EntrezGene

% vtools show annotation EntrezGene.DB


Annotation database EntrezGene (version 20131028)
Description:            Entrez Gene
  (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for
  gene-specific information. It does not include all known or predicted genes;
  instead Entrez Gene focuses on the genomes that have been completely
  sequenced, that have an active research community to contribute gene-
  specific information, or that are scheduled for intense sequence analysis.
  This database contains Entrez gene info database for Homo Sapiens,
  downloaded from ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sap
  iens.gene_info.gz.
Database type:          range
Reference genome hg19:  chr, start, end
  chr                   chromosome name, the same as field chromosome
  start                 Start location of the gene, retrieved from
                        EntrezGene2RefSeq.
  end                   End location of the gene, retrieved from
                        EntrezGene2RefSeq.
  tax_id                the unique identifier provided by NCBI Taxonomy for
                        the species or strain/isolate
  GeneID                the unique identifier for a gene (ASN1: geneid)
  Symbol                the default symbol for the gene (ASN1: gene->locus)
  LocusTag              the LocusTag value (ASN1:  gene->locus-tag)
  Synonyms              bar-delimited set of unofficial symbols for the gene
  dbXrefs               bar-delimited set of identifiers in other databases
                        for this gene.  The unit of the set is database:value.
  chromosome            the chromosome on which this gene is placed. for
                        mitochondrial genomes, the value 'MT' is used.
  map_location          the map location for this gene
  description           a descriptive name for this gene
  type_of_gene          the type assigned to the gene according to the list of
                        options. provided in http://www.ncbi.nlm.nih.gov/IEB/T
                        oolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entre
                        zgene.asn
  Symbol_from_nomenclature_authority If exists (not NULL), indicates that this
                        symbol is from a nomenclature authority
  Full_name_from_nomenclature_authority If exists (not NULL), indicates that
                        this full name is from a nomenclature authority
  Nomenclature_status   If exists (not NULL), indicates the status of the name
                        from the nomenclature authority (O for official, I for
                        interim)
  Other_designations    pipe-delimited set of some alternate descriptions that
                        have been assigned to a GeneID '-' indicates none is
                        being reported.
  Modification_date     the last date a gene record was updated, in YYYYMMDD
                        format

% vtools show annotation EntrezGene2RefSeq


Annotation database EntrezGene2RefSeq (version 20131028)
Description:            This database is a comprehensive report of the
  accessions that are related to a Entrez GeneID.  It includes sequences from
  the international sequence collaboration, Swiss-Prot, and RefSeq. This
  database only keeps record for human genome with reference genome Reference
  GRCh37.p13 Primary Assembly, and it also only keeps sequence on reference
  assembly (ref seq with assession type NC_).
Database type:          field
Reference genome *:     GeneID
  tax_id                the unique identifier provided by NCBI Taxonomy for
                        the species or strain/isolate
  GeneID                the unique identifier for a gene
  status                status of the RefSeq values are: INFERRED, MODEL, NA,
                        PREDICTED, PROVISIONAL, REVIEWED, SUPPRESSED,
                        VALIDATED
  RNA_nucleotide_accession_version may be null (-) for some genomes
  RNA_nucleotide_gi     the gi for an RNA nucleotide accession (e.g.
                        NP_047184.1, NC_004871.1)
  protein_accession_version will be null (-) for RNA-coding genes
  protein_gi            the gi for a protein accession, '-' if not applicable
  genomic_nucleotide_accession_version may be null (-) if a RefSeq was
                        provided after the genomic accession was submitted
  genomic_nucleotide_gi the gi for a genomic nucleotide accession, '-' if not
                        applicable
  start_position_on_the_genomic_accession position of the gene feature on the
                        genomic accession, adjusted to be 1-based
  end_position_on_the_genomic_accession position of the gene feature on the
                        genomic accession, adjusted to be 1-based
  orientation           orientation of the gene feature on the genomic
                        accession, '?' if not applicable
  assembly              the name of the assembly '-' if not applicable
  mature_peptide_accession_version will be null (-) if absent
  mature_peptide_gi     the gi for a mature peptide accession, '-' if not
                        applicable
  Symbol                the default symbol for the gene