0  structures 9  species 9  sequences

Family: Flavivirus-5UTR (RF03546)

Description: Flavivirus 5' UTR



This family is a member of clan (CL00129), which contains the following 3 members:

cHP DENV_SLA Flavivirus-5UTR

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Flavivirus 5' UTR. More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.



There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.


Formatting options

You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Alignment format:


Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

Secondary structure

This section shows a variety of different secondary structure representations for this family. More...

You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this RNA across different species. More...


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This page displays the predicted phylogenetic tree for the alignment. More...

This tree was built using the fasttree method.

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Note: You can also download the data file for the seed tree.

Motif matches

There are 3 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Motif Accession Motif Description Number of Hits Fraction of Hits Sum of Bits Image
7 RM00008 GNRA tetraloop 2 0.250 21.8 Match Image
7 RM00024 T-loop 3 0.375 30.0 Match Image
7 RM00030 U-turn motif 2 0.250 21.8 Match Image


This section shows the database cross-references that we have for this Rfam family.

Literature references

  1. 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. PUBMED:28587300

  2. Gebhard LG, Filomatori CV, Gamarnik AV Viruses. 2011;3:1739-1756. Functional RNA elements in the dengue virus genome. PUBMED:21994804

  3. 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. PUBMED:32292394

  4. Filomatori CV, Lodeiro MF, Alvarez DE, Samsa MM, Pietrasanta L, Gamarnik AV Genes Dev. 2006;20:2238-2249. A 5' RNA element promotes dengue virus RNA synthesis on a circular genome. PUBMED:16882970

  5. Yu L, Nomaguchi M, Padmanabhan R, Markoff L Virology. 2008;374:170-185. Specific requirements for elements of the 5' and 3' terminal regions in flavivirus RNA synthesis and viral replication. PUBMED:18234265

  6. Filomatori CV, Iglesias NG, Villordo SM, Alvarez DE, Gamarnik AV J Biol Chem. 2011;286:6929-6939. RNA sequences and structures required for the recruitment and activity of the dengue virus polymerase. PUBMED:21183683

  7. Alvarez DE, Lodeiro MF, Luduena SJ, Pietrasanta LI, Gamarnik AV J Virol. 2005;79:6631-6643. Long-range RNA-RNA interactions circularize the dengue virus genome. PUBMED:15890901

  8. Clyde K, Harris E; J Virol. 2006;80:2170-2182. RNA secondary structure in the coding region of dengue virus type 2 directs translation start codon selection and is required for viral replication. PUBMED:16474125

External database links

Curation and family details

This section shows the detailed information about the Rfam family. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.


Seed source Lamkiewicz K
Structure source Predicted; LocARNA 2.0.0RC8
Type Cis-reg;
Author Lamkiewicz KORCID logo
Alignment details
Alignment Number of
full 1
seed 8

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB
Gathering cutoff 80.0
Trusted cutoff 83.6
Noise cutoff 79.3
Covariance model Download