• Several projects to improve RefSeq services are currently in development by the NCBI, often in collaboration with research centers such as EMBL-EBI: Consensus CDS (CCDS): This project aims to identify a core set of human and mouse protein-coding regions and standardize sets of genes with high and consistent levels of genomic annotation quality. (wikipedia.org)
  • By doing that, the differences in transcripts annotation between RefSeq and Ensembl/GENCODE annotation systems are reduced. (wikipedia.org)
  • Some RefSeq records may incorporate expanded sequence and annotation information. (ibp.ac.cn)
  • In the master annotation file (.gff), I get the RefSeq-ID of every successful annotation, e.g. (stackexchange.com)
  • Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference? (stackexchange.com)
  • The refSeq annotation of the exons can easily be downloaded from the UCSC Table Browser, using the RefSeq Track. (seqanswers.com)
  • RefSeq: an update on prokaryotic genome annotation and curation. (cdc.gov)
  • Many components impact this transcript selection such as the size of the transcript, how many clinical submissions are present, and lastly, the huge effort associated with the MANE select transcript based on matching RefSeq and Ensembl selected transcripts. (goldenhelix.com)
  • Since many genes are represented by multiple RefSeq transcripts/proteins due to the biological process of alternative splicing, this complexity is problematic for studies such as comparative genomics or exchange of clinical variant data. (wikipedia.org)
  • The NCBI RefSeq Genes composite track shows zebrafish protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). (ucsc.edu)
  • This track was previously known as the 'RefSeq Genes' track. (ucsc.edu)
  • Does NCBI have a single, downloadable file containing all refSeq-annotated exons for all genes? (seqanswers.com)
  • To provide this increased depth of coverage and enable high multiplexing of samples, the xGen Exome Hyb Panel v2 targets only the coding sequences (CDS) of human coding genes in the RefSeq 109 database. (idtdna.com)
  • The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. (wikipedia.org)
  • The most important categories are: For more details and more categories, see Table 1 in Chapter 18 of the book The Reference Sequence (RefSeq) Database. (wikipedia.org)
  • According to the RefSeq release 213 (July 2022), the number of species represented in the database by counting distinct taxonomic IDs are as follows: The counts of accession and basepairs per molecule type are: GenBank Sequence analysis Sequence profiling tool Sequence motif UniProt List of sequenced eukaryotic genomes List of sequenced archaeal genomes Pruitt KD, Tatusova T, Maglott DR (January 2005). (wikipedia.org)
  • This track was produced at UCSC from RNA sequence data generated by scientists worldwide and curated by the NCBI RefSeq project . (nodai-genome.org)
  • Pruitt KD, Tatusova T, Maglott DR. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins . (nodai-genome.org)
  • INTERFACE RefSeq = Sequence ( Refany ) END RefSeq. (opencm3.net)
  • epidemiologically unlinked isolate RefSeq Assembly Accession GCF_001307335.1). (cdc.gov)
  • ACCESSION NC_040876 VERSION NC_040876.1 DBLINK BioProject: PRJNA485481 KEYWORDS RefSeq. (cdc.gov)
  • RefSeq All - all curated and predicted annotations provided by RefSeq. (ucsc.edu)
  • RefSeq Curated - subset of RefSeq All that includes only those annotations whose accessions begin with NM, NR, NP or YP. (ucsc.edu)
  • RefSeq Predicted - subset of RefSeq All that includes those annotations whose accessions begin with XM or XR. (ucsc.edu)
  • RefSeq Other - all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the RefSeq Curated or the RefSeq Predicted tracks. (ucsc.edu)
  • UCSC RefSeq - annotations generated from UCSC's realignment of RNAs with NM and NR accessions to the zebrafish genome. (ucsc.edu)
  • RefSeq is limited to major organisms for which sufficient data are available (121,461 distinct "named" organisms as of July 2022), while GenBank includes sequences for any organism submitted (approximately 504,000 formally described species). (wikipedia.org)
  • For each model organism, RefSeq aims to provide separate and linked records for the genomic DNA, the gene transcripts, and the proteins arising from those transcripts. (wikipedia.org)
  • 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, evolutionary conservation of the coding region etc. (wikipedia.org)
  • The "RefSeq Curated" track is NCBI's mapping of these transcripts to the genome. (ucsc.edu)
  • RefSeq Diffs - alignment differences between the zebrafish reference genome(s) and RefSeq curated transcripts. (ucsc.edu)
  • RefSeq Select (subset, only on hg38) - Subset of RefSeq Curated, transcripts marked as part of the RefSeq Select dataset. (ucsc.edu)
  • RefSeq HGMD (subset) - Subset of RefSeq Curated, transcripts annotated by the Human Gene Mutation Database. (ucsc.edu)
  • RefSeq Diffs - alignment differences between the human reference genome(s) and RefSeq transcripts. (ibp.ac.cn)
  • RefSeq HGMD - only show RefSeq Curated transcripts mentioned in the Human Gene Mutation Database. (ibp.ac.cn)
  • Drosophila transcripts from the NCBI RefSeq database were aligned against the D. melanogaster dm6 assembly using BLAT. (wustl.edu)
  • RefSeq release 212 is now available online , from the FTP site and through NCBI's Entrez programming utilities, E-utilities . (nih.gov)
  • All subtracks use coordinates provided by RefSeq, except for the UCSC RefSeq track, which UCSC produces by realigning the RefSeq RNAs to the genome. (ucsc.edu)
  • Another alignment track exists for these, the "UCSC RefSeq" track (see beloow). (ucsc.edu)
  • The RefSeq All , RefSeq Curated , RefSeq Predicted , and UCSC RefSeq tracks follow the display conventions for gene prediction tracks . (ucsc.edu)
  • RefSeq Alignments - alignments of RefSeq RNAs to the zebrafish genome provided by the RefSeq group, following the display conventions for PSL tracks . (ucsc.edu)
  • RefSeq Alignments - alignments of RefSeq RNAs to the human genome provided by the RefSeq group. (ibp.ac.cn)
  • The RefSeq Alignments track follows the display conventions for PSL tracks . (ibp.ac.cn)
  • The file 'GCF_000001405.28_knownrefseq_alignments.gff3' (or the most recent version) in the directory 'ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/alignments/' maps every refSeq exon to the current human genome build. (seqanswers.com)
  • Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. (ibp.ac.cn)
  • You can access RefSeq data through NCBI Datasets . (nih.gov)
  • Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. (ucsc.edu)
  • We are excited to announce that we have annotated over 1,000 eukaryotic species in RefSeq ! (nih.gov)
  • The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by RefSeq . (ucsc.edu)
  • Provisional: the RefSeq record has not yet been subject to individual review. (ibp.ac.cn)
  • RefSeq collection comprises different data types, with different origins, so it is necessary to establish standard categories and identifiers to store each data type. (wikipedia.org)
  • It is the most restricted RefSeq subset, targeting clinical diagnostics. (ucsc.edu)
  • Increasing clinical availability demografia-y-migracion/publicaciones-y-anuarios/ of molecular diagnostics might identify B. lonestari as an migraci%C3%B3n-internacional/estimaci%C3%B3n- poblaci%C3%B3n-extranjera-en-chile-2018/ emerging tickborne pathogen. (cdc.gov)
  • RefSeq supports the NIH Comparative Genomics Resource (CGR) , an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses for all eukaryotic organisms. (nih.gov)
  • RefSeq plays a huge role in variant filtering and analysis for both the single nucleotide, indel, and copy number analysis, all processed in the VarSeq software. (goldenhelix.com)
  • RefSeq release 218 is now available online and from the FTP site. (nih.gov)
  • RefSeq release 212 is available! (nih.gov)
  • Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted. (ibp.ac.cn)
  • For RNA-seq analysis, we advise using NCBI aligned tables like RefSeq All or RefSeq Curated. (ucsc.edu)