NCBI RefSeq Targeted Loci Project

Targeted loci are specific molecular markers such as protein coding or ribosomal RNA genes that are used for phylogenetic analysis

SCOPE

NCBI RefSeq Targeted Loci project includes markers from Archaea, Bacteria, and Fungi. Markers are represented by ribosomal RNA subunits in all three kingdoms and ITS (internal transcribed spacer) DNA sequences in Fungi. The RefSeq collection of targeted loci sequences is curated by NCBI staff.

TOOLS and ANALYSIS

BLAST

BLAST against the curated targeted loci database. Select "Sequences from type material" to limit your search to type only.

MOLE-BLAST is a tool that helps users find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results

16S ribosomal RNA project

The small subunit ribosomal RNA is a useful phylogenetic marker that has been used extensively for evolutionary analyses. The RefSeq dataset contains curated 16S ribosomal RNA sequences that correspond to bacteria and archaea type materials. The RefSeq records may contain corrections to the sequence or taxonomy as compared to the original INSD submission, and may have additional information added that is not found in the original. See more details on curation process.
16S RefSeq Nucleotide sequence records

5S ribosomal RNA project

5S ribosomal RNA is a small RNA molecule (length ~ 120 nt, molecular weight ~ 40kDa) . It is an integral part of the large ribosomal subunit in almost all known organisms with the exception of mitochondria of some fungi. The RefSeq 5S ribosomal RNA project represents a collection of curated complete and near full length Reference Sequence records for Archaea and Bacteria. This reference set is used in Prokaryotic Genome Annotation Pipeline.
5S RefSeq Nucleotide sequence records

23S ribosomal RNA project

The 23S ribosomal RNA is the largest rRNA in the microbial ribosome (~2800 nt) and is part of the 50S ribosomal subunit. The 23S rRNA is involved in the formation of peptide bonds during protein synthesis. Antibiotics which act by inhibiting translation, such as chloramphenicol, often bind to this region of the 23S rRNA. The RefSeq 23S ribosomal RNA project represents a collection of curated complete and near full length Reference Sequence records for Archaea and Bacteria. This set is used in Prokaryotic Genome Annotation Pipeline
23S Refseq Nucleotide sequence records

ITS (internal transcribed spacer) project

The Fungi RefSeq ITS project contains a curated and re-annotated set of sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived mostly from type material. Typically most useful for molecular systematics at the species level. The project is the result of an international collaboration of taxonomy experts in the mycological research community with NCBI. See more details on curation process.
ITS RefSeq Nucleotide sequence records

18S ribosomal RNA project

The 18S ribosomal RNA RefSeq project is the result of an international collaboration between a number of ribosomal RNA databases (including the AFTOL project) with NCBI to provide a curated set of complete and near full length reference sequence records. The nuclear small subunit ribosomal DNA (SSU rDNA) is widely used for phylogenetic and evolutionary analyses.
18S ribosomal RNA Nucleotide sequence records

28S ribosomal RNA project

The 28S ribosomal RNA RefSeq project is the result of an international collaboration between a number of ribosomal RNA databases (including the AFTOL project) with NCBI to provide a curated set of complete and near full length reference sequence records. The nuclear large subunit ribosomal DNA (LSU rDNA) is widely used for phylogenetic and evolutionary analyses.
28S ribosomal RNA Nucleotide sequence records

Last updated: 2017-11-28T15:45:04Z