21  structures 0  species 0  sequences

Motif: UNCG (RM00029)

Description: UNCG 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 21 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 1I6U 16 - 21
2 1J5E 1134 - 1140
2 1KUQ 8 - 13
2 1NBS 152 - 157
2 1S72 136 - 142
2 1UN6 15 - 64
2 1YKV 220 - 225
2 1YLS 220 - 225
2 1ZHO 15 - 20
2 2AVY 1449 - 1454
2 2AW4 1533 - 1538
2 2HW8 15 - 20
2 2J01 1691 - 1696
2 3kyl E 6 - 19
2 1ekz B 9 - 22
2 1p6v B 22 - 35
2 3izz A 12 - 25
2 2gip A 8 - 21
2 1ikd A 3 - 16
2 1f6x A 8 - 21
2 2l3e A 14 - 27

Family matches

There are 201 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 RF00002 5.8S ribosomal RNA 7 0.115 75.5 Match Image
3 RF00003 U1 spliceosomal RNA 48 0.480 512.0 Match Image
3 RF00004 U2 spliceosomal RNA 32 0.154 365.3 Match Image
3 RF00009 Nuclear RNase P 31 0.267 397.0 Match Image
3 RF00010 Bacterial RNase P class A 155 0.338 2427.3 Match Image
3 RF00011 Bacterial RNase P class B 32 0.281 419.1 Match Image
3 RF00012 Small nucleolar RNA U3 32 0.368 343.7 Match Image
3 RF00015 U4 spliceosomal RNA 35 0.206 481.2 Match Image
3 RF00018 CsrB/RsmB RNA family 19 0.500 157.5 Match Image
3 RF00020 U5 spliceosomal RNA 57 0.317 676.5 Match Image
3 RF00022 GcvB RNA 10 0.370 105.7 Match Image
3 RF00023 transfer-messenger RNA 57 0.119 636.7 Match Image
3 RF00024 Vertebrate telomerase RNA 21 0.568 237.4 Match Image
3 RF00026 U6 spliceosomal RNA 113 0.601 1320.7 Match Image
3 RF00028 Group I catalytic intron 3 0.250 30.3 Match Image
3 RF00030 RNase MRP 10 0.152 140.0 Match Image
3 RF00032 Histone 3' UTR stem-loop 7 0.152 61.2 Match Image
3 RF00033 MicF RNA 2 0.500 21.0 Match Image
3 RF00034 RprA RNA 4 0.308 35.3 Match Image
3 RF00045 Small nucleolar RNA SNORA73 family 8 0.121 97.3 Match Image
3 RF00061 Hepatitis C virus internal ribosome entry site 25 0.316 281.2 Match Image
3 RF00066 U7 small nuclear RNA 9 0.184 96.3 Match Image
3 RF00080 yybP-ykoY leader 5 0.172 58.2 Match Image
3 RF00090 Small nucleolar RNA SNORA74 7 0.292 61.3 Match Image
3 RF00096 U8 small nucleolar RNA 13 0.236 163.1 Match Image
3 RF00103 mir-1 microRNA precursor family 4 0.061 32.9 Match Image
3 RF00106 RNAI 4 0.400 40.4 Match Image
3 RF00114 Ribosomal S15 leader 10 0.128 105.1 Match Image
3 RF00126 ryfA RNA 9 1.000 184.7 Match Image
3 RF00128 Glm Y RNA activator of glmS mRNA 2 0.118 19.7 Match Image
3 RF00149 Small nucleolar RNA Z103 3 0.250 40.6 Match Image
3 RF00156 Small nucleolar RNA SNORA70 4 0.093 38.3 Match Image
3 RF00171 Tombusvirus 5' UTR 2 0.222 21.8 Match Image
3 RF00174 Cobalamin riboswitch 50 0.116 643.4 Match Image
3 RF00175 Human immunodeficiency virus type 1 dimerisation initiation site 2 0.029 16.6 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 88 0.889 2261.3 Match Image
3 RF00190 Small nucleolar RNA SNORA16B/SNORA16A family 4 0.138 36.5 Match Image
3 RF00191 Small nucleolar RNA SNORA57 7 0.269 67.3 Match Image
3 RF00195 RsmY RNA family 7 0.636 136.9 Match Image
3 RF00215 Tombus virus defective interfering (DI) RNA region 3 10 0.357 92.0 Match Image
3 RF00252 Alfalfa mosaic virus coat protein binding (CPB) RNA 4 0.222 35.2 Match Image
3 RF00262 sar RNA 4 1.000 40.8 Match Image
3 RF00263 Small nucleolar RNA SNORA68 5 0.192 42.9 Match Image
3 RF00345 Small nucleolar RNA snoR1 3 0.231 29.3 Match Image
3 RF00373 Archaeal RNase P 10 0.143 116.1 Match Image
3 RF00391 RtT RNA 6 0.105 49.9 Match Image
3 RF00428 Small nucleolar RNA SNORA38 5 0.200 50.8 Match Image
3 RF00435 Repression of heat shock gene expression (ROSE) element 4 0.308 47.2 Match Image
3 RF00444 PrrF RNA 8 0.444 82.1 Match Image
3 RF00449 HIF-1 alpha IRES 5 0.294 57.1 Match Image
3 RF00452 mir-172 microRNA precursor family 2 0.182 17.2 Match Image
3 RF00472 Small nucleolar RNA snR55/Z10 3 0.500 32.6 Match Image
3 RF00480 HIV Ribosomal frameshift signal 59 0.407 595.2 Match Image
3 RF00488 Yeast U1 spliceosomal RNA 2 0.400 23.1 Match Image
3 RF00506 Threonine operon leader 3 0.120 28.4 Match Image
3 RF00513 Tryptophan operon leader 7 0.318 63.9 Match Image
3 RF00514 Histidine operon leader 3 0.091 25.6 Match Image
3 RF00515 PyrR binding site 10 0.244 97.4 Match Image
3 RF00519 suhB 38 0.437 474.1 Match Image
3 RF00548 U11 spliceosomal RNA 8 0.111 96.1 Match Image
3 RF00551 Bicoid 3'-UTR regulatory element 3 0.200 29.6 Match Image
3 RF00557 Ribosomal protein L10 leader 23 0.237 234.8 Match Image
3 RF00558 Ribosomal protein L20 leader 4 0.093 41.0 Match Image
3 RF00598 Small nucleolar RNA SNORA76 5 0.227 46.2 Match Image
3 RF00618 U4atac minor spliceosomal RNA 13 0.213 176.1 Match Image
3 RF00619 U6atac minor spliceosomal RNA 13 0.210 185.3 Match Image
3 RF00625 Pseudomonas sRNA P11 14 0.933 123.9 Match Image
3 RF00627 Pseudomonas sRNA P15 3 0.136 28.0 Match Image
3 RF00629 Pseudomonas sRNA P24 7 0.500 64.1 Match Image
3 RF00630 Pseudomonas sRNA P26 9 0.333 82.7 Match Image
3 RF00639 microRNA mir-515 6 0.150 60.5 Match Image
3 RF00648 microRNA MIR396 5 0.192 45.8 Match Image
3 RF00664 microRNA mir-223 2 0.105 17.8 Match Image
3 RF00668 microRNA mir-302 6 0.136 54.9 Match Image
3 RF00675 microRNA mir-145 11 0.846 132.2 Match Image
3 RF00717 microRNA mir-315 8 0.500 75.4 Match Image
3 RF00727 microRNA bantam 3 0.273 24.6 Match Image
3 RF00763 microRNA mir-339 3 0.214 24.6 Match Image
3 RF00779 microRNA MIR474 4 0.364 33.8 Match Image
3 RF00802 microRNA mir-207 2 0.333 18.5 Match Image
3 RF00957 microRNA mir-663 2 0.167 16.5 Match Image
3 RF00959 microRNA mir-612 3 0.500 27.7 Match Image
3 RF01015 microRNA mir-885 3 1.000 28.7 Match Image
3 RF01036 microRNA mir-567 3 0.333 26.4 Match Image
3 RF01066 6C RNA 3 0.167 27.5 Match Image
3 RF01067 ATPC RNA motif 5 0.056 67.7 Match Image
3 RF01084 Pseudoknot of tRNA-like structure 5 0.625 50.0 Match Image
3 RF01116 Cyanobacterial functional RNA 1 7 0.189 84.1 Match Image
3 RF01188 Small nucleolar RNA snR56 2 0.125 20.9 Match Image
3 RF01219 Small nucleolar RNA snoR100 2 0.222 27.9 Match Image
3 RF01227 Small nucleolar RNA snoR83 3 0.429 31.9 Match Image
3 RF01233 Small nucleolar RNA U109 3 0.115 32.5 Match Image
3 RF01234 Small nucleolar RNA SNORA47 6 0.300 55.6 Match Image
3 RF01243 Small nucleolar RNA snR33 4 0.800 32.4 Match Image
3 RF01267 Small nucleolar RNA snR37 2 0.222 39.2 Match Image
3 RF01268 Small Cajal body-specific RNA 2 9 0.450 113.8 Match Image
3 RF01318 CRISPR RNA direct repeat element 4 0.333 41.6 Match Image
3 RF01322 CRISPR RNA direct repeat element 2 0.286 23.7 Match Image
3 RF01386 isrB Hfq binding RNA 3 1.000 37.4 Match Image
3 RF01400 istR Hfq binding RNA 7 1.000 113.9 Match Image
3 RF01411 BsrF 7 0.636 74.8 Match Image
3 RF01470 Listeria sRNA rli38 6 0.300 49.8 Match Image
3 RF01473 Listeria sRNA rli41 5 0.833 47.9 Match Image
3 RF01496 A. fumigatus sRNA Afu_182 5 0.263 78.4 Match Image
3 RF01502 Fungal signal recognition particle RNA 15 0.300 288.2 Match Image
3 RF01509 A. fumigatus snoRNA Afu_300 6 0.600 71.6 Match Image
3 RF01512 A. fumigatus sRNA Afu_309 4 0.400 61.7 Match Image
3 RF01656 Nematode sRNA ceN72-3_ceN74-2 4 0.308 40.4 Match Image
3 RF01673 PhrS 11 0.846 198.7 Match Image
3 RF01675 Pseudomonas sRNA CrcZ 16 0.842 310.8 Match Image
3 RF01687 Acido-Lenti-1 RNA 26 0.299 229.7 Match Image
3 RF01693 Bacteroidales-1 RNA 34 0.829 395.5 Match Image
3 RF01694 Bacteroides-1 RNA 7 0.175 59.2 Match Image
3 RF01695 C4 antisense RNA 223 0.489 3216.5 Match Image
3 RF01702 Cyano-2 RNA 7 0.123 66.1 Match Image
3 RF01706 Gut-1 RNA 23 0.605 262.8 Match Image
3 RF01715 Pedo-repair RNA 2 0.333 16.8 Match Image
3 RF01716 PhotoRC-I RNA 56 0.862 616.9 Match Image
3 RF01719 Pseudomon-1/ErsA RNA 3 0.158 43.1 Match Image
3 RF01728 STAXI RNA 24 0.800 523.9 Match Image
3 RF01732 asd RNA 15 0.484 188.0 Match Image
3 RF01736 flg-Rhizobiales RNA 2 0.154 21.7 Match Image
3 RF01740 gyrA RNA 2 0.111 18.7 Match Image
3 RF01743 leu/phe leader RNA from Lactococcus 9 1.000 86.0 Match Image
3 RF01746 mraW RNA 6 0.133 76.4 Match Image
3 RF01748 nuoG RNA 2 0.065 19.0 Match Image
3 RF01752 psaA RNA 21 0.677 447.4 Match Image
3 RF01754 radC RNA 15 0.115 146.6 Match Image
3 RF01758 sucA-II RNA 5 0.294 43.2 Match Image
3 RF01762 Whalefall-1 RNA 6 0.429 78.7 Match Image
3 RF01766 cspA thermoregulator 13 0.867 139.9 Match Image
3 RF01772 Pseudomonas rnk leader 8 0.533 120.3 Match Image
3 RF01773 Pseudomonas rpsL leader 2 0.222 35.6 Match Image
3 RF01793 ffh sRNA 12 0.135 108.5 Match Image
3 RF01794 sok antitoxin 11 0.121 92.8 Match Image
3 RF01814 rhtB sRNA 4 0.286 38.8 Match Image
3 RF01819 RNA Staph. aureus D 7 0.875 67.5 Match Image
3 RF01820 RNA Staph. aureus E 6 0.400 69.7 Match Image
3 RF01830 Salmonella enterica Typhi npcRNA 44 7 0.206 93.4 Match Image
3 RF01838 sobemovirus ribosomal frameshift elemental 4 0.800 60.1 Match Image
3 RF01844 SmY spliceosomal RNA 7 0.115 81.6 Match Image
3 RF01846 Fungal small nucleolar RNA U3 36 0.545 552.6 Match Image
3 RF01847 Plant small nucleolar RNA U3 5 0.208 50.5 Match Image
3 RF01848 ACEA small nucleolar RNA U3 8 0.286 99.2 Match Image
3 RF01849 Alphaproteobacteria transfer-messenger RNA 39 0.351 433.5 Match Image
3 RF01850 Betaproteobacteria transfer-messenger RNA 5 0.714 109.2 Match Image
3 RF01851 Cyanobacteria transfer-messenger RNA 9 0.333 140.2 Match Image
3 RF01857 Archaeal signal recognition particle RNA 15 0.283 136.2 Match Image
3 RF01867 caulobacter sRNA CC2171 7 0.538 73.4 Match Image
3 RF01872 Maternally expressed 3 conserved region 2 2 0.125 22.5 Match Image
3 RF01927 microRNA MIR1222 2 0.400 19.1 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 59 0.686 1201.2 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 57 0.626 1238.7 Match Image
3 RF02025 microRNA mir-3017 9 0.250 76.6 Match Image
3 RF02030 tp2 8 0.333 73.2 Match Image
3 RF02032 Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA 7 0.200 82.8 Match Image
3 RF02036 IMES-3 RNA motif 15 0.469 132.6 Match Image
3 RF02051 Enterobacterial sRNA STnc450 4 0.333 36.1 Match Image
3 RF02065 Enterobacterial sRNA STnc340 3 0.750 26.4 Match Image
3 RF02069 Enterobacterial sRNA STnc70 4 2.000 40.2 Match Image
3 RF02075 Enterobacterial sRNA STnc230 3 0.273 25.4 Match Image
3 RF02076 Gammaproteobacterial sRNA STnc100 17 0.708 299.3 Match Image
3 RF02079 Enterobacterial sRNA STnc180 5 0.500 78.7 Match Image
3 RF02100 Translational regulator of tfoXVC 2 0.200 20.7 Match Image
3 RF02143 Hydatidiform mole associated and imprinted conserved region 1 2 0.125 21.6 Match Image
3 RF02144 rsmX 16 1.000 331.7 Match Image
3 RF02165 Pvt1 oncogene conserved region 2 3 0.176 26.6 Match Image
3 RF02168 Pvt1 oncogene conserved region 5 5 0.217 50.7 Match Image
3 RF02189 ST7 overlapping transcript 4 conserved region 3 2 0.100 20.9 Match Image
3 RF02198 TTC28 antisense RNA 1 conserved region 1 2 0.143 17.4 Match Image
3 RF02221 sRNA-Xcc1 16 0.216 191.1 Match Image
3 RF02225 Proteobacterial sRNA sX6 6 0.750 66.6 Match Image
3 RF02240 Xanthomonadaceae sRNA Xoo1 4 0.800 53.0 Match Image
3 RF02241 Xanthomonadaceae sRNA Xoo2 3 1.000 27.0 Match Image
3 RF02249 Six3os1 conserved region 4 6 0.857 99.7 Match Image
3 RF02276 Hammerhead ribozyme (type II) 4 0.167 60.7 Match Image
3 RF02342 Alphaproteobacterial sRNA ar7 15 0.517 158.4 Match Image
3 RF02343 Alphaproteobacterial sRNA ar9 6 0.214 71.1 Match Image
3 RF02344 Alphaproteobacterial ar14 16 0.136 151.8 Match Image
3 RF02345 Alphaproteobacterial ar15 10 0.164 104.8 Match Image
3 RF02354 Bradyrhizobiaceae sRNA BjrC80 3 0.200 48.0 Match Image
3 RF02355 Bradyrhizobiaceae sRNA BjrC174 2 0.133 18.6 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 4 0.160 40.6 Match Image
3 RF02371 PyrG leader 7 0.700 59.1 Match Image
3 RF02399 Nitrogen stress-induced RNA 1 2 0.118 38.0 Match Image
3 RF02402 A. fumigatus snoRNA Afu_263 10 0.526 119.2 Match Image
3 RF02405 Pseudomonas sRNA P34 2 0.400 31.2 Match Image
3 RF02423 Burkholderia sRNA Bp1_Cand871_SIPHT 15 1.000 179.2 Match Image
3 RF02424 Burkholderia sRNA Bp2_Cand287_SIPHT 10 0.714 97.3 Match Image
3 RF02442 Streptococcus sRNA SpF66 8 0.889 83.6 Match Image
3 RF02455 Dianthovirus RNA2 cap-independent translation element 2 1.000 20.6 Match Image
3 RF02462 Ascomycota telomerase RNA 4 1.000 100.3 Match Image
3 RF02471 Actinobacteria sRNA Ms_IGR-5 3 0.143 31.2 Match Image
3 RF02501 Rhizobiales sRNA Atu_C7 3 1.000 25.0 Match Image
3 RF02502 Rhizobiales sRNA Atu_C8 8 0.296 85.1 Match Image
3 RF02509 Pyrrolysine insertion sequence mtbB 2 0.087 19.5 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 81 0.890 2169.7 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 89 0.873 1992.0 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 79 0.898 2528.8 Match Image
3 RF02679 Pistol ribozyme 5 0.111 88.4 Match Image
3 RF02684 Type-P5 twister ribozyme 4 0.267 62.1 Match Image

References

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

Literature references

  1. Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB J Math Biol. 2008;56:215-52. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. PUBMED:17694311

  2. Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB Nucleic Acids Res. 2009;37:4898-918. Classification and energetics of the base-phosphate interactions in RNA. PUBMED:19528080

  3. Molinaro M, Tinoco I Nucleic Acids Res. 1995;23:3056-63. Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: thermodynamic and spectroscopic applications. PUBMED:7544890

  4. Leulliot N, Baumruk V, Abdelkafi M, Turpin PY, Namane A, Gouyette C, Huynh-Dinh T, Ghomi M Nucleic Acids Res. 1999;27:1398-404. Unusual nucleotide conformations in GNRA and UNCG type tetraloop hairpins: evidence from Raman markers assignments. PUBMED:9973632

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:19528080
Structure source N/A
Type Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 31 18.10 59

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 8.0
Covariance model Download the Infernal CM for the motif here