In NCBI, NM_ is a specific accession prefix used within the RefSeq database to uniquely identify validated messenger RNA (mRNA) sequences.
Understanding NM_ Accession Numbers in NCBI
The National Center for Biotechnology Information (NCBI) serves as a critical resource for biomedical and genomic information globally. Within NCBI, the Reference Sequence (RefSeq) database stands out as a curated collection that provides a comprehensive, non-redundant set of sequences for genomic DNA, RNA transcripts, and proteins. Each of these sequences is assigned a unique identifier known as an accession number.
What Does NM_ Specifically Signify?
An NM_ accession number specifically designates a curated mRNA transcript sequence within the RefSeq database. Messenger RNA (mRNA) sequences are crucial as they carry the genetic information from DNA to the ribosomes, where it is translated into proteins. An NM_ accession provides a stable and consistent identifier for a particular mRNA sequence, which is essential for researchers tracking gene expression and function.
For instance, an accession like NM_000014.5 identifies a particular mRNA sequence within the RefSeq collection. The segment after the underscore (000014) represents the unique identifier for that specific transcript, while the number following the dot (.5) indicates the version of the sequence, with higher numbers denoting more recent updates or refinements.
The Importance of RefSeq Accessions
RefSeq accession numbers are fundamental in biological research for several key reasons:
- Stability and Persistence: Once an accession number is assigned, it remains stable. Even if the underlying sequence information is updated, only the version number changes, ensuring consistent referencing.
- Non-redundancy: The RefSeq project aims to provide a single, high-quality record for each naturally occurring molecule, thereby eliminating the redundancy often found in raw sequence submission databases.
- High-Quality Annotation: NM_ sequences are typically accompanied by rich, detailed annotations, including the gene name, organism, protein product, and precise genomic location, making them incredibly valuable for analysis.
Distinguishing RefSeq Accession Prefixes
While NM_ specifically identifies experimentally validated mRNA, other prefixes are used within the RefSeq database to categorize different types of molecules. Understanding these distinctions is vital for accurate data retrieval and interpretation in genomics.
Here's a table summarizing common RefSeq accession prefixes and their corresponding molecule types:
| Accession Prefix | Molecule Type | Description |
|---|---|---|
| NM_ | Messenger RNA (mRNA) | Represents fully curated and experimentally validated mRNA sequences, which are the primary templates for protein synthesis. |
| NR_ | Non-coding RNA (ncRNA) | Identifies RNA sequences that do not code for proteins but play various regulatory and structural roles, such as ribosomal RNA (rRNA) and transfer RNA (tRNA). |
| NZ_ | Assembled Genome (DNA) | Refers to whole genome shotgun (WGS) assemblies, often encompassing complete chromosomes or large contigs of genomic DNA. |
| XM_ | Predicted mRNA (mRNA) | Denotes computationally predicted mRNA sequences derived from genomic data. These sequences are often awaiting experimental validation and further curation. |
Note: Both NM and XM designate mRNA sequences. However, NM entries represent highly validated and curated transcripts, making them the preferred choice for robust research, whereas XM entries are computational predictions that may undergo further refinement or validation.
Practical Applications and How to Search
Researchers frequently leverage NM_ accession numbers in various molecular biology and genetics studies:
- Gene Expression Studies: To accurately identify and quantify specific mRNA transcripts, providing insights into gene activity.
- Genetic Variant Interpretation: For mapping genetic variations to specific transcript sequences to understand their potential impact on protein function and phenotype.
- Experimental Design: To retrieve the precise and most current mRNA sequence for applications such as gene cloning, primer design, and functional analysis.
To access information about a specific gene's mRNA, you can visit the NCBI Nucleotide database. Simply enter the NM_ accession number (e.g., NM_000014) into the search bar. This will direct you to a comprehensive record detailing the sequence, associated annotations, and links to related biological databases.
Why NM_ Sequences Are Highly Valued
For research requiring high confidence in the identity and structure of transcript sequences, NM entries are generally preferred over XM sequences. The rigorous curation process ensures that NM_ sequences accurately reflect known biological transcripts, thereby minimizing the risk of working with incorrectly predicted or incomplete data. This reliability makes them a foundational element in modern molecular biology and genetics research.
