Question about UCSC Genome Browser Negative Strand Annotation

[Morales, Diego Alejandro]

Good Evening,

My name is Diego Morales.  I am using UCSC Genome Browser and I have a question about the notation of genes on the negative strand.  

I have a gene ADH4:

Position: hg38 chr4:99,123,667-99,144,297 Size: 20,631 Total Exon Count: 9 Strand: -

I would like to know if the coordinates given on UCSC genome browser are read from 5' to 3' or 3' to 5' ?

Also, if they are read from 3' to 5', would that make 99,123,667 the TSS and 99,144,297 the 3' End?

Thank you,

Diego

[Robert Kuhn]

Hello, Diego,

The genomic coordinates are numbered from the p-arm telomere to the q-arm telomere

and have nothing to do with the direction of transcription of any annotation.

A gene or transcript annotated on the negative strand will be transcribed 5' to 3' on

the negative strand, so the larger coordinate represents the TSS and and smaller

coordinate the 3' end.  The sequence of the transcript will be the reverse complement

of the sequence on the positive strand.

best wishes and thanks for using the Genome Browser.

    --b0b kuhn

    ucsc genome bioinformatics group

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