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  1. 1. refGene
  2. 2. refGene_exon

The RefGene database was created from the UCSC database. RefGene specifies known human protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). If you would like to annotate your variants to genes, you can use the simpler refGene database. If you would like to determine the exons that your variants are in, use the refGene_exon database. See the available annotation fields for each database below.

Description of the database from NCBI:

RefSeqGene, a subset of NCBI's Reference Sequence (RefSeq) project, defines genomic sequences to be used as reference standards for well-characterized genes. These sequences, labeled with the keyword RefSeqGene in NCBI's nucleotide database, serve as a stable foundation for reporting mutations, for establishing conventions for numbering exons and introns, and for defining the coordinates of other variations. RefSeq mRNA and protein sequences have long been used for this purpose, but have the obvious weakness of not providing explicit coordinates for flanking or intronic sequence. RefSeq chromosome sequences do provide explicit coordinates no matter the relationship to any gene annotation, but have awkwardly large coordinate values that will change when the sequence is updated because of a re-assembly. Sequences of the RefSeqGene project counter both of these drawbacks by providing more stable gene-specific genomic sequence for each gene, as well as including upstream and downstream flanking regions. If modifications must be made to any RefSeqGene sequence, it will be versioned and tools will be provided to facilitate conversion of coordinates. The RefSeqGene sequences are aligned to reference chromosomes, and current and previous chromosome coordinates are available because of that re-alignment. The Clinical Remap tool make that conversion easy.

Although the majority of UCSC Known Genes (KG) are identical to RefSeq genes, there are some significant differences according to this post:

  • Not every RefSeq is a KG. Some RefSeqs were filtered out because they did not pass our gene-check processing step (e.g. RefSeqs with no start or stop codons, or bad reading frames are filtered out).
  • If there is a UniProt protein which maps well to a GenBank mRNA, and it passes the gene-check filter and there is no equal or better corresponding RefSeq, the mRNA/UniProt pair will be added to the KG data set.
  • UCSC KG is updated once in a few months. Our RefSeq track is updated nightly. So the refGene table may contains some latest RefSeq updates that came after the last KG build.

1.  refGene

% vtools show annotation refGene -v2
Annotation database refGene (version hg19_20130904)
Description:            Known human protein-coding and non-protein-coding
  genes taken from the NCBI RNA reference sequences collection (RefSeq).
Database type:          range
Number of records:      45,749
Distinct ranges:        32,293
Reference genome hg19:  chr, txStart, txEnd

Field:                  name
Type:                   string
Comment:                Gene name
Missing entries:        0
Unique Entries:         42,286

Field:                  chr
Type:                   string
Missing entries:        0
Unique Entries:         49

Field:                  strand
Type:                   string
Comment:                which DNA strand contains the observed alleles
Missing entries:        0
Unique Entries:         2

Field:                  txStart
Type:                   integer
Comment:                Transcription start position
Missing entries:        0
Unique Entries:         28,789
Range:                  6011 - 249200442

Field:                  txEnd
Type:                   integer
Comment:                Transcription end position
Missing entries:        0
Unique Entries:         28,737
Range:                  14409 - 249213345

Field:                  cdsStart
Type:                   integer
Comment:                Coding region start
Missing entries:        0
Unique Entries:         30,038
Range:                  6011 - 249211537

Field:                  cdsEnd
Type:                   integer
Comment:                Coding region end
Missing entries:        0
Unique Entries:         30,147
Range:                  14409 - 249212562

Field:                  exonCount
Type:                   integer
Comment:                Number of exons
Missing entries:        0
Unique Entries:         113
Range:                  1 - 363

Field:                  score
Type:                   integer
Comment:                Score
Missing entries:        0
Unique Entries:         1
Range:                  0 - 0

Field:                  name2
Type:                   string
Comment:                Alternative name
Missing entries:        0
Unique Entries:         23,953

Field:                  cdsStartStat
Type:                   string
Comment:                cds start stat, can be 'non', 'unk', 'incompl', and
                        'cmp1'
Missing entries:        0
Unique Entries:         3

Field:                  cdsEndStat
Type:                   string
Comment:                cds end stat, can be 'non', 'unk', 'incompl', and
                        'cmp1'
Missing entries:        0
Unique Entries:         3

2.  refGene_exon

% vtools show annotation refGene_exon -v2
Annotation database refGene_exon (version hg19_20130904)
Description:            RefGene specifies known human protein-coding and non-
  protein-coding genes taken from the NCBI RNA reference sequences collection
  (RefSeq). This database contains all exome regions of the refSeq genes.
Database type:          range
Number of records:      443,218
Distinct ranges:        240,821
Reference genome hg19:  chr, exon_start, exon_end

Field:                  name
Type:                   string
Comment:                Gene name
Missing entries:        0
Unique Entries:         42,286

Field:                  chr
Type:                   string
Missing entries:        0
Unique Entries:         49

Field:                  strand
Type:                   string
Comment:                which DNA strand contains the observed alleles
Missing entries:        0
Unique Entries:         2

Field:                  txStart
Type:                   integer
Comment:                Transcription start position
Missing entries:        0
Unique Entries:         28,789
Range:                  6011 - 249200442

Field:                  txEnd
Type:                   integer
Comment:                Transcription end position
Missing entries:        0
Unique Entries:         28,737
Range:                  14409 - 249213345

Field:                  cdsStart
Type:                   integer
Comment:                Coding region start
Missing entries:        0
Unique Entries:         30,038
Range:                  6011 - 249211537

Field:                  cdsEnd
Type:                   integer
Comment:                Coding region end
Missing entries:        0
Unique Entries:         30,147
Range:                  14409 - 249212562

Field:                  exonCount
Type:                   integer
Comment:                Number of exons
Missing entries:        0
Unique Entries:         113
Range:                  1 - 363

Field:                  exon_start
Type:                   integer
Comment:                exon start position
Missing entries:        0
Unique Entries:         235,886
Range:                  6011 - 249211478

Field:                  exon_end
Type:                   integer
Comment:                exon end position
Missing entries:        0
Unique Entries:         236,105
Range:                  6168 - 249213345

Field:                  score
Type:                   integer
Comment:                Score
Missing entries:        0
Unique Entries:         1
Range:                  0 - 0

Field:                  name2
Type:                   string
Comment:                Alternative name
Missing entries:        0
Unique Entries:         23,953

Field:                  cdsStartStat
Type:                   string
Comment:                cds start stat, can be 'non', 'unk', 'incompl', and
                        'cmp1'
Missing entries:        0
Unique Entries:         3

Field:                  cdsEndStat
Type:                   string
Comment:                cds end stat, can be 'non', 'unk', 'incompl', and
                        'cmp1'
Missing entries:        0
Unique Entries:         3