Tag: RefSeq

New RefSeq annotations for mouse, maize, sunflower and more!

New RefSeq annotations for mouse, maize, sunflower and more!

In August and September, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Amphiprion ocellaris (clown anemonefish)
  • Anopheles stephensi (Asian malaria mosquito)
  • Aplysia californica (California sea hare)
  • Bactrocera oleae (olive fruit fly)
  • Branchiostoma floridae (Florida lancelet)
  • Egretta garzetta (little egret)
  • Folsomia candida (springtail)
  • Fundulus heteroclitus (mummichog)
  • Halichoerus grypus (gray seal)
  • Helianthus annuus (common sunflower)
  • Homo sapiens (human)
  • Lynx canadensis (Canada lynx)
  • Molossus molossus (Pallas’s mastiff bat)
  • Monomorium pharaonis (pharaoh ant)
  • Mus musculus (house mouse)
  • Myotis myotis (bat)
  • Neolamprologus brichardi (lyretail cichlid)
  • Oncorhynchus keta (chum salmon)
  • Onychomys torridus (southern grasshopper mouse)
  • Oryzias melastigma (Indian medaka)
  • Phyllostomus discolor (pale spear-nosed bat)
  • Rousettus aegyptiacus (Egyptian rousette)
  • Sander lucioperca (pike-perch)
  • Zea mays (maize)

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

Learn more about the annotation of the new mouse reference assembly, GRCm39, here. This is the first coordinate-changing update to the mouse reference since the 2012 release of GRCm38.

Announcing the RefSeq annotation of mouse GRCm39!

NCBI RefSeq has finished its initial annotation of the new mouse reference assembly, GRCm39, recently released by the Genome Reference Consortium. This is the first coordinate-changing update to the mouse reference since the 2012 release of GRCm38, resolving over 400 issues, almost doubling the scaffold N50, closing almost half the gaps, and adding 1.9 Mb of sequence. It’s a big deal!Figure 1. The Genome Data Viewer showing the annotation for the mouse pseudoautosomal region that includes annotations of four genes that were previously missing: Sts, Nlgn4l, Akap17a, and 2510022D24Rik

Continue reading “Announcing the RefSeq annotation of mouse GRCm39!”

NCBI Datasets now provides downloads of gene data for more than 30 thousand organisms

NCBI Datasets now offers Gene tables: customizable tables of the genes you specify, with key gene information, and the ability to easily download a dataset of genomic, transcript and protein sequences.

Drag and drop a list of Gene IDs or gene symbols, and the data table shows your genes with up to 15 columns of metadata, including genomic coordinates, RefSeq transcript and protein accessions, Ensembl IDs and UniProt accessions, and other gene information. You can browse and select items in your table on the web, or download everything to your computer for later analysis (Figure 1).

Figure 1. The Data tables web download. Top panel. Enter or upload a list of gene identifiers or symbols. Bottom panel. The resulting table display allows you to browse results, download the table or the sequence data for the genes (genomic, transcripts, proteins).  Continue reading “NCBI Datasets now provides downloads of gene data for more than 30 thousand organisms”

The latest in COVID-19 related human gene annotation now in NCBI RefSeq and Gene

Interested in human genes involved in COVID-19 biology? NCBI’s RefSeq group has been hard at work compiling a set of human genes with roles in coronavirus infection and disease. You can now see and search for these genes and their regulatory elements in NCBI Gene and RefSeq.

Figure 1. Top section of the human ACE2 record in the Gene database. COVID-19 information can be found in the Summary and Annotation information sections.

Continue reading “The latest in COVID-19 related human gene annotation now in NCBI RefSeq and Gene”

RefSeq Release 202 is public

RefSeq release 202 is accessible online, via FTP and through NCBI’s Entrez programming utilities, E-utilities.

This full release incorporates genomic, transcript, and protein data available as of September 8, 2020, and contains 255,571,455 records, including 186,755,483 proteins, 33,077,068 RNAs, and sequences from 104,969  organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

Updated human genome Annotation Release 109.20200815
Updated Annotation Release 109.2020815 is an update of NCBI Homo sapiens Annotation Release 109. The annotation report is available here.

The annotation products are available in the sequence databases and on the FTP site.

This update includes around 15,000 updated RefSeq transcripts revised to use CAGE and polyA data to define 5′ and 3′ ends, and match the reference GRCh38 sequence.

Coronavirus host gene regulatory elements now annotated by RefSeq Functional Elements
The RefSeq Functional Elements project at NCBI has prioritized curation of experimentally validated regulatory elements for human host genes associated with SARS-CoV-2 entry into cells. The annotations include several enhancers, promoters, cis-regulatory elements and protein binding sites, among other feature types. We annotated 236 regulatory features for 27 distinct biological regions, including regulatory elements for the ABO, ACE2, ANPEP, CD209, CLEC4G, CLEC4M, CTSL, DPP4, and TMPRSS2 genes. More information can be found here.

New eukaryotic genome annotations
This release includes new annotations generated by NCBI’s eukaryotic genome annotation pipeline for 27 species, including:

  • maize annotation release 103, based on the new assembly Zm-B73-REFERENCE-NAM-5.0 (GCF_902167145.1)
  • marmoset annotation release 105, based on the new assembly Callithrix_jacchus_cj1700_1.1 (GCF_009663435.1)
  • Chinese hamster annotation release 104, based on the assembly CriGri_1.0 (GCF_000223135.1) and the new assembly CriGri-PICRH-1.0 (GCF_003668045.3)
  • Asian giant hornet annotation release 100, based on the new assembly V.mandarinia_Nanaimo_p1.0 (GCF_014083535.2)
  • Florida lancelet annotation release 100, based on the new assembly Bfl_VNyyK (GCF_000003815.2)
  • Anopheles stephensi annotation release 100, based on the new assembly UCI_ANSTEP_V1.0 (GCF_013141755.1)

Updated and improved collection of RefSeq representative genome assemblies now available
The collection of representative genome assemblies for Bacteria and Archaea contains 11,727 prokaryotic assemblies to represent their respective species. More information can be found here.

Updated protein family models used by PGAP available for download
Release 3.0 of the NCBI protein family models used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available.

This release contains 17,350 models: 12,864 HMMs built at NCBI (111 more than in release 2.0) and 4,486 TIGRFAM HMMs. In addition, since release 2.0, we have assigned product names to over 2,000 Pfam HMMs, bringing the total to 6,698 Pfam HMMs with names that can be transferred by PGAP to the annotated proteins they hit. More information can be found here.

Future change: Mouse Reference Assembly Update
RefSeq annotation of the new mouse GRCm39 assembly is in progress, and is expected to be included in the next release.

Updated and improved collection of RefSeq representative genome assemblies now available

We have updated the collection of representative genome assemblies for Bacteria and Archaea. As announced in April, this set is now recalculated three times a year. We selected a total of 11,727 prokaryotic assemblies to represent their respective species among the 192,000 assemblies in RefSeq. Six hundred and thirty-five species were included in the collection for the first time, while 395 organisms from undefined species (such as Bacillus bacterium) were removed. We were able to choose a higher-quality representative than in the previous set for 18% of Bacterial and Archaeal species due to improvements in the logic of the selection that is now based on the assembly length, number of pseudo CDSs called in the PGAP annotation, number of scaffolds, whether Gene IDs are available in the Gene database for the assembly that is currently representative, and type strain status. You can see the exact criteria in order of importance on the Prokaryotic RefSeq Genomes page. Now that the new selection process is in place, we expect future updates to have fewer changes. We will replace a representative only if the assembly has changed RefSeq status or if a substantially better assembly becomes available.

We have updated the database on the Microbial Nucleotide BLAST page as well as the basic nucleotide BLAST RefSeq Representative Genome Database, to reflect these changes.

You can download the reference and representative set from the Assembly resource. If you are interested in the annotation on these genomes, you can limit searches to proteins annotated on representative genomes by adding “refseq_select[filter]” to any query in the Protein database. For example, you can find all proteins annotated on representative genomes in the genus Klebsiella by using the query: “Klebsiella[organism] AND refseq_select[filter]“.  A BLAST database of proteins annotated on representative genomes will be coming soon. Stay tuned!

New annotations in RefSeq: white-tufted-ear marmoset, ruddy duck, and more

New annotations in RefSeq: white-tufted-ear marmoset, ruddy duck, and more

In June and July, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

Acipenser ruthenus (sterlet)
Anguilla anguilla (European eel)
Aphantopus hyperantus (ringlet)
Callithrix jacchus (white-tufted-ear marmoset)
Chelonus insularis (wasp)
Cricetulus griseus (Chinese hamster)
Cygnus atratus (black swan)
Drosophila subobscura (fly)
Electrophorus electricus (electric eel)
Etheostoma cragini (Arkansas darter)
Hippoglossus stenolepis (Pacific halibut)
Mirounga leonina (Southern elephant seal)
Morone saxatilis (striped sea-bass)
Mus musculus (house mouse)
Oxyura jamaicensis (ruddy duck)
Pan paniscus (pygmy chimpanzee)
Populus alba (eudicot)
Scophthalmus maximus (turbot)
Spodoptera frugiperda (fall armyworm)
Stegodyphus dumicola (spider)
Vitis riparia (eudicot)
Zootoca vivipara (common lizard)

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

New interaction data, downloads and track hub available for RefSeq Functional Elements 

We’ve added several new enhancements to the RefSeq Functional Elements dataset, which provides genome annotation and richly annotated RefSeq and Gene records for experimentally validated non-genic functional regions in human and mouse. Read on to see what we’ve done!

Continue reading “New interaction data, downloads and track hub available for RefSeq Functional Elements “

Major update for the NCBI RefSeq mouse GRCm38.p6 annotation

We have updated our annotation for the mouse reference genome, GRCm38.p6. It includes:

  • Markup for RefSeq Select, which identifies one representative transcript and protein for every protein-coding gene. Find features with the ‘tag=RefSeq Select’ attribute in GFF3 for those analyses where you need just a single transcript or protein for each coding gene. You can also find these RefSeqs in Entrez using the query ‘refseq_select[filter].’
  • Annotation updates made in the last year for over 2000 genes, including over 4000 new or revised curated transcripts. This includes targeted curation to ensure we are representing well-expressed and conserved transcripts for inclusion in RefSeq Select.
  • Annotation of over 2300 regulatory and other functional element features from over 900 biological regions. These are now identified with the source “RefSeqFE” in GFF3 column 2 for easy parsing.

When citing, please refer to this annotation as NCBI Mus musculus Annotation Release 108.20200622. You can find the data in:

This is our last update before upgrading to the new major assembly version just released by the Genome Reference Consortium, GRCm39. We expect to be cranking up our compute farm in the next few weeks to produce a full annotation based on our latest curation and extensive short (Illumina) and long (PacBio IsoSeq and nanopore) RNA-seq data, which should be released later this summer. Stay tuned!

Updated protein family models used by PGAP available for download

Release 3.0 of the NCBI protein family models used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available from our FTP site. You can search this collection of hidden Markov models (HMMs) against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.

The 3.0 release contains 17,350 models: 12,864 HMMs built at NCBI (111 more than in release 2.0) and 4,486 TIGRFAM HMMs. In addition, since release 2.0,  we have assigned product names to over 2,000 Pfam HMMs, bringing the total to 6,698 Pfam HMMs with names that can be transferred by PGAP to the annotated proteins they hit. You can access a table of these product names from the release directory.Prot_evidenceFigure 1. The evidence for name assignment for type III secretion system (T3SS) translocon subunit SctB (NF038055) showing the protein matches. Species-specific names for this highly variable component of T3SS include YopD, EspB, IpaC, SipC, etc. Instead, we used the standard moniker for core genes of T3SS, Sct, Secretion and cellular translocation (PMID 26520801,  PMID 9618447) providing a unified nomenclature for this secretion system.  Continue reading “Updated protein family models used by PGAP available for download”