3  structures 0  species 0  sequences

Clan: Flavivirus-5UTR (CL00129)


Flavivirus 5' UTR clan

The Flavivirus 5'-SLA clan contains the RNA families: RF02340 SLA_Flavivirus and RF03546 Flavivirus-5UTR

This clan contains 3 families and the total number of sequence regions in the clan is 176.

Literature references

  1. Lodeiro MF, Filomatori CV, Gamarnik AV, J Virol. 2009;83:993-1008.: Structural and functional studies of the promoter element for dengue virus RNA replication. 19004935
  2. Lee E, Bujalowski PJ, Teramoto T, Gottipati K, Scott SD, Padmanabhan R, Choi KH, Nat Commun. 2021;12:2530.: Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase. 33953197
  3. Ng WC, Soto-Acosta R, Bradrick SS, Garcia-Blanco MA, Ooi EE, Viruses. 2017; [Epub ahead of print]: The 5' and 3' Untranslated Regions of the Flaviviral Genome. 28587300
  4. Zeng M, Duan Y, Zhang W, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, Chen S, Cheng A, Front Microbiol. 2020;11:473.: Universal RNA Secondary Structure Insight Into Mosquito-Borne Flavivirus (MBFV) cis-Acting RNA Biology. 32292394


This clan contains the following 3 member families:

cHP DENV_SLA Flavivirus-5UTR


For those sequences which have a structure in the Protein DataBank, we generate a mapping between EMBL, PDB and Rfam coordinate systems. The table below shows the mapping between the Rfam families in this clan, the corresponding EMBL entries, and the region of the three-dimensional structures that are available for that sequence.

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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
Flavivirus-5UTR (RF03546) 1 (0.6%) View
DENV_SLA (RF02340) 83 (47.2%) View
cHP (RF00617) 92 (52.3%) View