Symbol report help

Table of Contents

• Core data fields
  • Species
  • Approved symbol
  • Approved name
  • Locus type
  • PGNC ID
  • Symbol status
  • Alias symbols
  • Alias names
  • Previous symbols
  • Previous names
  • Chromosomal location
  • Primary ID
• External resources
  • NCBI Gene
  • UniProt
  • Phytozome
  • Ensembl Gene
  • PubMed
  • CBI sequence viewer

Core data fields

Species

The Genbank common name for the species this gene belongs to as assigned by the NCBI.

Approved symbol

The official gene symbol approved by the VGNC, which is typically a short form of the gene name.

Approved name

The full gene name approved by the PGNC; corresponds to the approved symbol above.

Locus type

Specifies the genetic class of each gene entry. All PGNC locus types are listed below:

• gene with protein product - protein-coding genes (the protein may be predicted and of unknown function) (SO:0001217)

Currently we only have the locus type above but more will appear soon.

PGNC ID

A unique ID provided by the PGNC for each gene with an approved symbol. IDs are of the format PGNC:n, where n is a unique number. PGNC IDs remain stable even if a name or symbol changes.

Symbol status

Status of the symbol report, which can be either "Approved" or "Entry Withdrawn". Currently we have no "Entry Withdrawn" records.

Alias symbols

Alternative symbols that have been used to refer to the gene. Aliases may be from literature, from other databases or may be added to represent membership of a gene group.

Alias names

Alternative names for the gene. Aliases may be from literature, from other databases or may be added to represent membership of a gene group.

Previous symbols

This field displays any symbols that were previously PGNC-approved nomenclature.

Previous names

This field displays any names that were previously PGNC-approved nomenclature.

Chromosomal location

The chromosome in which the gene can be found.

Primary ID

The ID of the gene from the primary resource:

Populus trichocarpa

For this species the primary ID is the Phytozome gene ID (i.e. Potri ID). The Phytozome gene ID is a unique identifier for each gene in the Phytozome database.

External resources

NCBI Gene

The NCBI Gene resource at the NCBI provides curated sequence and descriptive information about genetic loci including official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites. We show the NCBI Gene ID and link to the NCBI Gene page for the gene.

UniProt

The UniProt Protein Knowledgebase is a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and high level of integration with other databases. We do not map to TrEMBL entries within UniProt, only to Swiss-Prot entries as these are manually annotated and reviewed. We show the UniProt ID and link to the UniProt page for the gene.

Phytozome

Phytozome is a plant comparative genomics portal, integrating plant genome sequences and annotation data. We show the Phytozome ID and link to the Phytozome page for the gene.

Ensembl Gene

The Ensembl Gene View displays data associated at the gene level such as orthologs, paralogs, regulatory regions and splice variants. We show the Ensembl Gene ID and link to the Ensembl Gene page for the gene.

PubMed

PubMed comprises more than 35 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites. We provide the PubMed ID which links to relevant publications that aided the curator(s) to assign the gene symbol and name.

CBI sequence viewer

Links to a jBrowser hosted by the CBI which aligns the gene to the assemblies.