Hi Alden,
These fields provide additional information about the status of the
start and end of a gene's coding region. The possible statuses are:
- none - no CDS specified from the sequence's data source.
- unk - unknown - not known if CDS start/end is complete.
- incmpl - the CDS start/end is incomplete
- cmpl - the CDS start/end is complete.
cdsStartStat refers to the cdsStart end of the gene, which is the start
codon for a positive strand gene and the stop codon for a negative
strand gene. cdsEndStat refers to the cdsEnd end of the gene, which is
the stop codon for a positive strand gene and the start codon for a
negative strand gene.
Please don't hesitate to contact the mail list again if you have any
further questions.
Katrina Learned
UCSC Genome Bioinformatics Group
Alden Huang wrote, On 02/18/11 16:32:
> Hi,
>
> I just had a quick question...
>
> In the description of the Gene Predictions table format used by UCSC,
> under specifically Gene Predictions (Extended), it lists two fields:
>
> string cdsStartStat; "enum('none','unk','incmpl','cmpl')"
> string cdsEndStat; "enum('none','unk','incmpl','cmpl')"
>
> I would simply like to know the significance of these particular fields.
>
> thanks,
>
> alden
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