Hover over the mRNA or annotated feature you want to color. Write down the "id" for that feature. Right-click on the track name to the left. Select "Color By...". In drop-down choose "Property", then select "id" in the next drop-down. Enter the "id" you wrote down in the tiny box and select your match and not-match colors. Click OK and only the feature with that id should be colored (assuming all IDs in your genome are unique).