3  structures 0  species 0  sequences

Motif: UMAC (RM00028)

Description: UMAC tetraloop

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 Tetraloop 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:
Download/view:

Structures

There are 3 PDB entires which have been used to build the motif model.

The table of results below may be sorted by clicking on the column titles, or restored to the original order here.

Original order PDB ID PDB chain ID PDB Residues
2 4A4S A 1 - 22
2 4A4R A 1 - 22
2 1JJ2 0 242 - 266

Family matches

There are 17 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 RF00102 VA RNA 21 0.389 296.5 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 31 0.313 428.7 Match Image
3 RF00195 RsmY RNA family 3 0.273 39.9 Match Image
3 RF00444 PrrF RNA 3 0.167 36.5 Match Image
3 RF00822 microRNA mir-274 2 0.286 25.7 Match Image
3 RF01066 6C RNA 2 0.111 27.0 Match Image
3 RF01405 STnc490 Hfq binding RNA 67 0.882 853.1 Match Image
3 RF01687 Acido-Lenti-1 RNA 34 0.391 571.2 Match Image
3 RF01772 Pseudomonas rnk leader 4 0.267 49.7 Match Image
3 RF01820 RNA Staph. aureus E 4 0.267 52.7 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 10 0.116 164.0 Match Image
3 RF02033 HNH endonuclease-associated RNA and ORF (HEARO) RNA 19 0.173 309.2 Match Image
3 RF02068 Enterobacterial sRNA STnc480 4 0.667 48.8 Match Image
3 RF02278 Betaproteobacteria toxic small RNA 6 0.118 85.9 Match Image
3 RF02399 Nitrogen stress-induced RNA 1 2 0.118 26.9 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 18 0.198 243.8 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 11 0.125 219.5 Match Image

References

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

Literature references

  1. Zhao Q, Huang HC, Nagaswamy U, Xia Y, Gao X, Fox GE Biopolymers. 2012;97:617-28. UNAC tetraloops: to what extent do they mimic GNRA tetraloops? PUBMED:22605553

  2. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, Pande N, Shang Z, Yu N, Gutell RR BMC Bioinformatics. 2002;3:2. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. PUBMED:11869452

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:22605553
Structure source N/A
Type Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 14 15.86 67

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