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Clan: C4-antisense-RNA (CL00128)


C4-antisense-RNA clan

The c4 antisense RNA clan include c4 antisense RNA RF01695, variant c4-2 antisense RNA RF02944 and variant c4-a1b1 antisense RNA RF03163. c4 antisense RNAs are used by phagues to inhibit the synthesis of antirepressor genes. It is proposed that c4 antisense RNAs are responsible for heteroimmunity in phagues.

This clan contains 3 families and the total number of sequence regions in the clan is 2,610.

Literature references

  1. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR;, Genome Biol. 2010;11:R31.: Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes. 20230605
  2. Weinberg Z, Lunse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR, Nucleic Acids Res. 2017;45:10811-10823.: Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. 28977401


This clan contains the following 3 member families:

C4 c4-2 c4-a1b1

Secondary structures

This tool allows you to view the secondary structure images of two clan members side-by-side. Choose the family structures using the two drop-down menus below.


The table below shows the number of occurrences of each family throughout the sequence database. In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this family. The rightmost column provides a link to the alignments tab for each family.

Rfam family Num. regions Alignment
c4-a1b1 (RF03163) 380 (14.6%) View
c4-2 (RF02944) 72 (2.8%) View
C4 (RF01695) 2,158 (82.7%) View