Flavivirus xrRNAs

The exoribonuclease-resistant RNA elements (xrRNA) are described throughout all groups of flaviviruses. Usually, each virus harbors two xrRNAs, xrRNA1 and xrRNA2, in the beginning of the 3 UTR [1].

This clan contains 7 families and the total number of sequence regions in the clan is 9.

Literature references

1. Pijlman GP, Funk A, Kondratieva N, Leung J, Torres S, van der Aa L, Liu WJ, Palmenberg AC, Shi PY, Hall RA, Khromykh AA, Cell Host Microbe. 2008;4:579-591.: A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity. 19064258
2. Szucs MJ, Nichols PJ, Jones RA, Vicens Q, Kieft JS, mBio. 2020;11:e02352-e02320.: A New Subclass of Exoribonuclease-Resistant RNA Found in Multiple Genera of Flaviviridae. 32994331
3. Vicens Q, Kieft JS, Comput Struct Biotechnol J. 2021;19:4373-4380.: Shared properties and singularities of exoribonuclease-resistant RNAs in viruses. 34471487

Members

This clan contains the following 7 member families:

Flavi_TBFV_xrRNA Flavi_NKV_xrRNA Flavi_ISFV_xrRNA Flavi_xrRNA Flavi_xrRNA_1a Flavi_xrRNA_1b Flavi_xrRNA_2

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
Flavi_xrRNA_2 (RF04363)	0 (0.0%)	View
Flavi_xrRNA_1b (RF04362)	3 (33.3%)	View
Flavi_xrRNA_1a (RF04361)	6 (66.7%)	View
Flavi_xrRNA (RF03547)	0 (0.0%)	View
Flavi_ISFV_xrRNA (RF03541)	0 (0.0%)	View
Flavi_NKV_xrRNA (RF03539)	0 (0.0%)	View
Flavi_TBFV_xrRNA (RF03536)	0 (0.0%)	View