RNA Splicing Flashcards: Exon Junctions & Isoforms

Question 1

What do you call the RNA precursor that’s processed into mature mRNA?

Accepted Answer

Pre-mRNA, or precursor messenger RNA.

Question 2

Can an exon contain bases in the 5′ untranslated region of a mature mRNA?

Accepted Answer

Yes. The 5′ untranslated region stays in the mature mRNA upstream of the translation start site.

Question 3

What two changes happen to a pre-mRNA segment when the intron between two exons is spliced out?

Accepted Answer

The intron is removed, and the two flanking exons are joined.

Question 4

In ordinary splicing within one pre-mRNA, what happens to the 5′ → 3′ order of the exons that are kept?

Accepted Answer

They stay in their original order. Splicing can change which exons are present.

Question 5

Write the mature RNA fragment, 5′ → 3′, after removing intron I1.

Pre-mRNA 5′ → 3′
E1 CACU | I1 GUAAG | E2 UUGC

Accepted Answer

5′-CACUUUGC-3′

Join CACU to UUGC.

Question 6

What is an exon–exon junction in a spliced RNA?

Accepted Answer

The point where the end of one exon joins the start of the next exon in that RNA.

Question 7

How can alternative splicing produce different RNA isoforms from the same gene?

Accepted Answer

Different splice patterns keep different parts of the precursor RNA, producing distinct mature RNA versions called isoforms.

Question 8

A pre-mRNA fragment has a 6-base exon, a 9-base intron, and a 4-base exon in that order. How many bases remain after the intron is removed?

Accepted Answer

10 bases. The two exons contribute 6 + 4.

Question 9

One mature RNA has exons E1 → E2 → E3. A second mature RNA from the same precursor has E1 → E3. What event accounts for the difference?

Accepted Answer

Exon skipping. The second RNA skips E2 and joins E1 directly to E3.

Question 10

Remove both introns. What’s the resulting RNA fragment, 5′ → 3′?

Pre-mRNA 5′ → 3′
E1 ACUG | I1 GUCAG | E2 CAA
I2 GUUAG | E3 GGUA

Accepted Answer

5′-ACUGCAAGGUA-3′

Join E1, E2, and E3 in that order.

Question 11

A mature RNA fragment consists of exons E1, E2, and E4 in that 5′ to 3′ order. Which exon–exon junctions does it contain?

Accepted Answer

E1 → E2 and E2 → E4. Each junction connects adjacent exons in the mature fragment.

Question 12

A mature RNA fragment contains a mapped E2 → E3 junction. Which candidate isoform matches?

Mature exon orders, 5′ → 3′
A: E1 → E2 → E3
B: E1 → E3

Accepted Answer

Isoform A. It places E2 immediately before E3.

Question 13

An mRNA isoform skips a 7-base exon. Compared with the isoform that includes it, how does the RNA length change if everything else is identical?

Accepted Answer

It decreases by 7 bases. The difference is the length of the skipped exon.

Question 14

What does intron retention mean when comparing mature RNA isoforms?

Accepted Answer

A sequence removed as an intron in one splice form remains in another mature form.

Question 15

A mature RNA isoform keeps I1 and removes I2. Write this fragment 5′ → 3′.

Pre-mRNA 5′ → 3′
E1 GGAC | I1 GUACAG | E2 AUUC
I2 GUGAG | E3 CUGA

Accepted Answer

5′-GGACGUACAGAUUCCUGA-3′

Keep E1–I1–E2 together and join E2 to E3.

Question 16

E1 and E2 are joined in this mature RNA fragment. Write the two bases on each side of the junction, with | at the join.

Exon sequences, 5′ → 3′
E1 AGUAC
E2 GCUUA

Accepted Answer

5′-AC|GC-3′

Take the last two bases of E1 and the first two of E2.

Question 17

The entire modeled mature fragment is 5′-GAGCUUACC-3′. Which of the two splice forms below makes it?

Exon sequences, 5′ → 3′
E1 GAGC
E2 CUAG
E3 UUACC

A: E1 → E2 → E3
B: E1 → E3

Accepted Answer

Isoform B. Joining E1 directly to E3 gives GAGCUUACC.

Question 18

In a pre-mRNA, an intron spans bases 37 through 47, including both endpoints. Mature isoform A removes it, and B retains it. If the rest of the sequence is identical, which isoform is longer and by how many bases?

Accepted Answer

Isoform B is 11 bases longer. Counting both endpoints gives 47 − 37 + 1 = 11 retained bases.

Question 19

A fragment contains an intron sequence between its two flanking exons. Does that evidence alone establish that it came from a mature RNA isoform with intron retention?

Accepted Answer

No. The same stretch can occur in a precursor whose intron hasn’t been removed yet. You need evidence that the RNA is mature.

Question 20

A mature RNA fragment skips E2 and removes both neighboring introns. Write the fragment 5′ → 3′.

Pre-mRNA 5′ → 3′
E1 UCCA | I1 GUAUG | E2 AGCUA
I2 GUGCAG | E3 UAGG

Accepted Answer

5′-UCCAUAGG-3′

Only E1 and E3 contribute bases.

Question 21

In the spliced fragment below, which two base positions meet at the E1 → E2 junction? Count from 1 at the 5′ end.

Exon sequences, 5′ → 3′
E1 CAGUACU
E2 AGCC

Accepted Answer

Positions 7 and 8. E1 ends at base 7, and E2 starts at base 8.

Question 22

A fragment from one of these mature RNAs spans the mapped E1 → E2 junction. Can you tell which candidate it came from?

Mature exon orders, 5′ → 3′
A: E1 → E2 → E3 → E4
B: E1 → E2 → E4

Accepted Answer

No. Both contain E1 → E2. A junction such as E2 → E4 would distinguish B from A.

Question 23

The full mature fragment is 12 bases long. Which candidate order fits these exon lengths?

E1: 4 bases     E2: 5 bases
E3: 3 bases     E4: 5 bases

A: E1 → E2 → E4
B: E1 → E3 → E4

Accepted Answer

Isoform B. Its exons total 4 + 3 + 5 = 12 bases. Isoform A has 14.

Question 24

Read this mature RNA in triplets from the indicated AUG at its 5′ end. Which codon crosses the E1 → E2 junction?

Exon sequences, 5′ → 3′
E1 AUGG
E2 CCUUA

Accepted Answer

GCC. The second codon uses the last G of E1 and the first two Cs of E2.

Question 25

After splicing out the intron, a student writes 5′-CUUGAAGC-3′. What’s the correct mature fragment?

Pre-mRNA 5′ → 3′
E1 AAGC | I1 GUUGAG | E2 CUUG

Accepted Answer

5′-AAGCCUUG-3′

The proposed answer puts E2 before E1.

Question 26

E2 is skipped. Write the three bases just upstream and the one base just downstream of the new E1 → E3 junction, in 5′ → 3′ order. Mark the join with |.

Exon sequences, 5′ → 3′
E1 CUAGCU
E2 UGGG
E3 AUCGA

Accepted Answer

5′-GCU|A-3′

The left side comes from the end of E1, and the right side starts E3.

Question 27

A mature fragment has a mapped E1 → E4 junction. Which of these two candidate exon orders is compatible?

Mature exon orders, 5′ → 3′
A: E1 → E2 → E4
B: E1 → E3 → E4

Accepted Answer

Neither. Each candidate keeps an exon between E1 and E4.

Question 28

A student counts 10 RNA bases in 5′-GAUC|CUGAA-3′ by including the | that marks the join. What’s the base count?

Accepted Answer

9 bases. There are 4 bases before the junction and 5 after it.

Question 29

Two RNA isoforms have different exon junctions in their 5′ untranslated regions and identical translated sequences. Does the junction difference by itself imply different amino acid sequences?

Accepted Answer

No. Those junctions fall outside the translated sequence, so the two RNAs can encode the same amino acid sequence.

Question 30

This mature isoform retains I1 and removes I2. A student writes 5′-ACCGUGAGGCU-3′. What’s the correct fragment?

Pre-mRNA 5′ → 3′
E1 ACCG | I1 GUCUAG | E2 UGA
I2 GUAUAG | E3 GGCU

Accepted Answer

5′-ACCGGUCUAGUGAGGCU-3′

Restore the retained I1 sequence between E1 and E2.

Question 31

The bases in 5′-GAC|ACUUGU-3′ are correct, but the E1 → E2 marker is misplaced. Where should | go?

Exon sequences, 5′ → 3′
E1 GACA
E2 CUUGU

Accepted Answer

5′-GACA|CUUGU-3′

The boundary follows all four bases of E1.

Question 32

A short mature RNA fragment reads 5′-CGAC-3′. Does it distinguish these candidate isoforms?

Exon sequences, 5′ → 3′
E1 UCGACG
E2 AGUU
E3 CUCA

A: E1 → E2 → E3
B: E1 → E3

Accepted Answer

No. Both candidates contain CGAC inside their shared E1 sequence.

Question 33

A complete mature fragment is 13 bases long. Can length alone choose between these candidate exon orders?

E1: 5 bases     E2: 4 bases
E3: 4 bases     E4: 4 bases

A: E1 → E2 → E4
B: E1 → E3 → E4

Accepted Answer

No. Both total 13 bases. The sequence or a mapped junction could distinguish them.

Question 34

Translation starts at the AUG in E1. If the mature isoform skips E2, what codon immediately follows AUG?

Exon sequences, 5′ → 3′
E1 AUGU
E2 GCA
E3 UCAG

Accepted Answer

UUC. The codon uses the last U of E1 and the first two bases of E3.

Question 35

E1 lies entirely in the 5′ untranslated region. Both exons are kept and I1 is removed. Write the whole mature RNA fragment, 5′ → 3′.

Pre-mRNA 5′ → 3′
E1 UACGA | I1 GUAGAG | E2 AUGCCU

Accepted Answer

5′-UACGAAUGCCU-3′

Include the untranslated exon in the mature RNA.

Question 36

In this mature isoform I1 is retained and I2 is excised. Which exon–exon junction is formed within the shown fragment?

Pre-mRNA block order, 5′ → 3′
E1 → I1 → E2 → I2 → E3

Accepted Answer

E2 → E3. Retained I1 still lies between E1 and E2.

Question 37

A short mature RNA fragment reads 5′-AUGC-3′. Which candidate isoform or isoforms could contain it?

Exon sequences, 5′ → 3′
E1 CUCAU
E2 UAUGCA
E3 GCAU

A: E1 → E2 → E3
B: E1 → E3

Accepted Answer

Both. AUGC lies within E2 in A and crosses E1 → E3 in B.

Question 38

How many bases longer is mature fragment A than B?

Pre-mRNA order, 5′ → 3′
E1 (4) → I1 (6) → E2 (5) → I2 (7) → E3 (3)
A keeps E1, I1, E2, and E3.
B keeps E1 and E3 only.

Accepted Answer

11 bases longer. A includes the 6 bases of I1 and the 5 bases of E2 that B lacks.

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RNA Splicing Flashcards: Exon Junctions & Isoforms

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