174 lines
60 KiB
HTML
174 lines
60 KiB
HTML
<!DOCTYPE html>
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/*# sourceURL=/css/ampshared.css*/</style><meta property="og:locale" content="en_US"><meta property="og:type" content="article"><meta property="og:title" content="New Annotations in RefSeq! - NCBI Insights"><meta property="og:description" content="In April, May, and June, the NCBI Eukaryotic Genome Annotation Pipeline released eighty-two new annotations in RefSeq! Highlights: Homo sapiens (human) T2T-CHM13v2.0 now includes many more alternative splice variants Homo sapiens (human) GRCh38.p14 includes all transcripts from MANE v1.2, and includes over 78,000 new RefSeq Functional Element (RefSeqFE) features added since our last annotation in 2022 Mus musculus (house mouse) GRCm39 … Continue reading New Annotations in RefSeq! →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2023/07/24/new-annotations-in-refseq/"><meta property="og:site_name" content="NCBI Insights"><meta property="article:publisher" content="https://www.facebook.com/ncbi.nlm"><meta property="article:published_time" content="2023-07-24T16:46:08+00:00"><meta property="article:modified_time" content="2023-08-02T14:22:37+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg"><meta property="og:image:width" content="1100"><meta property="og:image:height" content="734"><meta 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<h1 class="amp-wp-title">New Annotations in RefSeq!</h1>
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<time datetime="2023-07-24T16:46:08+00:00">
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2 years ago </time>
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<amp-img width="1024" height="683" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?fit=1024%2C683&ssl=1" class="attachment-large size-large wp-post-image amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" alt="Peregrine falcon in flight" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=300%2C200&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=1024%2C683&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=150%2C100&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=768%2C512&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=270%2C180&ssl=1 270w" sizes="auto, (max-width: 1024px) 100vw, 1024px" data-hero-candidate="" layout="intrinsic" disable-inline-width="" data-hero i-amphtml-ssr i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjY4MyIgd2lkdGg9IjEwMjQiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><img class="i-amphtml-fill-content i-amphtml-replaced-content" decoding="async" loading="lazy" alt="Peregrine falcon in flight" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?fit=1024%2C683&ssl=1" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?w=1100&ssl=1 1100w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=300%2C200&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=1024%2C683&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=150%2C100&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=768%2C512&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2023/07/iStock-180825415-e1689952782128.jpg?resize=270%2C180&ssl=1 270w" sizes="auto, (max-width: 1024px) 100vw, 1024px"></amp-img> <p class="wp-caption-text">
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Peregrine Falcon in flight </p>
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</figure>
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<div class="amp-wp-article-content">
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<p>In April, May, and June, the <a class="external-link" title="Follow link" href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724" target="_blank" rel="nofollow noopener">NCBI Eukaryotic Genome Annotation Pipeline</a> released <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/?accession=GCF_027475565.1,GCF_019202715.1,GCF_026212465.1,GCF_022539595.1,GCF_027943255.1,GCF_947563725.1,GCF_949987535.1,GCF_026745355.1,GCF_900634795.4,GCF_947242115.1,GCF_026225935.1,GCF_029407905.1,GCF_950005125.1,GCF_029603195.1,GCF_903798145.1,GCF_022539665.1,GCF_023375885.1,GCF_026230105.1,GCF_027744805.1,GCF_945859705.1,GCF_028583425.1,GCF_029931775.1,GCF_945859685.1,GCF_023638135.1,GCF_023634085.1,GCF_023634155.1,GCF_026213295.1,GCF_029281585.1,GCF_028858705.1,GCF_030028045.1,GCF_029227915.1,GCF_029499605.1,GCF_029633865.1,GCF_028641065.1,GCF_012489685.1,GCF_024334085.1,GCF_015342785.2,GCF_030028575.1,GCF_030020395.1,GCF_937616625.2,GCF_029852145.1,GCF_027580225.1,GCF_027887165.1,GCF_022376915.1,GCF_000001635.27,GCF_905146905.1,GCF_029582105.1,GCF_947568905.1,GCF_029289425.1,GCF_028858775.1,GCF_019649055.1,GCF_932274485.2,GCF_009829125.3,GCF_028554395.1,GCF_024763615.1,GCF_002837175.3,GCF_027474105.1,GCF_028885655.1,GCF_028885625.1,GCF_029017545.1,GCF_907164565.1,GCF_029220125.1,GCF_000801105.2,GCF_015227675.2,GCF_029890125.1,GCF_029448725.1,GCF_021018895.1,GCF_009176505.1,GCF_947179165.1,GCF_027595985.1,GCF_029834395.1,GCF_020520425.1,GCF_028878055.1,GCF_021117445.2,GCF_003711565.1,GCF_029784135.1,GCF_015846415.1,GCF_024868665.1,GCF_026930045.1,GCF_029784155.1,GCF_023065955.2,GCF_029784165.1">eighty-two new annotations</a> in <a class="external-link" title="Follow link" href="https://www.ncbi.nlm.nih.gov/refseq/about/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724" target="_blank" rel="nofollow noopener">RefSeq</a>!</p>
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<p><strong>Highlights</strong>:</p>
|
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<ul>
|
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<li>Homo sapiens (human) <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009914755.1/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724">T2T-CHM13v2.0</a> now includes many more alternative splice variants</li>
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<li>Homo sapiens (human) <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724">GRCh38.p14</a> includes all transcripts from <a href="https://www.ncbi.nlm.nih.gov/refseq/MANE/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724">MANE</a> v1.2, and includes over 78,000 new <a class="external-link" href="https://www.ncbi.nlm.nih.gov/refseq/functionalelements/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724" target="_blank" rel="nofollow noopener">RefSeq Functional Element</a> (RefSeqFE) features added since our last annotation in 2022</li>
|
||
<li>Mus musculus (house mouse) <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724">GRCm39</a> integrates curation for over 3,000 genes and 14,000 transcripts since September 2020</li>
|
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<li>Rattus norvegicus (Norway rat) <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_015227675.2/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724">mRatBN7.2</a>, including curation of over 5000 genes since our last annotation in 2021</li>
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</ul>
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<p><strong>New annotations</strong>: </p>
|
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<ul>
|
||
<li>Acinonyx jubatus (cheetah)</li>
|
||
<li>Actinidia eriantha (eudicot)</li>
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<li>Amaranthus tricolor (eudicot)</li>
|
||
<li>Amphiprion ocellaris (clown anemonefish)</li>
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||
<li>Anastrepha obliqua (fly)</li>
|
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<li>Argiope bruennichi (spider)</li>
|
||
<li>Balaenoptera acutorostrata (minke whale)</li>
|
||
<li>Beta vulgaris subsp. vulgaris (beet)</li>
|
||
<li>Betta splendens (Siamese fighting fish)</li>
|
||
<li>Biomphalaria glabrata (bloodfluke planorb)</li>
|
||
<li>Boleophthalmus pectinirostris (great blue-spotted mudskipper)</li>
|
||
<li>Bubalus carabanensis (carabao)</li>
|
||
<li>Chionomys nivalis (European snow vole)</li>
|
||
<li>Condylostylus longicornis (fly)</li>
|
||
<li>Danio aesculapii (bony fish)</li>
|
||
<li>Daphnia carinata (crustacean)</li>
|
||
<li>Dermacentor andersoni (tick)</li>
|
||
<li>Diorhabda sublineata (beetle)</li>
|
||
<li>Dunckerocampus dactyliophorus (ringed pipefish)</li>
|
||
<li>Episyrphus balteatus (marmalade hoverfly)</li>
|
||
<li>Eublepharis macularius (Leopard gecko)</li>
|
||
<li>Euleptes europaea (tarantolino)</li>
|
||
<li>Eupeodes corollae (fly)</li>
|
||
<li>Falco biarmicus (lanner falcon)</li>
|
||
<li>Falco cherrug (Saker falcon)</li>
|
||
<li>Falco peregrinus (peregrine falcon) <em>(pictured)</em></li>
|
||
<li>Gadus chalcogrammus (walleye pollock)</li>
|
||
<li>Gorilla gorilla gorilla (western lowland gorilla)</li>
|
||
<li>Grus americana (Whooping crane)</li>
|
||
<li>Hippopotamus amphibius kiboko (hippopotamus)</li>
|
||
<li>Hydractinia symbiolongicarpus (hydrozoan)</li>
|
||
<li>Hyla sarda (Sardinian treefrog)</li>
|
||
<li>Lampris incognitus (smalleye Pacific opah)</li>
|
||
<li>Leucoraja erinacea (little skate)</li>
|
||
<li>Lotus japonicus (eudicot)</li>
|
||
<li>Lutzomyia longipalpis (fly)</li>
|
||
<li>Lytechinus pictus (painted urchin)</li>
|
||
<li>Malurus melanocephalus (red-backed fairy wren)</li>
|
||
<li>Manis pentadactyla (Chinese pangolin)</li>
|
||
<li>Mercurialis annua (annual mercury)</li>
|
||
<li>Microplitis mediator (wasp)</li>
|
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<li>Misgurnus anguillicaudatus (oriental weatherfish)</li>
|
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<li>Monodelphis domestica (gray short-tailed opossum)</li>
|
||
<li>Moschus berezovskii (Chinese forest musk deer)</li>
|
||
<li>Mus musculus (house mouse)</li>
|
||
<li>Nyctereutes procyonoides (raccoon dog)</li>
|
||
<li>Oenanthe melanoleuca (bird)</li>
|
||
<li>Ostrea edulis (bivalve)</li>
|
||
<li>Pan paniscus (pygmy chimpanzee)</li>
|
||
<li>Pan troglodytes (chimpanzee)</li>
|
||
<li>Paramacrobiotus metropolitanus (tardigrade)</li>
|
||
<li>Patella vulgata (common limpet)</li>
|
||
<li>Periophthalmus magnuspinnatus (bony fish)</li>
|
||
<li>Pezoporus wallicus (ground parrot)</li>
|
||
<li>Phlebotomus papatasi (fly)</li>
|
||
<li>Physeter catodon (sperm whale)</li>
|
||
<li>Poeciliopsis prolifica (blackstripe livebearer)</li>
|
||
<li>Pongo pygmaeus (Bornean orangutan)</li>
|
||
<li>Prosopis cineraria (eudicot)</li>
|
||
<li>Psammomys obesus (fat sand rat)</li>
|
||
<li>Pseudoliparis swirei (bony fish)</li>
|
||
<li>Raphanus sativus (radish)</li>
|
||
<li>Rattus norvegicus (Norway rat)</li>
|
||
<li>Rhinichthys klamathensis goyatoka (bony fish)</li>
|
||
<li>Salvelinus fontinalis (brook trout)</li>
|
||
<li>Seriola aureovittata (bony fish)</li>
|
||
<li>Sitodiplosis mosellana (orange wheat blossom midge)</li>
|
||
<li>Solanum dulcamara (climbing nightshade)</li>
|
||
<li>Sorex araneus (European shrew)</li>
|
||
<li>Sorex cinereus (cinereus shrew)</li>
|
||
<li>Spinacia oleracea (spinach)</li>
|
||
<li>Symphalangus syndactylus (siamang)</li>
|
||
<li>Syzygium oleosum (eudicot)</li>
|
||
<li>Takifugu flavidus (sansaifugu)</li>
|
||
<li>Toxorhynchites rutilus septentrionalis (mosquito)</li>
|
||
<li>Triplophysa dalaica (bony fish)</li>
|
||
<li>Triplophysa rosa (bony fish)</li>
|
||
<li>Uloborus diversus (spider)</li>
|
||
<li>Uranotaenia lowii (mosquito)</li>
|
||
<li>Ursus arctos (brown bear)</li>
|
||
<li>Wyeomyia smithii (pitcher-plant mosquito)</li>
|
||
</ul>
|
||
<p><span data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00">View the full list of annotated eukaryotes available in the</span><a class="external-link amp-wp-c5d79b2" title="Follow link" href="https://www.ncbi.nlm.nih.gov/genome/gdv/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724" target="_blank" rel="nofollow noopener" data-amp-original-style="font-size: 1.125rem; background-color: #ffffff;"> Genome Data Viewer (GDV) genome browser</a><span data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00">. You can download genome sequence and metadata using the </span><a class="external-link amp-wp-c5d79b2" title="Follow link" href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/download-genome/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724" target="_blank" rel="nofollow noopener" data-amp-original-style="font-size: 1.125rem; background-color: #ffffff;">NCBI Datasets command line tool</a><span data-amp-original-style="font-size: 1.125rem;" class="amp-wp-2917c00">.</span></p>
|
||
<h5>Stay up to date</h5>
|
||
<p>RefSeq is part of the <a href="https://www.ncbi.nlm.nih.gov/comparative-genomics-resource/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724">NIH Comparative Genomics Resource (CGR). </a><span data-contrast="none">CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration. </span><span data-ccp-props='{"134233117":true,"134233118":true,"201341983":0,"335559739":160,"335559740":240}'> </span></p>
|
||
<p>CGR is also making it easier to navigate between data and tools. To see this list and find out what’s in the RefSeq annotation pipeline, check out the <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=refseq-update-20230724">new table</a> in NCBI Datasets with information on the latest eukaryotic RefSeq annotations.</p>
|
||
<p><a class="external-link" href="https://public.govdelivery.com/accounts/USNLMOCPL/subscriber/new?topic_id=USNLMOCPL_50%22" rel="nofollow">Join our mailing list</a> to keep up to date with RefSeq and other CGR news.</p>
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<h5>Questions?</h5>
|
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<p><span data-contrast="auto">If you have questions or would like to provide feedback, please reach out to us at </span><a href="mailto:info@ncbi.nlm.nih.gov"><span data-contrast="none">info@ncbi.nlm.nih.gov</span></a><span data-contrast="auto">. </span><span data-ccp-props='{"201341983":0,"335559739":0,"335559740":240}'> </span></p>
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