Togavirus 5' plus strand cis-regulatory element

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Togavirus 5' plus strand cis-regulatory element
Predicted secondary structure and sequence conservation of Toga_5_CRE
Rfam RF00470
Other data
RNA type Cis-reg
Domain(s) Viruses
SO 0000233
PDB structures PDBe

The Togavirus 5' plus strand cis-regulatory element is an RNA element which is thought to be essential for both plus and minus strand RNA synthesis. [1]

Togaviridae is a family of viruses. Humans, mammals, birds, and mosquitoes serve as natural hosts. Currently, 31 species are placed in this family in a single genus. Diseases associated with alphaviruses include arthritis and encephalitis.

Cis-regulatory elements (CREs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphogenesis, the development of anatomy, and other aspects of embryonic development, studied in evolutionary developmental biology.

Genus Alphavirus belongs to the family Togaviridae. Alpha viruses contain secondary structural motifs in the 5' UTR that allow them to avoid detection by IFIT1. [2]

<i>Alphavirus</i> genus of viruses

In biology and immunology, an Alphavirus belongs to group IV of the Baltimore classification of the Togaviridae family of viruses, according to the system of classification based on viral genome composition introduced by David Baltimore in 1971. Alphaviruses, like all other group IV viruses, have a positive sense, single-stranded RNA genome. There are thirty alphaviruses able to infect various vertebrates such as humans, rodents, fish, birds, and larger mammals such as horses as well as invertebrates. Transmission between species and individuals occurs mainly via mosquitoes, making the alphaviruses a member of the collection of arboviruses – or arthropod-borne viruses. Alphavirus particles are enveloped, have a 70 nm diameter, tend to be spherical, and have a 40 nm isometric nucleocapsid.

IFIT1 protein-coding gene in the species Homo sapiens

Interferon-induced protein with tetratricopeptide repeats 1 is a protein that in humans is encoded by the IFIT1 gene.

See also

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Bamboo mosaic potexvirus (BaMV) cis-regulatory element

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Bamboo mosaic virus satellite RNA cis-regulatory element

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Enteroviral 3 UTR element

In molecular biology, the enteroviral 3' UTR element is an RNA structure found in the 3' UTR of various enteroviruses. The overall structure forms the origin of replication (OriR) for the initiation of (-) strand RNA synthesis. Pseudoknots have also been predicted in this structure.

Enterovirus 5 cloverleaf cis-acting replication element

The Enterovirus 5' cloverleaf cis-acting replication element is an RNA element found in the 5' UTR of Enterovirus genomes. The element has a cloverleaf like secondary structure and is known to be a multifunctional cis-acting replication element (CRE), required for the initiation of negative strand RNA synthesis.

Enterovirus cis-acting replication element

Enterovirus cis-acting replication element is a small RNA hairpin in the coding region of protein 2C as the site in PV1(M) RNA that is used as the primary template for the in vitro uridylylation. The first step in the replication of the plus-stranded poliovirus RNA is the synthesis of a complementary minus strand. This process is initiated by the covalent attachment of uridine monophosphate (UMP) to the terminal protein VPg, yielding VPgpU and VPgpUpU.

Equine arteritis virus leader TRS hairpin (LTH)

The equine arteritis virus leader transcription-regulating sequence hairpin (LTH) is as RNA element that is thought to be a key structural element in discontinuous subgenomic RNA synthesis and is critical for leader transcription-regulating sequences (TRS) function. Similar structures have been predicted in other arteriviruses and coronaviruses.

Potato virus X cis-acting regulatory element

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Rotavirus cis-acting replication element

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Rubella virus 3 cis-acting element

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Human rhinovirus internal cis-acting regulatory element

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Tombusvirus 3 UTR region IV

Tombusvirus 3' UTR is an important cis-regulatory region of the Tombus virus genome.

Tombusvirus 5 UTR

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Turnip crinkle virus (TCV) repressor of minus strand synthesis H5

The TCV hairpin 5 (H5) is an RNA element found in the turnip crinkle virus. This RNA element is composed of a stem-loop that contains a large symmetrical internal loop (LSL). H5 can repress minus-strand synthesis when the 3' side of the LSL pairs with the 4 bases at the 3'-terminus of the RNA(GCCC-OH).


The Upstream pseudoknot (UPSK) domain is an RNA element found in the turnip yellow mosaic virus, beet virus Q, barley stripe mosaic virus and tobacco mosaic virus, which is thought to be needed for efficient transcription. Disruption of the pseudoknot structure gives rise to a 50% drop in transcription efficiency. This element acts in conjunction with the Tymovirus/Pomovirus tRNA-like 3' UTR element to enhance translation.

Cis-acting replication elements bring together the 5' and 3' ends during replication of positive-sense single-stranded RNA viruses and double-stranded RNA viruses.


  1. Frolov I, Hardy R, Rice CM (November 2001). "Cis-acting RNA elements at the 5' end of Sindbis virus genome RNA regulate minus- and plus-strand RNA synthesis". RNA. 7 (11): 1638–1651. doi:10.1017/S135583820101010X. PMC   1370205 . PMID   11720292.
  2. Hyde JL, Gardner CL, Kimura T, White JP, Liu G, Trobaugh DW, Huang C, Tonelli M, Paessler S, Takeda K, Klimstra WB, Amarasinghe GK, Diamond MS (February 2014). "A viral RNA structural element alters host recognition of nonself RNA". Science. 343 (6172): 783–787. doi:10.1126/science.1248465. PMC   4209899 . PMID   24482115.

Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families.