diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/BoxGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/BoxGlyph.ts
index 5ddd8baf..df190ad8 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/BoxGlyph.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/BoxGlyph.ts
@@ -175,7 +175,7 @@ function drawTooltip(
   if (!position) {
     return
   }
-  const { layoutIndex, layoutRow } = position
+  const { featureRow, layoutIndex, layoutRow } = position
   const { bpPerPx, displayedRegions, offsetPx } = lgv
   const displayedRegion = displayedRegions[layoutIndex]
   const { refName, reversed } = displayedRegion
@@ -191,7 +191,7 @@ function drawTooltip(
       coord: reversed ? max : min,
       regionNumber: layoutIndex,
     })?.offsetPx ?? 0) - offsetPx
-  const top = layoutRow * apolloRowHeight
+  const top = (layoutRow + featureRow) * apolloRowHeight
   const widthPx = length / bpPerPx
 
   const featureType = `Type: ${feature.type}`
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts
index 32ed3777..25b34b32 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts
@@ -291,9 +291,32 @@ function getFeatureFromLayout(
 ): AnnotationFeature | undefined {
   const featureInThisRow: AnnotationFeature[] = featuresForRow(feature)[row]
   for (const f of featureInThisRow) {
+    let featureObj
     if (bp >= f.min && bp <= f.max && f.parent) {
-      return f
+      featureObj = f
     }
+    if (!featureObj) {
+      continue
+    }
+    if (
+      featureObj.type === 'CDS' &&
+      featureObj.parent &&
+      featureObj.parent.type === 'mRNA'
+    ) {
+      const { cdsLocations } = featureObj.parent
+      for (const cdsLoc of cdsLocations) {
+        for (const loc of cdsLoc) {
+          if (bp >= loc.min && bp <= loc.max) {
+            return featureObj
+          }
+        }
+      }
+
+      // If mouse position is in the intron region, return the mRNA
+      return featureObj.parent
+    }
+    // If mouse position is in a feature that is not a CDS, return the feature
+    return featureObj
   }
   return feature
 }