{"id":14122,"date":"2024-10-28T09:47:17","date_gmt":"2024-10-28T13:47:17","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=14122"},"modified":"2024-11-04T14:06:59","modified_gmt":"2024-11-04T19:06:59","slug":"mane-v1-4-mane-select-non-coding-genes","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/10\/28\/mane-v1-4-mane-select-non-coding-genes\/","title":{"rendered":"MANE v1.4 with MANE Select for Non-Coding Genes"},"content":{"rendered":"<p><span data-contrast=\"auto\">The next release (v1.4) of <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/MANE\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\"><span data-contrast=\"none\">Matched Annotation from NCBI and EMBL-EBI (MANE)<\/span><\/a><span data-contrast=\"auto\"> is here!\u00a0 MANE is a <\/span><a href=\"https:\/\/www.nature.com\/articles\/s41586-022-04558-8\"><span data-contrast=\"none\">collaborative dataset<\/span><\/a><span data-contrast=\"auto\"> produced jointly by NCBI and EMBL-EBI that provides a representative transcript (MANE Select) for human protein-coding genes, to be used as universal standards for variant reporting and browser display. A second transcript, MANE Plus Clinical, is provided for genes where MANE Select alone is not sufficient to report all known variants. The new MANE release adds another important component to this high-value dataset \u2013 non-coding genes, some of which are known to be <\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37968332\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\"><span data-contrast=\"none\">associated with human disease.<\/span><\/a><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><!--more--><\/p>\n<h5><b><span data-contrast=\"auto\">What\u2019s new?<\/span><\/b><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">This release, built from RefSeq Annotation <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/annotation_euk\/Homo_sapiens\/GCF_000001405.40-RS_2024_08\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\"><span data-contrast=\"none\">GCF_000001405.40-RS_2024_08<\/span><\/a><span data-contrast=\"auto\"> and Ensembl release 114, contains 19,338 MANE Select and 66 MANE Plus Clinical transcripts. It also includes the first batch of fifty non-coding genes that are associated with human disease, chosen based on publications and input from collaborating groups.\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"4\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">For example, this set includes the small nuclear RNA gene <i data-stringify-type=\"italic\">RNU4ATAC<\/i><i>,<\/i> implicated in <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK589232\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\"><i>RNU4ATAC<\/i> Spectrum Disorder<\/a>, and the long noncoding RNA (lncRNA) gene <i>MALAT1,<\/i> reported as a <a href=\"https:\/\/www.nature.com\/articles\/s41598-023-35639-x\">therapeutic target<\/a> in several types of cancer, including breast cancer.\u00a0\u00a0<\/span><\/li>\n<\/ul>\n<p><span data-contrast=\"auto\">A new data file included on the FTP site provides information about genes where the original MANE Select was updated. The MANE set is intended to be stable, however rare updates are made in response to issues flagged by quality assurance tests, new published data, or external datasets. Look for the list in this file: <\/span><a href=\"https:\/\/ftp.ncbi.nih.gov\/refseq\/MANE\/MANE_human\/release_1.4\/MANE.GRCh38.v1.4.changed_select_accessions.txt.gz\"><span data-contrast=\"none\">MANE.GRCh38.v1.4.changed_select_accessions.txt.gz<\/span><\/a><span data-contrast=\"auto\">.\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"4\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"2\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">For example, the decision to switch MANE Select transcript for <i>IL36B<\/i> (GeneID: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gene\/27177?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\">27177<\/a>) from <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NM_014438.5?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\">NM_014438.5<\/a> (ENST00000259213.9) to <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NM_173178.3?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\">NM_173178.3<\/a> (ENST00000327407.2) was informed by the higher per-residue model confidence score (pLDDT score) of the AlphaFold prediction for <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/NM_173178.3?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\">NM_173178.3<\/a>. This is one of the eight MANE Select switches made based on the analysis in <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36519529\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\">Sommer et al., 2022<\/a>.<\/span><\/li>\n<\/ul>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"14125\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/10\/28\/mane-v1-4-mane-select-non-coding-genes\/malat1_manev1-4\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?fit=1741%2C249&amp;ssl=1\" data-orig-size=\"1741,249\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;1&quot;}\" data-image-title=\"MALAT1_MANEv1-4\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?fit=300%2C43&amp;ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?fit=1024%2C146&amp;ssl=1\" class=\"alignright size-full wp-image-14125\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?resize=1108%2C158&#038;ssl=1\" alt=\"Screenshot of MANE table\" width=\"1108\" height=\"158\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?w=1741&amp;ssl=1 1741w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?resize=300%2C43&amp;ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?resize=1024%2C146&amp;ssl=1 1024w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?resize=150%2C21&amp;ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?resize=768%2C110&amp;ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?resize=1536%2C220&amp;ssl=1 1536w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/10\/MALAT1_MANEv1-4.jpg?resize=270%2C39&amp;ssl=1 270w\" sizes=\"auto, (max-width: 1108px) 100vw, 1108px\" \/><b><i><span data-contrast=\"auto\">Figure:<\/span><\/i><\/b><i><span data-contrast=\"auto\"> Genome Data Viewer displaying the lncRNA gene MALAT1 (NCBI GeneID:378938) with the MANE v1.4 track (top) showing the MANE Select NR_002819.5 and all transcripts included in RefSeq Annotation GCF_000001405.40-RS_2024_08 (bottom).<\/span><\/i><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"auto\">Access the Data<\/span><\/b><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"2\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\"><a href=\"https:\/\/ftp.ncbi.nih.gov\/refseq\/MANE\/MANE_human\/release_1.4\">Download the MANE dataset<\/a>\u00a0\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"2\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">View MANE Select records in the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/nuccore?term=%22mane+ensembl+match%22%5BProperties%5D&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\">Nucleotide<\/a> or <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/protein\/?term=%22mane+ensembl+match%22%5BProperties%5D&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\">Protein<\/a> databases\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"2\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Interactively explore MANE sequence data in the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gdv?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\">Genome Data Viewer<\/a>\u00a0<\/span><\/li>\n<\/ul>\n<h5><b><span data-contrast=\"auto\">Learn more<\/span><\/b><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">For more information, check out our <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/MANE\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=mane-1.4-20241028\"><span data-contrast=\"none\">help documentation<\/span><\/a><span data-contrast=\"auto\">.<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"auto\">Stay up to date\u202f\u202f<\/span><\/b><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">Follow us on social\u202f<\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"auto\">\u202fand\u202f<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_52\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"auto\">\u202fto keep up to date with MANE and other NCBI news.\u202f\u202f\u202f<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"auto\">We want to hear from you! \u202f\u202f\u202f<\/span><\/b><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">We want your feedback! If you have questions or would like to provide feedback, please reach out to us at MANE-help@ncbi.nlm.nih.gov.<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The next release (v1.4) of Matched Annotation from NCBI and EMBL-EBI (MANE) is here!\u00a0 MANE is a collaborative dataset produced jointly by NCBI and EMBL-EBI that provides a representative transcript (MANE Select) for human protein-coding genes, to be used as universal standards for variant reporting and browser display. A second transcript, MANE Plus Clinical, is &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/10\/28\/mane-v1-4-mane-select-non-coding-genes\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">MANE v1.4 with MANE Select for Non-Coding Genes<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":14126,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"MANE v1.4 with MANE Select for Non-Coding Genes","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[574293891,782519,3064946,9715],"table_tags":[],"class_list":["post-14122","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-genome-data-viewer","tag-mane","tag-nucleotide","tag-protein"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>MANE v1.4 with MANE Select for Non-Coding Genes - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/10\/28\/mane-v1-4-mane-select-non-coding-genes\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"MANE v1.4 with MANE Select for Non-Coding Genes - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"The next release (v1.4) of Matched Annotation from NCBI and EMBL-EBI (MANE) is here!\u00a0 MANE is a collaborative dataset produced jointly by NCBI and EMBL-EBI that provides a representative transcript (MANE Select) for human protein-coding genes, to be used as universal standards for variant reporting and browser display. 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