1- chr7 | 94656324 | 94656580 | NM_015068.3_exon_0_0_chr7_94656325_f |
2- chr7 | 94663333 | 94664513 | NM_015068.3_exon_1_0_chr7_94663334_f |
3- chr7 | 94664513 | 94669695 | NM_015068.3_exon_2_0_chr7_94664514_f |
Hello Keyvan,
Thank you for using the UCSC Genome Browser and your inquiry.
The "exons" in the output are actually aligned blocks of sequence, i.e. regions of the genome that align without gaps to the transcript sequence. Usually, alignment gaps between these regions are caused by introns in the reference genome, so calling the aligned blocks "exons" is usually accurate. However, in this case, the second exon is interrupted by an anomalous alignment gap that happens to have length 0 on the reference genome. We internally store our coordinates as zero-based half-open coordinates, and you can find more information about our coordinate system from the following blog post:
http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/
You can see the zero-length false "intron" in question from the following MySQL query in the ncbiRefSeqCurated table for NM_015068.3:
Note that the second exonEnd is equal to the third exonStart (94664513) -- there is an alignment gap of length 0 on the reference genome. Usually, this means that the reference genome is missing a base from the transcript, requiring an alignment gap. However, this case is even rarer, and if you click into the details page for NM_015068.3, there is a note:
protein translation is dependent on -1 ribosomal frameshift; isoform 1 is encoded by transcript variant 1.
So it seems like the reference genome is not missing a base after all, but rather a ribosomal hiccup is required for correct transcription.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
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