2  structures 106  species 1881  sequences

Family: IRE_I (RF00037)

Description: Iron response element I

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.

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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:
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Download

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

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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

Selections

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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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Trees

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.

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_I family has been found.

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References

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

Literature references

  1. Hentze MW, Caughman SW, Rouault TA, Barriocanal JG, Dancis A, Harford JB, Klausner RD Science. 1987;238:1570-1573. Identification of the iron-responsive element for the translational regulation of human ferritin mRNA. PUBMED:3685996

  2. Sammarco MC, Ditch S, Banerjee A, Grabczyk E J Biol Chem. 2008;283:4578-4587. Ferritin L and H subunits are differentially regulated on a post-transcriptional level. PUBMED:18160403

  3. Zhang D, Albert DW, Kohlhepp P, D-Pham DQ, Winzerling JJ Insect Mol Biol. 2001;10:531-539. Repression of Manduca sexta ferritin synthesis by IRP1/IRE interaction. PUBMED:11903622

  4. Nichol H, Winzerling J Insect Biochem Mol Biol. 2002;32:1699-1710. Structured RNA upstream of insect cap distal iron responsive elements enhances iron regulatory protein-mediated control of translation. PUBMED:12429122

  5. Huang TS, Melefors O, Lind MI, Soderhall K Insect Biochem Mol Biol. 1999;29:1-9. An atypical iron-responsive element (IRE) within crayfish ferritin mRNA and an iron regulatory protein 1 (IRP1)-like protein from crayfish hepatopancreas. PUBMED:10070739

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 1,820
seed 61

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 23.44 -Z 549862.597050 --mxsize 128 CM SEQDB
Gathering cutoff 34.0
Trusted cutoff 34.0
Noise cutoff 33.9
Covariance model Download