# SSU Peaks Positions & ORF

**URL:** <https://www.alphagenomecommunity.com/t/ssu-peaks-positions-orf/649>\
**Category:** Help & Support\
**Created:** [September 10, 2025, 3:36pm UTC](https://www.alphagenomecommunity.com/t/ssu-peaks-positions-orf/649 "2025-09-10T15:36:17Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![Selenium](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/selenium/32/546_2.png) [@Selenium](https://www.alphagenomecommunity.com/u/Selenium)\
**Post date:** [September 10, 2025, 3:36pm UTC](https://www.alphagenomecommunity.com/t/ssu-peaks-positions-orf/649/1 "2025-09-10T15:36:17Z")

</div>

Hello,

A quick question regarding positions for peaks. If I run a given variant, expected to cause an intronic cryptic splice site change (both donor and acceptor gain, for instance), and have the following peak data print out for the most relevant peaks in splice-site usage:

ALT SSU(+) peak metadata (±250 bp around variant):  
peak\_bp height left\_height right\_height global\_bin window\_bin bin\_size\_bp distance\_to\_center\_bp abs\_distance\_bp  
144410630 0.2700 0.0000 0.0002 524288 250 1 1 1  
144410738 0.1858 0.0010 0.0011 524397 359 1 109 109

Do the peaks specify the positions of the new canonical donor and acceptor, or the first/last nt of the pseudoexon itself? I.e. what are the positions for the hypothesised ORF?

Thank you

---

<div class="post-metadata">

**Author:** ![Jun\_Cheng](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/jun_cheng/32/23_2.png) [@Jun\_Cheng](https://www.alphagenomecommunity.com/u/Jun_Cheng)\
**Post date:** [September 10, 2025, 5:26pm UTC](https://www.alphagenomecommunity.com/t/ssu-peaks-positions-orf/649/2 "2025-09-10T17:26:13Z")

</div>

Not sure I read your metadata correctly. AG SSU predict usage of splice sites, we define splice sites as first and last base of exons. Therefore the new peaks in ALT SSU are likely corresponding to the first/last base of the cryptic exon. You can also check the splice junction and RNAseq predictions.

---

<div class="post-metadata">

**Author:** ![Selenium](https://yyz2.discourse-cdn.com/watermelon/user_avatar/www.alphagenomecommunity.com/selenium/32/546_2.png) [@Selenium](https://www.alphagenomecommunity.com/u/Selenium)\
**Post date:** [September 10, 2025, 7:00pm UTC](https://www.alphagenomecommunity.com/t/ssu-peaks-positions-orf/649/3 "2025-09-10T19:00:04Z")

</div>

Thank you that’s really helpful.

So a given exon would be the SSU peaks inclusive (0-based). Ie for the above example with peaks at 144410630 And 144410738, the cryptic exon length is 109 bases?