diff --git a/packages/apollo-cli/package.json b/packages/apollo-cli/package.json
index 54d9e1078..e1af85fb9 100644
--- a/packages/apollo-cli/package.json
+++ b/packages/apollo-cli/package.json
@@ -85,7 +85,7 @@
     "@istanbuljs/esm-loader-hook": "^0.2.0",
     "@istanbuljs/nyc-config-typescript": "^1.0.2",
     "@oclif/test": "^3.1.3",
-    "@types/chai": "^4",
+    "@types/chai": "^4.3.19",
     "@types/cli-progress": "^3",
     "@types/inquirer": "^9.0.7",
     "@types/mocha": "^10",
diff --git a/packages/apollo-shared/package.json b/packages/apollo-shared/package.json
index 22934e8f8..1b91a530f 100644
--- a/packages/apollo-shared/package.json
+++ b/packages/apollo-shared/package.json
@@ -26,8 +26,11 @@
   "devDependencies": {
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
+    "@types/chai": "^4.3.19",
     "@types/node": "^18.14.2",
     "@types/rimraf": "^3",
+    "chai": "^5.1.1",
+    "chai-exclude": "^3.0.0",
     "glob": "^11.0.0",
     "mobx": "^6.6.1",
     "mobx-state-tree": "^5.1.7",
diff --git a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts
index 6a412af5d..b6abc8f0a 100644
--- a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts
+++ b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts
@@ -1,11 +1,16 @@
 /* eslint-disable @typescript-eslint/no-floating-promises */
-import { strict as assert } from 'node:assert'
 import { describe, it } from 'node:test'
-import gff from '@gmod/gff'
+import { readFileSync } from 'node:fs'
+
+import gff, { GFF3Feature } from '@gmod/gff'
+import { assert, use } from 'chai'
+import chaiExclude from 'chai-exclude'
 
 import { gff3ToAnnotationFeature } from './gff3ToAnnotationFeature'
 import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
+use(chaiExclude)
+
 const testCases: [string, string, AnnotationFeatureSnapshot][] = [
   [
     'a feature with no children',
@@ -23,18 +28,173 @@ const testCases: [string, string, AnnotationFeatureSnapshot][] = [
       },
     },
   ],
+  [
+    'a feature with two children',
+    `ctgA	est	EST_match	1050	3202	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 1 654
+ctgA	est	match_part	1050	1500	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 1 451
+ctgA	est	match_part	3000	3202	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 452 654
+`,
+    {
+      _id: '66cf9fbb4e947fa2c27d3d6a',
+      refSeq: 'ctgA',
+      type: 'EST_match',
+      min: 1049,
+      max: 3202,
+      strand: 1,
+      children: {
+        '66cf9fbb4e947fa2c27d3d68': {
+          _id: '66cf9fbb4e947fa2c27d3d68',
+          refSeq: 'ctgA',
+          type: 'match_part',
+          min: 1049,
+          max: 1500,
+          strand: 1,
+          attributes: {
+            gff_source: ['est'],
+            gff_name: ['agt830.5'],
+            gff_target: ['agt830.5 1 451'],
+          },
+        },
+        '66cf9fbb4e947fa2c27d3d69': {
+          _id: '66cf9fbb4e947fa2c27d3d69',
+          refSeq: 'ctgA',
+          type: 'match_part',
+          min: 2999,
+          max: 3202,
+          strand: 1,
+          attributes: {
+            gff_source: ['est'],
+            gff_name: ['agt830.5'],
+            gff_target: ['agt830.5 452 654'],
+          },
+        },
+      },
+      attributes: {
+        gff_source: ['est'],
+        gff_id: ['Match1'],
+        gff_name: ['agt830.5'],
+        gff_target: ['agt830.5 1 654'],
+      },
+    },
+  ],
 ]
 
+interface AnnotationFeatureSnapshotWithChildrenArray
+  extends Omit<AnnotationFeatureSnapshot, 'children'> {
+  children?: AnnotationFeatureSnapshotWithChildrenArray[]
+}
+
+function childrenToArray(
+  feature: AnnotationFeatureSnapshot,
+): AnnotationFeatureSnapshotWithChildrenArray {
+  const { children } = feature
+  if (!children) {
+    return feature as AnnotationFeatureSnapshotWithChildrenArray
+  }
+  const childrenArray = Object.values(children).map((child) =>
+    childrenToArray(child),
+  )
+  return { ...feature, children: childrenArray }
+}
+
 function compareFeatures(
   feature1: AnnotationFeatureSnapshot,
   feature2: AnnotationFeatureSnapshot,
 ) {
-  assert.deepEqual(
-    { ...feature1, _id: undefined },
-    { ...feature2, _id: undefined },
+  assert.deepEqualExcludingEvery(
+    childrenToArray(feature1),
+    childrenToArray(feature2),
+    '_id',
   )
 }
 
+function readFeatureFile(fn: string): GFF3Feature[] {
+  const lines = readFileSync(fn).toString().split('\n')
+  const feature: string[] = []
+  for (const line of lines) {
+    if (!line.startsWith('#')) {
+      feature.push(line)
+    }
+  }
+  const inGff = gff.parseStringSync(feature.join('\n')) as GFF3Feature[]
+  return inGff
+}
+
+function readAnnotationFeatureSnapshot(fn: string): AnnotationFeatureSnapshot {
+  const lines = readFileSync(fn).toString()
+  return JSON.parse(lines) as AnnotationFeatureSnapshot
+}
+
+const [ex1, ex2, ex3, ex4] = readFeatureFile(
+  'test_data/gene_representations.gff3',
+)
+
+describe('gff3ToAnnotationFeature examples', () => {
+  it('Convert one CDS', () => {
+    const actual = gff3ToAnnotationFeature(
+      readFeatureFile('test_data/one_cds.gff3')[0],
+    )
+    const expected = readAnnotationFeatureSnapshot('test_data/one_cds.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert two CDSs', () => {
+    const actual = gff3ToAnnotationFeature(
+      readFeatureFile('test_data/two_cds.gff3')[0],
+    )
+    const expected = readAnnotationFeatureSnapshot('test_data/two_cds.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert example 1', () => {
+    const actual = gff3ToAnnotationFeature(ex1)
+    const txt = JSON.stringify(actual, null, 2)
+
+    assert.equal(txt.match(/"type": "CDS"/g)?.length, 4)
+    assert.equal(txt.match(/"type": "TF_binding_site"/g)?.length, 1)
+
+    const expected = readAnnotationFeatureSnapshot('test_data/example01.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert example 2', () => {
+    const actual = gff3ToAnnotationFeature(ex2)
+    const txt = JSON.stringify(actual, null, 2)
+    assert.equal(txt.match(/"type": "CDS"/g)?.length, 4)
+    const expected = readAnnotationFeatureSnapshot('test_data/example02.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert example 3', () => {
+    // NB: In example 3 (and in the other examples) mRNA10003 produces two proteins.
+    // In the other examples the two proteins are identified by sharing the same cds id.
+    // In example 3 instead each cds has a unique id so the two proteins are identified by the order they
+    // appear in the gff.
+    const actual = gff3ToAnnotationFeature(ex3)
+    const txt = JSON.stringify(actual, null, 2)
+    assert.equal(txt.match(/"type": "CDS"/g)?.length, 4)
+
+    // const expected = readAnnotationFeatureSnapshot('test_data/example03.json')
+    // compareFeatures(actual, expected)
+  })
+  it('Convert example 4', () => {
+    const ft = JSON.stringify(ex4, null, 2)
+    assert.equal(ft.match(/"type": "five_prime_UTR"/g)?.length, 6)
+    assert.equal(ft.match(/"type": "three_prime_UTR"/g)?.length, 3)
+
+    const actual = gff3ToAnnotationFeature(ex4)
+    const txt = JSON.stringify(actual, null, 2)
+    assert.equal(txt.match(/"type": "CDS"/g)?.length, 4)
+    assert.equal(txt.match(/prime_UTR/g), null)
+
+    const expected = readAnnotationFeatureSnapshot('test_data/example04.json')
+    compareFeatures(actual, expected)
+  })
+  it('Convert braker gff', () => {
+    const [gffFeature] = readFeatureFile('test_data/braker.gff')
+    const actual = gff3ToAnnotationFeature(gffFeature)
+    const txt = JSON.stringify(actual, null, 2)
+    assert.equal(txt.match(/intron/g), null)
+    assert.equal(txt.match(/_codon/g), null)
+  })
+})
+
 describe('gff3ToAnnotationFeature', () => {
   for (const testCase of testCases) {
     const [description, featureLine, convertedFeature] = testCase
diff --git a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts
index c07c1d31b..cd4c368d9 100644
--- a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts
+++ b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts
@@ -158,7 +158,10 @@ function convertChildren(
     const [firstChildFeatureLocation] = childFeature
     if (
       firstChildFeatureLocation.type === 'three_prime_UTR' ||
-      firstChildFeatureLocation.type === 'five_prime_UTR'
+      firstChildFeatureLocation.type === 'five_prime_UTR' ||
+      firstChildFeatureLocation.type === 'intron' ||
+      firstChildFeatureLocation.type === 'start_codon' ||
+      firstChildFeatureLocation.type === 'stop_codon'
     ) {
       continue
     }
@@ -232,20 +235,17 @@ function processCDS(
       groupedLocations.push([location])
       continue
     }
-    const lastGroupLastLocation = lastGroup.at(-1)
-    if (!lastGroupLastLocation) {
-      throw new Error('Got group with no locations')
-    }
-    if (
+    const overlaps = lastGroup.some((lastGroupLoc) =>
       doesIntersect2(
         /* eslint-disable @typescript-eslint/no-non-null-assertion */
-        lastGroupLastLocation.start!,
-        lastGroupLastLocation.end!,
+        lastGroupLoc.start!,
+        lastGroupLoc.end!,
         location.start!,
         location.end!,
         /* eslint-enable @typescript-eslint/no-non-null-assertion */
-      )
-    ) {
+      ),
+    )
+    if (overlaps) {
       groupedLocations.push([location])
     } else {
       lastGroup.push(location)
diff --git a/packages/apollo-shared/test_data/braker.gff b/packages/apollo-shared/test_data/braker.gff
new file mode 100644
index 000000000..27feccfcd
--- /dev/null
+++ b/packages/apollo-shared/test_data/braker.gff
@@ -0,0 +1,13 @@
+##gff-version	3
+CM033580.1	AUGUSTUS	gene	15529	16566	0.92	-	.	ID=g1;
+CM033580.1	AUGUSTUS	mRNA	15529	16566	0.92	-	.	ID=g1.t1;Parent=g1;
+CM033580.1	AUGUSTUS	stop_codon	15529	15531	.	-	0	ID=g1.t1.stop1;Parent=g1.t1;
+CM033580.1	AUGUSTUS	CDS	15529	15659	0.92	-	2	ID=g1.t1.CDS1;Parent=g1.t1;
+CM033580.1	AUGUSTUS	exon	15529	15659	.	-	.	ID=g1.t1.exon1;Parent=g1.t1;
+CM033580.1	AUGUSTUS	intron	15660	16112	0.96	-	.	ID=g1.t1.intron1;Parent=g1.t1;
+CM033580.1	AUGUSTUS	CDS	16113	16314	0.96	-	0	ID=g1.t1.CDS2;Parent=g1.t1;
+CM033580.1	AUGUSTUS	exon	16113	16314	.	-	.	ID=g1.t1.exon2;Parent=g1.t1;
+CM033580.1	AUGUSTUS	intron	16315	16536	0.96	-	.	ID=g1.t1.intron2;Parent=g1.t1;
+CM033580.1	AUGUSTUS	CDS	16537	16566	0.99	-	0	ID=g1.t1.CDS3;Parent=g1.t1;
+CM033580.1	AUGUSTUS	exon	16537	16566	.	-	.	ID=g1.t1.exon3;Parent=g1.t1;
+CM033580.1	AUGUSTUS	start_codon	16564	16566	.	-	0	ID=g1.t1.start1;Parent=g1.t1;
diff --git a/packages/apollo-shared/test_data/example01.gff3 b/packages/apollo-shared/test_data/example01.gff3
new file mode 100644
index 000000000..bdedf2aa0
--- /dev/null
+++ b/packages/apollo-shared/test_data/example01.gff3
@@ -0,0 +1,26 @@
+##gff-version 3
+##sequence-region   chr1 1000 9000
+#example01
+chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN
+chr1	.	TF_binding_site	1000	1012	.	+	.	ID=tfbs10001;Parent=gene10001
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10002;Parent=gene10001;Name=EDEN.2
+chr1	.	mRNA	1300	9000	.	+	.	ID=mRNA10003;Parent=gene10001;Name=EDEN.3
+chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001,mRNA10002
+chr1	.	exon	1300	1500	.	+	.	ID=exon10002;Parent=mRNA10003
+chr1	.	exon	3000	3902	.	+	.	ID=exon10003;Parent=mRNA10001,mRNA10003
+chr1	.	exon	5000	5500	.	+	.	ID=exon10004;Parent=mRNA10001,mRNA10002,mRNA10003
+chr1	.	exon	7000	9000	.	+	.	ID=exon10005;Parent=mRNA10001,mRNA10002,mRNA10003
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1
+chr1	.	CDS	3000	3902	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2
+chr1	.	CDS	3301	3902	.	+	0	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3
+chr1	.	CDS	3391	3902	.	+	0	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4
diff --git a/packages/apollo-shared/test_data/example01.json b/packages/apollo-shared/test_data/example01.json
new file mode 100644
index 000000000..161b7a135
--- /dev/null
+++ b/packages/apollo-shared/test_data/example01.json
@@ -0,0 +1,236 @@
+{
+  "_id": "66e049f17b9cedae9ad89108",
+  "refSeq": "chr1",
+  "type": "gene",
+  "min": 999,
+  "max": 9000,
+  "strand": 1,
+  "children": {
+    "66e049f17b9cedae9ad890f5": {
+      "_id": "66e049f17b9cedae9ad890f5",
+      "refSeq": "chr1",
+      "type": "TF_binding_site",
+      "min": 999,
+      "max": 1012,
+      "strand": 1,
+      "attributes": {
+        "gff_id": ["tfbs10001"]
+      }
+    },
+    "66e049f17b9cedae9ad890fb": {
+      "_id": "66e049f17b9cedae9ad890fb",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 1049,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "66e049f17b9cedae9ad890f6": {
+          "_id": "66e049f17b9cedae9ad890f6",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 1049,
+          "max": 1500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10002"]
+          }
+        },
+        "66e049f17b9cedae9ad890f7": {
+          "_id": "66e049f17b9cedae9ad890f7",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 2999,
+          "max": 3902,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10003"]
+          }
+        },
+        "66e049f17b9cedae9ad890f8": {
+          "_id": "66e049f17b9cedae9ad890f8",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10004"]
+          }
+        },
+        "66e049f17b9cedae9ad890f9": {
+          "_id": "66e049f17b9cedae9ad890f9",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 6999,
+          "max": 9000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10005"]
+          }
+        },
+        "66e049f17b9cedae9ad890fa": {
+          "_id": "66e049f17b9cedae9ad890fa",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 1200,
+          "max": 7600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds10001"],
+            "gff_name": ["edenprotein.1"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA10001"],
+        "gff_name": ["EDEN.1"]
+      }
+    },
+    "66e049f17b9cedae9ad89100": {
+      "_id": "66e049f17b9cedae9ad89100",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 1049,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "66e049f17b9cedae9ad890fc": {
+          "_id": "66e049f17b9cedae9ad890fc",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 1049,
+          "max": 1500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10002"]
+          }
+        },
+        "66e049f17b9cedae9ad890fd": {
+          "_id": "66e049f17b9cedae9ad890fd",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10004"]
+          }
+        },
+        "66e049f17b9cedae9ad890fe": {
+          "_id": "66e049f17b9cedae9ad890fe",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 6999,
+          "max": 9000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10005"]
+          }
+        },
+        "66e049f17b9cedae9ad890ff": {
+          "_id": "66e049f17b9cedae9ad890ff",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 1200,
+          "max": 7600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds10002"],
+            "gff_name": ["edenprotein.2"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA10002"],
+        "gff_name": ["EDEN.2"]
+      }
+    },
+    "66e049f17b9cedae9ad89107": {
+      "_id": "66e049f17b9cedae9ad89107",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 1299,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "66e049f17b9cedae9ad89101": {
+          "_id": "66e049f17b9cedae9ad89101",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 1299,
+          "max": 1500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10001"]
+          }
+        },
+        "66e049f17b9cedae9ad89102": {
+          "_id": "66e049f17b9cedae9ad89102",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 2999,
+          "max": 3902,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10003"]
+          }
+        },
+        "66e049f17b9cedae9ad89103": {
+          "_id": "66e049f17b9cedae9ad89103",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10004"]
+          }
+        },
+        "66e049f17b9cedae9ad89104": {
+          "_id": "66e049f17b9cedae9ad89104",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 6999,
+          "max": 9000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10005"]
+          }
+        },
+        "66e049f17b9cedae9ad89105": {
+          "_id": "66e049f17b9cedae9ad89105",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 3300,
+          "max": 7600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds10003"],
+            "gff_name": ["edenprotein.3"]
+          }
+        },
+        "66e049f17b9cedae9ad89106": {
+          "_id": "66e049f17b9cedae9ad89106",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 3390,
+          "max": 7600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds10004"],
+            "gff_name": ["edenprotein.4"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA10003"],
+        "gff_name": ["EDEN.3"]
+      }
+    }
+  },
+  "attributes": {
+    "gff_id": ["gene10001"],
+    "gff_name": ["EDEN"]
+  }
+}
diff --git a/packages/apollo-shared/test_data/example02.json b/packages/apollo-shared/test_data/example02.json
new file mode 100644
index 000000000..089705a3e
--- /dev/null
+++ b/packages/apollo-shared/test_data/example02.json
@@ -0,0 +1,225 @@
+{
+  "_id": "66e049609048deab4117a33e",
+  "refSeq": "chr1",
+  "type": "gene",
+  "min": 10999,
+  "max": 19000,
+  "strand": 1,
+  "children": {
+    "66e049609048deab4117a331": {
+      "_id": "66e049609048deab4117a331",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 11049,
+      "max": 19000,
+      "strand": 1,
+      "children": {
+        "66e049609048deab4117a32c": {
+          "_id": "66e049609048deab4117a32c",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 11049,
+          "max": 11500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20001"]
+          }
+        },
+        "66e049609048deab4117a32d": {
+          "_id": "66e049609048deab4117a32d",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 12999,
+          "max": 13902,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20004"]
+          }
+        },
+        "66e049609048deab4117a32e": {
+          "_id": "66e049609048deab4117a32e",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 14999,
+          "max": 15500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20006"]
+          }
+        },
+        "66e049609048deab4117a32f": {
+          "_id": "66e049609048deab4117a32f",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 16999,
+          "max": 19000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20009"]
+          }
+        },
+        "66e049609048deab4117a330": {
+          "_id": "66e049609048deab4117a330",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 11200,
+          "max": 17600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds20001"],
+            "gff_name": ["edenprotein.1"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA20001"],
+        "gff_name": ["EDEN.1"]
+      }
+    },
+    "66e049609048deab4117a336": {
+      "_id": "66e049609048deab4117a336",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 11049,
+      "max": 19000,
+      "strand": 1,
+      "children": {
+        "66e049609048deab4117a332": {
+          "_id": "66e049609048deab4117a332",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 11049,
+          "max": 11500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20002"]
+          }
+        },
+        "66e049609048deab4117a333": {
+          "_id": "66e049609048deab4117a333",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 14999,
+          "max": 15500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20007"]
+          }
+        },
+        "66e049609048deab4117a334": {
+          "_id": "66e049609048deab4117a334",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 16999,
+          "max": 19000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20010"]
+          }
+        },
+        "66e049609048deab4117a335": {
+          "_id": "66e049609048deab4117a335",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 11200,
+          "max": 17600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds20002"],
+            "gff_name": ["edenprotein.2"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA20002"],
+        "gff_name": ["EDEN.2"]
+      }
+    },
+    "66e049609048deab4117a33d": {
+      "_id": "66e049609048deab4117a33d",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 11299,
+      "max": 19000,
+      "strand": 1,
+      "children": {
+        "66e049609048deab4117a337": {
+          "_id": "66e049609048deab4117a337",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 11299,
+          "max": 11500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20003"]
+          }
+        },
+        "66e049609048deab4117a338": {
+          "_id": "66e049609048deab4117a338",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 12999,
+          "max": 13902,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20005"]
+          }
+        },
+        "66e049609048deab4117a339": {
+          "_id": "66e049609048deab4117a339",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 14999,
+          "max": 15500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20008"]
+          }
+        },
+        "66e049609048deab4117a33a": {
+          "_id": "66e049609048deab4117a33a",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 16999,
+          "max": 19000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon20011"]
+          }
+        },
+        "66e049609048deab4117a33b": {
+          "_id": "66e049609048deab4117a33b",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 13300,
+          "max": 17600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds20003"],
+            "gff_name": ["edenprotein.3"]
+          }
+        },
+        "66e049609048deab4117a33c": {
+          "_id": "66e049609048deab4117a33c",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 13390,
+          "max": 17600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds20004"],
+            "gff_name": ["edenprotein.4"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA20003"],
+        "gff_name": ["EDEN.3"]
+      }
+    }
+  },
+  "attributes": {
+    "gff_id": ["gene20001"],
+    "gff_name": ["EDEN"]
+  }
+}
diff --git a/packages/apollo-shared/test_data/example04.json b/packages/apollo-shared/test_data/example04.json
new file mode 100644
index 000000000..83d8928d6
--- /dev/null
+++ b/packages/apollo-shared/test_data/example04.json
@@ -0,0 +1,225 @@
+{
+  "_id": "66e0555fae0bd7cfcd69912d",
+  "refSeq": "chr1",
+  "type": "gene",
+  "min": 30999,
+  "max": 39000,
+  "strand": 1,
+  "children": {
+    "66e0555fae0bd7cfcd699120": {
+      "_id": "66e0555fae0bd7cfcd699120",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 31049,
+      "max": 39000,
+      "strand": 1,
+      "children": {
+        "66e0555fae0bd7cfcd69911b": {
+          "_id": "66e0555fae0bd7cfcd69911b",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 31049,
+          "max": 31500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40001"]
+          }
+        },
+        "66e0555fae0bd7cfcd69911c": {
+          "_id": "66e0555fae0bd7cfcd69911c",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 32999,
+          "max": 33902,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40003"]
+          }
+        },
+        "66e0555fae0bd7cfcd69911d": {
+          "_id": "66e0555fae0bd7cfcd69911d",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 34999,
+          "max": 35500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40004"]
+          }
+        },
+        "66e0555fae0bd7cfcd69911e": {
+          "_id": "66e0555fae0bd7cfcd69911e",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 36999,
+          "max": 39000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40005"]
+          }
+        },
+        "66e0555fae0bd7cfcd69911f": {
+          "_id": "66e0555fae0bd7cfcd69911f",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 31200,
+          "max": 37600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds40001"],
+            "gff_name": ["edenprotein.1"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA40001"],
+        "gff_name": ["EDEN.1"]
+      }
+    },
+    "66e0555fae0bd7cfcd699125": {
+      "_id": "66e0555fae0bd7cfcd699125",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 31049,
+      "max": 39000,
+      "strand": 1,
+      "children": {
+        "66e0555fae0bd7cfcd699121": {
+          "_id": "66e0555fae0bd7cfcd699121",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 31049,
+          "max": 31500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40001"]
+          }
+        },
+        "66e0555fae0bd7cfcd699122": {
+          "_id": "66e0555fae0bd7cfcd699122",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 34999,
+          "max": 35500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40004"]
+          }
+        },
+        "66e0555fae0bd7cfcd699123": {
+          "_id": "66e0555fae0bd7cfcd699123",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 36999,
+          "max": 39000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40005"]
+          }
+        },
+        "66e0555fae0bd7cfcd699124": {
+          "_id": "66e0555fae0bd7cfcd699124",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 31200,
+          "max": 37600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds40002"],
+            "gff_name": ["edenprotein.2"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA40002"],
+        "gff_name": ["EDEN.2"]
+      }
+    },
+    "66e0555fae0bd7cfcd69912c": {
+      "_id": "66e0555fae0bd7cfcd69912c",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 31299,
+      "max": 39000,
+      "strand": 1,
+      "children": {
+        "66e0555fae0bd7cfcd699126": {
+          "_id": "66e0555fae0bd7cfcd699126",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 31299,
+          "max": 31500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40002"]
+          }
+        },
+        "66e0555fae0bd7cfcd699127": {
+          "_id": "66e0555fae0bd7cfcd699127",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 32999,
+          "max": 33902,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40003"]
+          }
+        },
+        "66e0555fae0bd7cfcd699128": {
+          "_id": "66e0555fae0bd7cfcd699128",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 34999,
+          "max": 35500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40004"]
+          }
+        },
+        "66e0555fae0bd7cfcd699129": {
+          "_id": "66e0555fae0bd7cfcd699129",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 36999,
+          "max": 39000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon40005"]
+          }
+        },
+        "66e0555fae0bd7cfcd69912a": {
+          "_id": "66e0555fae0bd7cfcd69912a",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 33300,
+          "max": 37600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds40003"],
+            "gff_name": ["edenprotein.3"]
+          }
+        },
+        "66e0555fae0bd7cfcd69912b": {
+          "_id": "66e0555fae0bd7cfcd69912b",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 33390,
+          "max": 37600,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds40004"],
+            "gff_name": ["edenprotein.4"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA40003"],
+        "gff_name": ["EDEN.3"]
+      }
+    }
+  },
+  "attributes": {
+    "gff_id": ["gene40001"],
+    "gff_name": ["EDEN"]
+  }
+}
diff --git a/packages/apollo-shared/test_data/example05.gff3 b/packages/apollo-shared/test_data/example05.gff3
new file mode 100644
index 000000000..70031fe06
--- /dev/null
+++ b/packages/apollo-shared/test_data/example05.gff3
@@ -0,0 +1,30 @@
+##gff-version 3
+# example 5
+chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN;testid=t003
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10002;Parent=gene10001;Name=EDEN.2;testid=t005
+chr1	.	mRNA	1300	9000	.	+	.	ID=mRNA10003;Parent=gene10001;Name=EDEN.3;testid=t006
+chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001,mRNA10002;testid=t007
+chr1	.	exon	1300	1500	.	+	.	ID=exon10002;Parent=mRNA10003;testid=t008
+chr1	.	exon	3000	3902	.	+	.	ID=exon10003;Parent=mRNA10001,mRNA10003;testid=t009
+chr1	.	exon	5000	5500	.	+	.	ID=exon10004;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t010
+chr1	.	exon	7000	9000	.	+	.	ID=exon10005;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t011
+chr1	.	five_prime_UTR	1050	1200	.	+	.	ID=five_prime_UTR10001;Parent=mRNA10001,mRNA10002;testid=t012
+chr1	.	five_prime_UTR	1300	1500	.	+	.	ID=five_prime_UTR10002;Parent=mRNA10003;testid=t013
+chr1	.	five_prime_UTR	3000	3300	.	+	.	ID=five_prime_UTR10003;Parent=mRNA10003;testid=t014
+chr1	.	five_prime_UTR	3000	3390	.	+	.	ID=five_prime_UTR10004;Parent=mRNA10003;testid=t015
+chr1	.	five_prime_UTR	3000	3390	.	+	.	ID=five_prime_UTR10004;Parent=mRNA10003;testid=t016
+chr1	.	three_prime_UTR	7601	9000	.	+	.	ID=three_prime_UTR10001;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t017
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t018
+chr1	.	CDS	3000	3902	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t019
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t020
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t021
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t022
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t023
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t024
+chr1	.	CDS	3301	3902	.	+	0	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t025
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t026
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t027
+chr1	.	CDS	3391	3902	.	+	0	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t028
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t029
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t030
diff --git a/packages/apollo-shared/test_data/example06.gff3 b/packages/apollo-shared/test_data/example06.gff3
new file mode 100644
index 000000000..a762a0936
--- /dev/null
+++ b/packages/apollo-shared/test_data/example06.gff3
@@ -0,0 +1,30 @@
+##gff-version 3
+# example 6
+chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN;testid=t003
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10002;Parent=gene10001;Name=EDEN.2;testid=t005
+chr1	.	mRNA	1300	9000	.	+	.	ID=mRNA10003;Parent=gene10001;Name=EDEN.3;testid=t006
+chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001,mRNA10002;testid=t007
+chr1	.	exon	1300	1500	.	+	.	ID=exon10002;Parent=mRNA10003;testid=t008
+chr1	.	exon	3000	3902	.	+	.	ID=exon10003;Parent=mRNA10001,mRNA10003;testid=t009
+chr1	.	exon	5000	5500	.	+	.	ID=exon10004;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t010
+chr1	.	exon	7000	9000	.	+	.	ID=exon10005;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t011
+chr1	.	five_prime_UTR	1050	1200	.	+	.	ID=five_prime_UTR10001;Parent=mRNA10001,mRNA10002;testid=t012
+chr1	.	five_prime_UTR	1300	1500	.	+	.	ID=five_prime_UTR10002;Parent=mRNA10003;testid=t013
+chr1	.	five_prime_UTR	3000	3300	.	+	.	ID=five_prime_UTR10003;Parent=mRNA10003;testid=t014
+chr1	.	five_prime_UTR	3000	3390	.	+	.	ID=five_prime_UTR10004;Parent=mRNA10003;testid=t015
+chr1	.	five_prime_UTR	3000	3390	.	+	.	ID=five_prime_UTR10004;Parent=mRNA10003;testid=t016
+chr1	.	three_prime_UTR	7601	9000	.	+	.	ID=three_prime_UTR10001;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t017
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t018
+chr1	.	CDS	3000	3902	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t019
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t020
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t021
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t022
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t023
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t024
+chr1	.	CDS	3301	3902	.	+	0	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t025
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t026
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t027
+chr1	.	CDS	3391	3902	.	+	0	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t028
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t029
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t030
diff --git a/packages/apollo-shared/test_data/example07.gff3 b/packages/apollo-shared/test_data/example07.gff3
new file mode 100644
index 000000000..c1bb5fcab
--- /dev/null
+++ b/packages/apollo-shared/test_data/example07.gff3
@@ -0,0 +1,30 @@
+##gff-version 3
+# example 2
+chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN;testid=t003
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10002;Parent=gene10001;Name=EDEN.2;testid=t005
+chr1	.	mRNA	1300	9000	.	+	.	ID=mRNA10003;Parent=gene10001;Name=EDEN.3;testid=t006
+chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001;testid=t007
+chr1	.	exon	1050	1500	.	+	.	ID=exon10002;Parent=mRNA10002;testid=t008
+chr1	.	exon	1300	1500	.	+	.	ID=exon10003;Parent=mRNA10003;testid=t009
+chr1	.	exon	3000	3902	.	+	.	ID=exon10004;Parent=mRNA10001;testid=t010
+chr1	.	exon	3000	3902	.	+	.	ID=exon10005;Parent=mRNA10003;testid=t011
+chr1	.	exon	5000	5500	.	+	.	ID=exon10006;Parent=mRNA10001;testid=t012
+chr1	.	exon	5000	5500	.	+	.	ID=exon10007;Parent=mRNA10002;testid=t013
+chr1	.	exon	5000	5500	.	+	.	ID=exon10008;Parent=mRNA10003;testid=t014
+chr1	.	exon	7000	9000	.	+	.	ID=exon10009;Parent=mRNA10001;testid=t015
+chr1	.	exon	7000	9000	.	+	.	ID=exon20010;Parent=mRNA10002;testid=t016
+chr1	.	exon	7000	9000	.	+	.	ID=exon20011;Parent=mRNA10003;testid=t017
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t018
+chr1	.	CDS	3000	3902	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t019
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t020
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t021
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t022
+chr1	.	CDS	5000	5500	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t023
+chr1	.	CDS	7000	7600	.	+	0	ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t024
+chr1	.	CDS	3301	3902	.	+	0	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t025
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t026
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t027
+chr1	.	CDS	3391	3902	.	+	0	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t028
+chr1	.	CDS	5000	5500	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t029
+chr1	.	CDS	7000	7600	.	+	1	ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t030
diff --git a/packages/apollo-shared/test_data/gene_mrna.gff3 b/packages/apollo-shared/test_data/gene_mrna.gff3
new file mode 100644
index 000000000..55efcbad7
--- /dev/null
+++ b/packages/apollo-shared/test_data/gene_mrna.gff3
@@ -0,0 +1,4 @@
+##gff-version 3
+##sequence-region   ctgA 1000 2000
+ctgA	example	gene	1000	2000	.	.	.	ID=gene01;Name=geneA;Alias=hga
+ctgA	example	mRNA	1000	2000	.	.	.	Parent=gene01;Name=mrnaA;Alias=hga
diff --git a/packages/apollo-cli/test_data/gene_representations.gff3 b/packages/apollo-shared/test_data/gene_representations.gff3
similarity index 96%
rename from packages/apollo-cli/test_data/gene_representations.gff3
rename to packages/apollo-shared/test_data/gene_representations.gff3
index e3ebe11c0..b9aff4134 100644
--- a/packages/apollo-cli/test_data/gene_representations.gff3
+++ b/packages/apollo-shared/test_data/gene_representations.gff3
@@ -110,64 +110,6 @@ chr1	.	CDS	37000	37600	.	+	1	ID=cds40003;Parent=mRNA40003;Name=edenprotein.3
 chr1	.	CDS	33391	33902	.	+	0	ID=cds40004;Parent=mRNA40003;Name=edenprotein.4
 chr1	.	CDS	35000	35500	.	+	1	ID=cds40004;Parent=mRNA40003;Name=edenprotein.4
 chr1	.	CDS	37000	37600	.	+	1	ID=cds40004;Parent=mRNA40003;Name=edenprotein.4
-# example 5
-chr1	.	gene	41000	49000	.	+	.	ID=gene50001;Name=EDEN
-chr1	.	mRNA	41050	49000	.	+	.	ID=mRNA50001;Parent=gene50001;Name=EDEN.1
-chr1	.	mRNA	41050	49000	.	+	.	ID=mRNA50002;Parent=gene50001;Name=EDEN.2
-chr1	.	mRNA	41300	49000	.	+	.	ID=mRNA50003;Parent=gene50001;Name=EDEN.3
-chr1	.	exon	41050	41500	.	+	.	ID=exon50001;Parent=mRNA50001,mRNA50002
-chr1	.	exon	41300	41500	.	+	.	ID=exon50002;Parent=mRNA50003
-chr1	.	exon	43000	43902	.	+	.	ID=exon50003;Parent=mRNA50001,mRNA50003
-chr1	.	exon	45000	45500	.	+	.	ID=exon50004;Parent=mRNA50001,mRNA50002,mRNA50003
-chr1	.	exon	47000	49000	.	+	.	ID=exon50005;Parent=mRNA50001,mRNA50002,mRNA50003
-chr1	.	five_prime_UTR	41050	41200	.	+	.	ID=five_prime_UTR50001;Parent=mRNA50001,mRNA50002
-chr1	.	five_prime_UTR	41300	41500	.	+	.	ID=five_prime_UTR50002;Parent=mRNA50003
-chr1	.	five_prime_UTR	43000	43300	.	+	.	ID=five_prime_UTR50003;Parent=mRNA50003
-chr1	.	five_prime_UTR	43000	43390	.	+	.	ID=five_prime_UTR50004;Parent=mRNA50003
-chr1	.	five_prime_UTR	43000	43390	.	+	.	ID=five_prime_UTR50004;Parent=mRNA50003
-chr1	.	three_prime_UTR	47601	49000	.	+	.	ID=three_prime_UTR50001;Parent=mRNA50001,mRNA50002,mRNA50003
-chr1	.	CDS	41201	41500	.	+	0	ID=cds50001;Parent=mRNA50001;Name=edenprotein.1
-chr1	.	CDS	43000	43902	.	+	0	ID=cds50001;Parent=mRNA50001;Name=edenprotein.1
-chr1	.	CDS	45000	45500	.	+	0	ID=cds50001;Parent=mRNA50001;Name=edenprotein.1
-chr1	.	CDS	47000	47600	.	+	0	ID=cds50001;Parent=mRNA50001;Name=edenprotein.1
-chr1	.	CDS	41201	41500	.	+	0	ID=cds50002;Parent=mRNA50002;Name=edenprotein.2
-chr1	.	CDS	45000	45500	.	+	0	ID=cds50002;Parent=mRNA50002;Name=edenprotein.2
-chr1	.	CDS	47000	47600	.	+	0	ID=cds50002;Parent=mRNA50002;Name=edenprotein.2
-chr1	.	CDS	43301	43902	.	+	0	ID=cds50003;Parent=mRNA50003;Name=edenprotein.3
-chr1	.	CDS	45000	45500	.	+	1	ID=cds50003;Parent=mRNA50003;Name=edenprotein.3
-chr1	.	CDS	47000	47600	.	+	1	ID=cds50003;Parent=mRNA50003;Name=edenprotein.3
-chr1	.	CDS	43391	43902	.	+	0	ID=cds50004;Parent=mRNA50003;Name=edenprotein.4
-chr1	.	CDS	45000	45500	.	+	1	ID=cds50004;Parent=mRNA50003;Name=edenprotein.4
-chr1	.	CDS	47000	47600	.	+	1	ID=cds50004;Parent=mRNA50003;Name=edenprotein.4
-# example 6
-chr1	.	gene	51000	59000	.	+	.	ID=gene60001;Name=EDEN
-chr1	.	mRNA	51050	59000	.	+	.	ID=mRNA60001;Parent=gene60001;Name=EDEN.1
-chr1	.	mRNA	51050	59000	.	+	.	ID=mRNA60002;Parent=gene60001;Name=EDEN.2
-chr1	.	mRNA	51300	59000	.	+	.	ID=mRNA60003;Parent=gene60001;Name=EDEN.3
-chr1	.	exon	51050	51500	.	+	.	ID=exon60001;Parent=mRNA60001,mRNA60002
-chr1	.	exon	51300	51500	.	+	.	ID=exon60002;Parent=mRNA60003
-chr1	.	exon	53000	53902	.	+	.	ID=exon60003;Parent=mRNA60001,mRNA60003
-chr1	.	exon	55000	55500	.	+	.	ID=exon60004;Parent=mRNA60001,mRNA60002,mRNA60003
-chr1	.	exon	57000	59000	.	+	.	ID=exon60005;Parent=mRNA60001,mRNA60002,mRNA60003
-chr1	.	five_prime_UTR	51050	51200	.	+	.	ID=five_prime_UTR60001;Parent=mRNA60001,mRNA60002
-chr1	.	five_prime_UTR	51300	51500	.	+	.	ID=five_prime_UTR60002;Parent=mRNA60003
-chr1	.	five_prime_UTR	53000	53300	.	+	.	ID=five_prime_UTR60003;Parent=mRNA60003
-chr1	.	five_prime_UTR	53000	53390	.	+	.	ID=five_prime_UTR60004;Parent=mRNA60003
-chr1	.	five_prime_UTR	53000	53390	.	+	.	ID=five_prime_UTR60004;Parent=mRNA60003
-chr1	.	three_prime_UTR	57601	59000	.	+	.	ID=three_prime_UTR60001;Parent=mRNA60001,mRNA60002,mRNA60003
-chr1	.	CDS	51201	51500	.	+	0	ID=cds60001;Parent=mRNA60001;Name=edenprotein.1
-chr1	.	CDS	53000	53902	.	+	0	ID=cds60001;Parent=mRNA60001;Name=edenprotein.1
-chr1	.	CDS	55000	55500	.	+	0	ID=cds60001;Parent=mRNA60001;Name=edenprotein.1
-chr1	.	CDS	57000	57600	.	+	0	ID=cds60001;Parent=mRNA60001;Name=edenprotein.1
-chr1	.	CDS	51201	51500	.	+	0	ID=cds60002;Parent=mRNA60002;Name=edenprotein.2
-chr1	.	CDS	55000	55500	.	+	0	ID=cds60002;Parent=mRNA60002;Name=edenprotein.2
-chr1	.	CDS	57000	57600	.	+	0	ID=cds60002;Parent=mRNA60002;Name=edenprotein.2
-chr1	.	CDS	53301	53902	.	+	0	ID=cds60003;Parent=mRNA60003;Name=edenprotein.3
-chr1	.	CDS	55000	55500	.	+	1	ID=cds60003;Parent=mRNA60003;Name=edenprotein.3
-chr1	.	CDS	57000	57600	.	+	1	ID=cds60003;Parent=mRNA60003;Name=edenprotein.3
-chr1	.	CDS	53391	53902	.	+	0	ID=cds60004;Parent=mRNA60003;Name=edenprotein.4
-chr1	.	CDS	55000	55500	.	+	1	ID=cds60004;Parent=mRNA60003;Name=edenprotein.4
-chr1	.	CDS	57000	57600	.	+	1	ID=cds60004;Parent=mRNA60003;Name=edenprotein.4
 ##FASTA
 >chr1
 cattgttgcggagttgaacaACGGCATTAGGAACACTTCCGTCTCtcacttttatacgat
diff --git a/packages/apollo-shared/test_data/one_cds.gff3 b/packages/apollo-shared/test_data/one_cds.gff3
new file mode 100644
index 000000000..81626f6e3
--- /dev/null
+++ b/packages/apollo-shared/test_data/one_cds.gff3
@@ -0,0 +1,9 @@
+##gff-version 3
+##sequence-region   chr1 1000 9000
+#example01
+chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN;testid=t003
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004,t001,t004
+chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001;testid=t007
+chr1	.	exon	5000	5500	.	+	.	ID=exon10004;Parent=mRNA10001;testid=t010
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t012,t013,t014
+chr1	.	CDS	5000	5000	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t015,t014
diff --git a/packages/apollo-shared/test_data/one_cds.json b/packages/apollo-shared/test_data/one_cds.json
new file mode 100644
index 000000000..185f5579c
--- /dev/null
+++ b/packages/apollo-shared/test_data/one_cds.json
@@ -0,0 +1,67 @@
+{
+  "_id": "66d70e4ccc30b55b65e5f619",
+  "refSeq": "chr1",
+  "type": "gene",
+  "min": 999,
+  "max": 9000,
+  "strand": 1,
+  "children": {
+    "66d70e4ccc30b55b65e5f618": {
+      "_id": "66d70e4ccc30b55b65e5f618",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 1049,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "66d70e4ccc30b55b65e5f615": {
+          "_id": "66d70e4ccc30b55b65e5f615",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 1049,
+          "max": 1500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10001"],
+            "testid": ["t007"]
+          }
+        },
+        "66d70e4ccc30b55b65e5f616": {
+          "_id": "66d70e4ccc30b55b65e5f616",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10004"],
+            "testid": ["t010"]
+          }
+        },
+        "66d70e4ccc30b55b65e5f617": {
+          "_id": "66d70e4ccc30b55b65e5f617",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 1200,
+          "max": 5000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds10001"],
+            "gff_name": ["edenprotein.1"],
+            "testid": ["t012", "t013", "t014", "t015"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA10001"],
+        "gff_name": ["EDEN.1"],
+        "testid": ["t004", "t001", "t004"]
+      }
+    }
+  },
+  "attributes": {
+    "gff_id": ["gene10001"],
+    "gff_name": ["EDEN"],
+    "testid": ["t003"]
+  }
+}
diff --git a/packages/apollo-shared/test_data/two_cds.gff3 b/packages/apollo-shared/test_data/two_cds.gff3
new file mode 100644
index 000000000..fd58a8a33
--- /dev/null
+++ b/packages/apollo-shared/test_data/two_cds.gff3
@@ -0,0 +1,9 @@
+##gff-version 3
+##sequence-region   chr1 1000 9000
+#example01
+chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN;testid=t003
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004,t001,t004
+chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001;testid=t007
+chr1	.	exon	5000	5500	.	+	.	ID=exon10004;Parent=mRNA10001;testid=t010
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t012,t013,t014
+chr1	.	CDS	5000	5000	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t014
diff --git a/packages/apollo-shared/test_data/two_cds.json b/packages/apollo-shared/test_data/two_cds.json
new file mode 100644
index 000000000..6500195a7
--- /dev/null
+++ b/packages/apollo-shared/test_data/two_cds.json
@@ -0,0 +1,67 @@
+{
+  "_id": "66d70f3b9c7a7460925687a3",
+  "refSeq": "chr1",
+  "type": "gene",
+  "min": 999,
+  "max": 9000,
+  "strand": 1,
+  "children": {
+    "66d70f3b9c7a7460925687a2": {
+      "_id": "66d70f3b9c7a7460925687a2",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 1049,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "66d70f3b9c7a74609256879f": {
+          "_id": "66d70f3b9c7a74609256879f",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 1049,
+          "max": 1500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10001"],
+            "testid": ["t007"]
+          }
+        },
+        "66d70f3b9c7a7460925687a0": {
+          "_id": "66d70f3b9c7a7460925687a0",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10004"],
+            "testid": ["t010"]
+          }
+        },
+        "66d70f3b9c7a7460925687a1": {
+          "_id": "66d70f3b9c7a7460925687a1",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 1200,
+          "max": 5000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds10001"],
+            "gff_name": ["edenprotein.1"],
+            "testid": ["t012", "t013", "t014"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA10001"],
+        "gff_name": ["EDEN.1"],
+        "testid": ["t004", "t001", "t004"]
+      }
+    }
+  },
+  "attributes": {
+    "gff_id": ["gene10001"],
+    "gff_name": ["EDEN"],
+    "testid": ["t003"]
+  }
+}
diff --git a/yarn.lock b/yarn.lock
index f51810c29..890e5c4df 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -330,7 +330,7 @@ __metadata:
     "@oclif/core": "npm:^3.18.2"
     "@oclif/plugin-help": "npm:^6.0.8"
     "@oclif/test": "npm:^3.1.3"
-    "@types/chai": "npm:^4"
+    "@types/chai": "npm:^4.3.19"
     "@types/cli-progress": "npm:^3"
     "@types/inquirer": "npm:^9.0.7"
     "@types/mocha": "npm:^10"
@@ -591,9 +591,12 @@ __metadata:
     "@jbrowse/core": "npm:^2.13.1"
     "@nestjs/common": "npm:^10.1.0"
     "@nestjs/core": "npm:^10.1.0"
+    "@types/chai": "npm:^4.3.19"
     "@types/node": "npm:^18.14.2"
     "@types/rimraf": "npm:^3"
     bson-objectid: "npm:^2.0.4"
+    chai: "npm:^5.1.1"
+    chai-exclude: "npm:^3.0.0"
     generic-filehandle: "npm:^3.0.0"
     glob: "npm:^11.0.0"
     jwt-decode: "npm:^3.1.2"
@@ -9323,13 +9326,20 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@types/chai@npm:*, @types/chai@npm:^4":
+"@types/chai@npm:*":
   version: 4.3.11
   resolution: "@types/chai@npm:4.3.11"
   checksum: 10c0/0c216ac4a19bfbf8318bb104d32e50704ee2ffc4b538b976c4326e6638fee121462402caa570662227a2a218810388aadb14bdbd3d3d474ec300b00695db448a
   languageName: node
   linkType: hard
 
+"@types/chai@npm:^4.3.19":
+  version: 4.3.19
+  resolution: "@types/chai@npm:4.3.19"
+  checksum: 10c0/8fd573192e486803c4d04185f2b0fab554660d9a1300dbed5bde9747ab8bef15f462a226f560ed5ca48827eecaf8d71eed64aa653ff9aec72fb2eae272e43a84
+  languageName: node
+  linkType: hard
+
 "@types/cli-progress@npm:^3, @types/cli-progress@npm:^3.11.5":
   version: 3.11.5
   resolution: "@types/cli-progress@npm:3.11.5"
@@ -11562,6 +11572,13 @@ __metadata:
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+"assertion-error@npm:^2.0.1":
+  version: 2.0.1
+  resolution: "assertion-error@npm:2.0.1"
+  checksum: 10c0/bbbcb117ac6480138f8c93cf7f535614282dea9dc828f540cdece85e3c665e8f78958b96afac52f29ff883c72638e6a87d469ecc9fe5bc902df03ed24a55dba8
+  languageName: node
+  linkType: hard
+
 "ast-types-flow@npm:^0.0.7":
   version: 0.0.7
   resolution: "ast-types-flow@npm:0.0.7"
@@ -12882,6 +12899,17 @@ __metadata:
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+"chai-exclude@npm:^3.0.0":
+  version: 3.0.0
+  resolution: "chai-exclude@npm:3.0.0"
+  dependencies:
+    fclone: "npm:^1.0.11"
+  peerDependencies:
+    chai: ">= 5"
+  checksum: 10c0/c0bbe2f29398e9a9338e0aa86835668b701bf220e49ec24cf80d58f3b322b4a9dd332e3052c757f97ea5ba2c0086c64c7014a3b07862fa370480f350ceac4066
+  languageName: node
+  linkType: hard
+
 "chai@npm:*, chai@npm:^4.3.10":
   version: 4.3.10
   resolution: "chai@npm:4.3.10"
@@ -12897,6 +12925,19 @@ __metadata:
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   linkType: hard
 
+"chai@npm:^5.1.1":
+  version: 5.1.1
+  resolution: "chai@npm:5.1.1"
+  dependencies:
+    assertion-error: "npm:^2.0.1"
+    check-error: "npm:^2.1.1"
+    deep-eql: "npm:^5.0.1"
+    loupe: "npm:^3.1.0"
+    pathval: "npm:^2.0.0"
+  checksum: 10c0/e7f00e5881e3d5224f08fe63966ed6566bd9fdde175863c7c16dd5240416de9b34c4a0dd925f4fd64ad56256ca6507d32cf6131c49e1db65c62578eb31d4566c
+  languageName: node
+  linkType: hard
+
 "chalk-template@npm:0.4.0":
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   resolution: "chalk-template@npm:0.4.0"
@@ -13029,6 +13070,13 @@ __metadata:
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   linkType: hard
 
+"check-error@npm:^2.1.1":
+  version: 2.1.1
+  resolution: "check-error@npm:2.1.1"
+  checksum: 10c0/979f13eccab306cf1785fa10941a590b4e7ea9916ea2a4f8c87f0316fc3eab07eabefb6e587424ef0f88cbcd3805791f172ea739863ca3d7ce2afc54641c7f0e
+  languageName: node
+  linkType: hard
+
 "check-more-types@npm:2.24.0, check-more-types@npm:^2.24.0":
   version: 2.24.0
   resolution: "check-more-types@npm:2.24.0"
@@ -14677,6 +14725,13 @@ __metadata:
   languageName: node
   linkType: hard
 
+"deep-eql@npm:^5.0.1":
+  version: 5.0.2
+  resolution: "deep-eql@npm:5.0.2"
+  checksum: 10c0/7102cf3b7bb719c6b9c0db2e19bf0aa9318d141581befe8c7ce8ccd39af9eaa4346e5e05adef7f9bd7015da0f13a3a25dcfe306ef79dc8668aedbecb658dd247
+  languageName: node
+  linkType: hard
+
 "deep-extend@npm:^0.6.0":
   version: 0.6.0
   resolution: "deep-extend@npm:0.6.0"
@@ -16775,6 +16830,13 @@ __metadata:
   languageName: node
   linkType: hard
 
+"fclone@npm:^1.0.11":
+  version: 1.0.11
+  resolution: "fclone@npm:1.0.11"
+  checksum: 10c0/dbe3ebd0883edeec2998874bf951aa03198d727f1091351b22af250ff53e227ee94872487ae88ba7280b2469fb164a7d4dd4e5ece10afd4988ab4712f49bc43b
+  languageName: node
+  linkType: hard
+
 "fd-slicer@npm:~1.1.0":
   version: 1.1.0
   resolution: "fd-slicer@npm:1.1.0"
@@ -21199,6 +21261,15 @@ __metadata:
   languageName: node
   linkType: hard
 
+"loupe@npm:^3.1.0":
+  version: 3.1.1
+  resolution: "loupe@npm:3.1.1"
+  dependencies:
+    get-func-name: "npm:^2.0.1"
+  checksum: 10c0/99f88badc47e894016df0c403de846fedfea61154aadabbf776c8428dd59e8d8378007135d385d737de32ae47980af07d22ba7bec5ef7beebd721de9baa0a0af
+  languageName: node
+  linkType: hard
+
 "lower-case@npm:^2.0.2":
   version: 2.0.2
   resolution: "lower-case@npm:2.0.2"
@@ -24600,6 +24671,13 @@ __metadata:
   languageName: node
   linkType: hard
 
+"pathval@npm:^2.0.0":
+  version: 2.0.0
+  resolution: "pathval@npm:2.0.0"
+  checksum: 10c0/602e4ee347fba8a599115af2ccd8179836a63c925c23e04bd056d0674a64b39e3a081b643cc7bc0b84390517df2d800a46fcc5598d42c155fe4977095c2f77c5
+  languageName: node
+  linkType: hard
+
 "pause-stream@npm:0.0.11":
   version: 0.0.11
   resolution: "pause-stream@npm:0.0.11"