table genePredExt
"A gene prediction with some additional info."
(
string name; "Name of gene (usually transcript_id from GTF)"
string chrom; "Chromosome name"
char[1] strand; "+ or - for strand"
uint txStart; "Transcription start position"
uint txEnd; "Transcription end position"
uint cdsStart; "Coding region start"
uint cdsEnd; "Coding region end"
uint exonCount; "Number of exons"
uint[exonCount] exonStarts; "Exon start positions"
uint[exonCount] exonEnds; "Exon end positions"
int score; "Score"
string name2; "Alternate name (e.g. gene_id from GTF)"
- string cdsStartStat; "enum('none','unk','incmpl','cmpl')"
- string cdsEndStat; "enum('none','unk','incmpl','cmpl')"
+ string cdsStartStat; "Status of CDS start annotation (none, unknown, incomplete, or complete)"
+ string cdsEndStat; "Status of CDS end annotation (none, unknown, incomplete, or complete)"
lstring exonFrames; "Exon frame offsets {0,1,2}"
)
Gene Predictions and RefSeq Genes with Gene Names
A version of genePred that associates the gene name with the gene prediction information. In alternative-splicing situations, each transcript has a row in this table.
table refFlat
"A gene prediction with additional geneName field."
(
string geneName; "Name of gene as it appears in Genome Browser."
string name; "Name of gene"
string chrom; "Chromosome name"