transcriptional start site for negative strand gene

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Tara Henagan

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Jun 27, 2013, 5:28:47 PM6/27/13

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UCSC Genome Bioinformatics,

When looking at information from a UCSC table database on genes that are coded on the negative DNA strand, such as PPARG1A, is the column that lists the coordinate for the transcription start site (txStart) really the transcription start site or is it really the transcription end site? (In the latter case then the column named txEnd would actually be the transcription start site coordinate for the gene on a negative strand?) For example, in human PPARG1A, the txStart on chr4 is 23793643 and the txEnd is 23891700. Are these true for the negative strand, or is 23793643 actually the txEnd and 23891700 actually the txStart?

Thank you,

Tara

Pauline Fujita

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Jul 11, 2013, 6:50:50 PM7/11/13

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Hello Tara,

You are correct the txStart and cdsStart coordinates in the UCSC
Genome Browser tables always refer to the lowest-numbered coordinates
(and cdsEnd and txEnd to the highest-numbered coordinates). Thus this
explains what you are seeing for PPARGC1A.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu