0  structures 0  species 0  sequences

Motif: HuR_binding (RM00009)

Description: HuR binding site

Summary

Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled ELAVL1 but we are unable to retrieve the article content at this time. More...

Alignments

You can either download the motif alignment or view it directly in your browser window. More...

Formatting options

You can view or download motif 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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Family matches

There are 21 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. 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 Family Accession Family Description Number of Hits Fraction of Hits Sum of Bits Image
3 RF00022 GcvB RNA 3 0.111 37.5 Match Image
3 RF00025 Ciliate telomerase RNA 2 0.100 27.4 Match Image
3 RF00028 Group I catalytic intron 3 0.250 38.9 Match Image
3 RF00096 U8 small nucleolar RNA 8 0.145 103.1 Match Image
3 RF00443 Small nucleolar RNA SNORA27 10 0.417 132.0 Match Image
3 RF00488 Yeast U1 spliceosomal RNA 3 0.600 36.9 Match Image
3 RF00563 Small nucleolar RNA SNORA53 14 0.500 173.6 Match Image
3 RF00630 Pseudomonas sRNA P26 6 0.222 72.4 Match Image
3 RF01050 Saccharomyces telomerase 5 0.385 70.8 Match Image
3 RF01249 Small nucleolar RNA snR190 2 0.200 26.0 Match Image
3 RF01263 Small nucleolar RNA snR191 2 0.182 27.4 Match Image
3 RF01265 Small nucleolar RNA snR42 2 0.400 27.4 Match Image
3 RF01272 Small nucleolar RNA snR86 2 0.400 28.0 Match Image
3 RF01583 small nucleolar RNA snoR01 2 0.667 25.6 Match Image
3 RF01590 small nucleolar RNA snoR14 2 0.500 26.5 Match Image
3 RF01794 sok antitoxin 22 0.242 307.3 Match Image
3 RF01848 ACEA small nucleolar RNA U3 6 0.214 73.9 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 11 0.121 158.5 Match Image
3 RF02076 Gammaproteobacterial sRNA STnc100 2 0.083 25.0 Match Image
3 RF02452 Bacillus sRNA ncr1575 4 0.138 49.4 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 27 0.307 520.5 Match Image

References

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

Literature references

  1. López de Silanes I, Zhan M, Lal A, Yang X, Gorospe M Proc Natl Acad Sci U S A. 2004;101:2987-92. Identification of a target RNA motif for RNA-binding protein HuR. PUBMED:14981256

  2. Dassi E, Zuccotti P, Leo S, Provenzani A, Assfalg M, D'Onofrio M, Riva P, Quattrone A Nucleic Acids Res. 2013 Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR. PUBMED:23376935

External database links

Curation and motif details

This section shows the detailed information about the Rfam motif. 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 Published; PMID:14981256
Structure source N/A
Type Specific Recognition Motif
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 9 17.00 37

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 12.0
Covariance model Download the Infernal CM for the motif here