what does 'none','unk','incmpl','cmpl' in UCSC refgene tables mean

Question

[mt1022]

when I download human refseq gene table from UCSC table download, there are two columns (cdsstartstat, cdsendstat) with values from {'none','unk','incmpl','cmpl'}. What do these values mean?

Answer 1

[Maximilian Haeussler]

It's explained in hgc.c https://github.com/ucscGenomeBrowser/kent/blob/ae4aa88945e566f60c950226ab06cbd2ee749789/src/hg/hgc/hgc.c#L2443

void printCdsStatus(enum cdsStatus cdsStatus)
/* print a description of a genePred cds status */
{
switch (cdsStatus)
    {
    case cdsNone:        /* "none" - No CDS (non-coding)  */
        printf("none (non-coding)<br>\n");
        break;
    case cdsUnknown:     /* "unk" - CDS is unknown (coding, but not known)  */
        printf("unknown (coding, but not known)<br>\n");
        break;
    case cdsIncomplete:  /* "incmpl" - CDS is not complete at this end  */
        printf("<em>not</em> complete<br>\n");
        break;
    case cdsComplete:    /* "cmpl" - CDS is complete at this end  */
        printf("complete<br>\n");
        break;
    }
}

[mt1022]

thanks for your timely answer.

Answer 2

[PoGibas]

http://lmgtfy.com/?q=cdsStartStat&l=1

Answer from UCSC support forum (2010):

• none - no CDS specified
• unk - unknown if CDS start/end is complete
• incmpl - CDS start/end is incomplete
• cmpl - CDS start/end is complete

[mt1022]

thanks for your timely answer.