10  structures 11  species 87  sequences

Family: HIV-1_DIS (RF00175)

Description: Human immunodeficiency virus type 1 dimerisation initiation site


Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Retroviral Psi packaging element. 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...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


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.


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 structures on which the HIV-1_DIS family has been found.

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Motif matches

There are 1 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 RM00029 UNCG tetraloop 2 0.029 16.6 Match Image


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

Literature references

  1. McBride MS, Panganiban AT J Virol 1997;71:2050-2058. Position dependence of functional hairpins important for human immunodeficiency virus type 1 RNA encapsidation in vivo. PUBMED:9032337

  2. McBride MS, Schwartz MD, Panganiban AT J Virol 1997;71:4544-4554. Efficient encapsidation of human immunodeficiency virus type 1 vectors and further characterization of cis elements required for encapsidation. PUBMED:9151848

  3. McBride MS, Panganiban AT J Virol 1996;70:2963-2973. The human immunodeficiency virus type 1 encapsidation site is a multipartite RNA element composed of functional hairpin structures. PUBMED:8627772

  4. Gallego J, Greatorex J, Zhang H, Yang B, Arunachalam S, Fang J, Seamons J, Lea S, Pomerantz RJ, Lever AM J Biol Chem 2003;278:40385-40391. Rev binds specifically to a purine loop in the SL1 region of the HIV-1 leader RNA. PUBMED:12851400

  5. Lawrence DC, Stover CC, Noznitsky J, Wu Z, Summers MF J Mol Biol 2003;326:529-542. Structure of the intact stem and bulge of HIV-1 Psi-RNA stem-loop SL1. PUBMED:12559920

  6. Amarasinghe GK, De Guzman RN, Turner RB, Chancellor KJ, Wu ZR, Summers MF J Mol Biol 2000;301:491-511. NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition. PUBMED:10926523

  7. Pappalardo L, Kerwood DJ, Pelczer I, Borer PN J Mol Biol 1998;282:801-818. Three-dimensional folding of an RNA hairpin required for packaging HIV-1. PUBMED:9743628

  8. Kerwood DJ, Cavaluzzi MJ, Borer PN Biochemistry 2001;40:14518-14529. Structure of SL4 RNA from the HIV-1 packaging signal. PUBMED:11724565

  9. Berkhout B, van Wamel JL J Virol. 1996;70:6723-6732. Role of the DIS hairpin in replication of human immunodeficiency virus type 1. PUBMED:8794309

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 Bateman A
Structure source Published; PMID:8627772
Type Cis-reg;
Author Bateman AORCID logo, Daub JORCID logo
Alignment details
Alignment Number of
full 17
seed 70

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
Gathering cutoff 35.0
Trusted cutoff 35.0
Noise cutoff 34.9
Covariance model Download