaMaglott2005" class="citation journal cs1"><a href="Kim_D._Pruitt" title="Kim D. Pruitt">Pruitt KD</a>, Tatusova T, <a href="Donna_R._Maglott" title="Donna R. Maglott">Maglott DR</a> (January 2005). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979">"NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins"</a>. Nucleic Acids Research. 33 (Database issue): D501 – D504. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fnar%2Fgki025">10.1093/nar/gki025</a>. <a href="PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979">539979</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/15608248">15608248</a>.</cite>

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<li id="cite_note-pmid10637631-3"><a href="#cite_ref-pmid10637631_3-0">^</a> <cite id="CITEREFPruittKatzSicotteMaglott2000" class="citation journal cs1">Pruitt KD, Katz KS, Sicotte H, Maglott DR (January 2000). "Introducing RefSeq and LocusLink: curated human genome resources at the NCBI". Trends in Genetics. 16 (1): 44–47. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1016%2Fs0168-9525%2899%2901882-x">10.1016/s0168-9525(99)01882-x</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/10637631">10637631</a>.</cite>

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<li id="cite_note-:0-4">^ <a href="#cite_ref-:0_4-0">a</a> <a href="#cite_ref-:0_4-1">b</a> <a href="#cite_ref-:0_4-2">c</a> <cite class="citation report cs1"><a rel="nofollow" class="external text" href="https://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/">RefSeq Release 213 Statistics</a> (Report). <a href="National_Library_of_Medicine" class="mw-redirect" title="National Library of Medicine">National Library of Medicine</a>. 11 July 2022. Retrieved 20 July 2022.</cite>

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</ol></div></div>

<div class="mw-heading mw-heading2"><h2 id="Sources">Sources</h2></div>

<ul><li> This article incorporates <a href="Copyright_status_of_works_by_the_federal_government_of_the_United_States" title="Copyright status of works by the federal government of the United States">public domain material</a> from <cite class="citation cs1"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=handbook.TOC&depth=2">NCBI Handbook</a>. <a href="National_Center_for_Biotechnology_Information" title="National Center for Biotechnology Information">National Center for Biotechnology Information</a>.</cite></li></ul>

<div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2></div>

<ul><li><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/refseq/">RefSeq</a></li>

<li><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/books/NBK21105/#ch1.Appendix_GenBank_RefSeq_TPA_and_UniP">GenBank, RefSeq, TPA and UniProt: What's in a Name?</a></li></ul></div><div><div class="zim-footer">

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