30

Task 2.2

There are also certain RNA motifs, also called regulatory RNA elements, that perform a spe­

cific function. Name and explain different RNA elements, such as IREs or riboswitches.

Task 2.3

What criteria do I have to consider in order to analyze an RNA (RNA molecule) for

RNA motifs?

Task 2.4

Explain how to identify regulatory RNA elements.

Task 2.5

Which of the following statements about regulatory RNA elements is correct (multiple

answers possible)?

(A) Regulatory RNA elements are not found in humans.

(B) For RNA motif searches, it’s enough if I just look at the sequence.

(C) I can find many RNA families in the Rfam database.

(D) IRE and riboswitches are examples of regulatory RNA elements.

(E) It is best to combine several criteria (sequence, structure and energy) for an RNA

motif search.

Task 2.6

Example: Find by hand (Ctrl + F or grep or Perl script) a typical conserved IRE motif

(CAGUGN or CAGTGN) in the following sequence:

> RNAanalyzer.

A T A A G A G A C C A C A A G C G A C C C G C A G G G C C A G A C G T T C T T C G C C G A G A G T C G

TCGGGGTTTCCTGCTTCAACAGTGCTTGGACGGAACCCGGCGCTCGTTCCCCACCCC

GGCCGGCCGCCCATAGCCAGCCCTCCGTCACCTCTTCACCGCACCCTCGGACTGCCCC

A A G G C C C C C G C C G C C G C T C C A G C G C C G C G C A G C C A C C G C C G C C G C C G C C G C C T C

T C C T T A G T C G C C G C C A T G A C G A C C G C G T C C A C C T C G C A G G T G C G C C A G A A C T A C C

A C C A G G A C T C A G A G G C C G C C A T C A A C C G C C A G A T C A A C C T G G A G C T C T A C G C C

T C C T A C G T T T A C C T G T C C A T G T C T T A C T A C T T T G A C C G C G A T G A T G T G G C T T T

G A A G A A C T T T G C C A A A T A C T T T C T T C A C C A A T C T C A T G A G G A G A G G G A A C A T

G C T G A G A A A C T G A T G A A G C T G C A G A A C C A A C G A G G T G G C C G A A T C T T C C T T

C A G G A T A T C A A G A A A C C A G A C T G T G A T G A C T G G G A G A G C G G G C T G A A T G C A

A T G G A G T G T G C A T T A C A T T T G G A A A A A A A T G T G A A T C A G T C A C T A C T G G A A C T G C A

C A A A C T G G C C A C T G A C A A A A A T G A C C C C C A T T T G T G T G A C T T C A T T G A G A C A C A T

TACCTGAATGAGCAGGTGAAAGCCATCAAAGAATTGGGTGACCACGTGACCAACTTGCGCAA

GATGGGAGCGCCCGAATCTGGCTTGGCGGAATATCTCTTTGACAAGCACACCCTGGGAG

A C A G T G A T A A T G A A A G C T A A G C C T C G G G C T A A T T T C C C C A T A G C C G T G G G G T G A C T

TCCCTGGTCACCAAGGCAGTGCATGCATGTTGGGGTTTCCTTTACCTTTTCTATAAG

T T G T A C C A A A A C A T C C A C T T A A G T T C T T T G A T T T G T A C C A T T C C T T C A A A T A A A G

AAATTTGGTACCCAGGTGTTGTCTTTGAGGTCTTGGGATGAATCAGAAATCTATCCAGGC

TATCTTCCAGATTCCTTAAGTGCCGTTGT

2  Magic RNA