The UC’s will only use 10-11th grades in their GPA calculation but will look at all grades 9-11th for the a-g course requirements.
You can use the UC GPA calculator to calculate your Unweighted UC GPA, Capped weighted UC GPA and Fully weighted UC GPA at the end of Junior year to see how you stand. An upward trend in your grades will definitely help.
https://rogerhub.com/gpa-calculator-uc/
If your counselor states that all grades including quarter grades are listed on your transcript, then you would need to submit these grades to the colleges in which you apply. Most colleges can be more lenient on lower than average grades received Freshman year but for selective colleges, they could have an impact.