1  structure 217  species 1202  sequences

Family: IRE_II (RF02253)

Description: Iron response element II

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Iron response element. More...

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

Sequences

Alignment

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.

Viewer:

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/view:

Download

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

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Click on a node to select that node and its sub-tree.

Clear selection

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...

Tree controls

Hide

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

Loading...

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.

Trees

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

This tree was built using the fasttree method.

Label the trees using or

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

Structures

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 IRE_II family has been found.

Loading structure mapping...

References

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

Literature references

  1. Koeller DM, Casey JL, Hentze MW, Gerhardt EM, Chan LN, Klausner RD, Harford JB Proc Natl Acad Sci U S A. 1989;86:3574-3578. A cytosolic protein binds to structural elements within the iron regulatory region of the transferrin receptor mRNA. PUBMED:2498873

  2. Lymboussaki A, Pignatti E, Montosi G, Garuti C, Haile DJ, Pietrangelo A J Hepatol. 2003;39:710-715. The role of the iron responsive element in the control of ferroportin1/IREG1/MTP1 gene expression. PUBMED:14568251

  3. Kohler SA, Henderson BR, Kuhn LC J Biol Chem. 1995;270:30781-30786. Succinate dehydrogenase b mRNA of Drosophila melanogaster has a functional iron-responsive element in its 5'-untranslated region. PUBMED:8530520

  4. Gunshin H, Allerson CR, Polycarpou-Schwarz M, Rofts A, Rogers JT, Kishi F, Hentze MW, Rouault TA, Andrews NC, Hediger MA FEBS Lett. 2001;509:309-316. Iron-dependent regulation of the divalent metal ion transporter. PUBMED:11741608

  5. Cmejla R, Petrak J, Cmejlova J Biochem Biophys Res Commun. 2006;341:158-166. A novel iron responsive element in the 3'UTR of human MRCKalpha. PUBMED:16412980

  6. Gray NK, Pantopoulos K, Dandekar T, Ackrell BA, Hentze MW Proc Natl Acad Sci U S A. 1996;93:4925-4930. Translational regulation of mammalian and Drosophila citric acid cycle enzymes via iron-responsive elements. PUBMED:8643505

  7. Dandekar T, Stripecke R, Gray NK, Goossen B, Constable A, Johansson HE, Hentze MW EMBO J. 1991;10:1903-1909. Identification of a novel iron-responsive element in murine and human erythroid delta-aminolevulinic acid synthase mRNA. PUBMED:2050126

  8. Sanchez M, Galy B, Dandekar T, Bengert P, Vainshtein Y, Stolte J, Muckenthaler MU, Hentze MW J Biol Chem. 2006;281:22865-22874. Iron regulation and the cell cycle: identification of an iron-responsive element in the 3'-untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy. PUBMED:16760464

  9. Sanchez M, Galy B, Muckenthaler MU, Hentze MW Nat Struct Mol Biol. 2007;14:420-426. Iron-regulatory proteins limit hypoxia-inducible factor-2alpha expression in iron deficiency. PUBMED:17417656

  10. Wingert RA, Galloway JL, Barut B, Foott H, Fraenkel P, Axe JL, Weber GJ, Dooley K, Davidson AJ, Schmid B, Paw BH, Shaw GC, Kingsley P, Palis J, Schubert H, Chen O, Kaplan J, Zon LI Nature. 2005;436:1035-1039. Deficiency of glutaredoxin 5 reveals Fe-S clusters are required for vertebrate haem synthesis. PUBMED:16110529

  11. Alen C, Sonenshein AL Proc Natl Acad Sci U S A. 1999;96:10412-10417. Bacillus subtilis aconitase is an RNA-binding protein. PUBMED:10468622

  12. Kohler SA, Menotti E, Kuhn LC J Biol Chem. 1999;274:2401-2407. Molecular cloning of mouse glycolate oxidase. High evolutionary conservation and presence of an iron-responsive element-like sequence in the mRNA. PUBMED:9891009

  13. Lin E, Graziano JH, Freyer GA J Biol Chem. 2001;276:27685-27692. Regulation of the 75-kDa subunit of mitochondrial complex I by iron. PUBMED:11313346

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.

Curation

Seed source Leipuviene, R. and Theil, E.C.
Structure source Published; PMID:17849083
Type Cis-reg;
Author Stevens S, Gardner PPORCID logo, Brown C
Alignment details
Alignment Number of
sequences
full 1,173
seed 29

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 25.45 -Z 549862.597050 CM SEQDB
Gathering cutoff 27.0
Trusted cutoff 27.0
Noise cutoff 26.9
Covariance model Download