46  structures 0  species 0  sequences

Motif: GNRA (RM00008)

Description: GNRA 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:
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Structures

There are 46 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 3OWI A 41 - 61
2 2CDM B 2 - 17
2 1C04 13 - 18
2 1G1X 588 - 651
2 1GRZ 149 - 154
2 1HMH 104 - 114
2 1HQ1 153 - 158
2 1HR2 149 - 154
2 1J5E 1012 - 1017
2 1JID 146 - 151
2 1KH6 28 - 33
2 1KXK 33 - 38
2 1L9A 146 - 151
2 1LNG 208 - 213
2 1M5O 74 - 79
2 1MFQ 197 - 202
2 1MME 154 - 164
2 1MZP 25 - 30
2 1NBS 204 - 209
2 1NYI 111 - 116
2 1Q96 13 - 18
2 1Q9A 2658 - 2663
2 1QZW 201 - 206
2 1RLG 9 - 14
2 1S72 1054 - 1060
2 1U6B 23 - 28
2 1U9S 204 - 209
2 1UN6 82 - 94
2 1X8W 149 - 154
2 1Y0Q 101 - 106
2 1Y69 2353 - 2358
2 2A2E 178 - 183
2 2AVY 1012 - 1017
2 2AW4 1222 - 1227
2 2BTE 46 - 51
2 2EZ6 11 - 16
2 2GIS 49 - 54
2 2J01 1222 - 1227
2 2NZ4 108 - 113
2 2OIU 10 - 15
2 2PXL 153 - 158
2 2R8S 149 - 154
2 2V3C 208 - 213
2 2Z75 113 - 118
2 430D 13 - 18
2 488D 154 - 164

Family matches

There are 369 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 RF00001 5S ribosomal RNA 279 0.392 2678.1 Match Image
3 RF00004 U2 spliceosomal RNA 18 0.087 162.3 Match Image
3 RF00007 U12 minor spliceosomal RNA 11 0.177 125.0 Match Image
3 RF00008 Hammerhead ribozyme (type III) 8 0.098 81.7 Match Image
3 RF00009 Nuclear RNase P 49 0.422 580.3 Match Image
3 RF00010 Bacterial RNase P class A 453 0.989 17762.2 Match Image
3 RF00011 Bacterial RNase P class B 102 0.895 2028.5 Match Image
3 RF00012 Small nucleolar RNA U3 16 0.184 174.1 Match Image
3 RF00013 6S / SsrS RNA 33 0.221 312.3 Match Image
3 RF00014 DsrA RNA 3 0.600 24.0 Match Image
3 RF00017 Metazoan signal recognition particle RNA 71 0.780 1144.2 Match Image
3 RF00018 CsrB/RsmB RNA family 23 0.605 261.7 Match Image
3 RF00021 Spot 42 RNA 11 0.579 103.0 Match Image
3 RF00022 GcvB RNA 8 0.296 98.0 Match Image
3 RF00023 transfer-messenger RNA 153 0.321 1591.1 Match Image
3 RF00024 Vertebrate telomerase RNA 14 0.378 179.1 Match Image
3 RF00028 Group I catalytic intron 10 0.833 178.6 Match Image
3 RF00029 Group II catalytic intron 77 0.837 991.9 Match Image
3 RF00030 RNase MRP 33 0.500 351.5 Match Image
3 RF00040 RNase E 5' UTR element 6 1.000 59.5 Match Image
3 RF00050 FMN riboswitch (RFN element) 30 0.208 312.3 Match Image
3 RF00062 HgcC family RNA 5 1.000 55.8 Match Image
3 RF00064 HgcG RNA 4 0.800 69.4 Match Image
3 RF00066 U7 small nuclear RNA 3 0.061 25.3 Match Image
3 RF00078 MicA sRNA 8 0.471 69.9 Match Image
3 RF00079 OmrA-B family 11 0.478 124.4 Match Image
3 RF00080 yybP-ykoY leader 8 0.276 71.3 Match Image
3 RF00082 SraG RNA 3 0.429 23.2 Match Image
3 RF00083 GlmZ RNA activator of glmS mRNA 5 0.238 37.3 Match Image
3 RF00084 CsrC RNA family 2 0.500 22.1 Match Image
3 RF00096 U8 small nucleolar RNA 5 0.091 56.5 Match Image
3 RF00099 Small nucleolar RNA SNORD22 11 0.224 91.5 Match Image
3 RF00100 7SK RNA 3 0.067 29.9 Match Image
3 RF00101 SraC/RyeA RNA 10 0.769 133.0 Match Image
3 RF00102 VA RNA 12 0.222 95.3 Match Image
3 RF00107 FinP 3 0.500 26.3 Match Image
3 RF00113 Short Intergenic Abundant RNA 4 0.235 36.0 Match Image
3 RF00126 ryfA RNA 8 0.889 91.3 Match Image
3 RF00127 t44 RNA 13 0.167 140.7 Match Image
3 RF00142 Small nucleolar RNA Z118/Z121/Z120 4 0.571 41.1 Match Image
3 RF00156 Small nucleolar RNA SNORA70 13 0.302 100.6 Match Image
3 RF00162 SAM riboswitch (S box leader) 63 0.145 669.2 Match Image
3 RF00166 PrrB/RsmZ RNA family 8 0.216 97.9 Match Image
3 RF00168 Lysine riboswitch 18 0.383 168.1 Match Image
3 RF00169 Bacterial small signal recognition particle RNA 102 0.391 850.9 Match Image
3 RF00174 Cobalamin riboswitch 175 0.407 2194.2 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 99 1.000 8325.7 Match Image
3 RF00191 Small nucleolar RNA SNORA57 4 0.154 33.1 Match Image
3 RF00199 SL2 RNA 21 0.700 224.8 Match Image
3 RF00222 Bag-1 internal ribosome entry site (IRES) 13 0.867 142.4 Match Image
3 RF00223 bip internal ribosome entry site (IRES) 6 0.667 47.6 Match Image
3 RF00224 FGF-2 internal ribosome entry site (IRES) 5 0.833 45.6 Match Image
3 RF00226 n-myc internal ribosome entry site (IRES) 4 0.667 34.8 Match Image
3 RF00229 Picornavirus internal ribosome entry site (IRES) 37 0.402 378.2 Match Image
3 RF00230 T-box leader 10 0.208 98.3 Match Image
3 RF00233 Tymovirus/Pomovirus/Furovirus tRNA-like 3' UTR element 2 0.071 15.7 Match Image
3 RF00234 glmS glucosamine-6-phosphate activated ribozyme 11 0.611 125.7 Match Image
3 RF00239 mir-124 microRNA precursor family 4 0.071 34.3 Match Image
3 RF00261 L-myc internal ribosome entry site (IRES) 11 1.000 239.7 Match Image
3 RF00286 Small Cajal body specific RNA 8 3 0.136 28.6 Match Image
3 RF00302 Small nucleolar RNA SNORA65 2 0.143 16.4 Match Image
3 RF00350 Small nucleolar RNA Z152/R70/R12/ 3 0.333 26.6 Match Image
3 RF00357 Small nucleolar RNA R44/J54/Z268 family 5 0.172 40.2 Match Image
3 RF00368 sroB RNA 16 1.000 261.4 Match Image
3 RF00369 sroC RNA 2 0.333 16.8 Match Image
3 RF00373 Archaeal RNase P 59 0.843 1238.6 Match Image
3 RF00379 ydaO/yuaA leader 26 0.245 300.0 Match Image
3 RF00380 ykoK leader 114 0.726 1177.8 Match Image
3 RF00391 RtT RNA 17 0.298 158.6 Match Image
3 RF00397 Small nucleolar RNA SNORA14 3 0.167 24.7 Match Image
3 RF00405 Small nucleolar RNA SNORA44 9 0.333 80.9 Match Image
3 RF00408 Small nucleolar RNA SNORA1 3 0.103 26.0 Match Image
3 RF00415 Small nucleolar RNA SNORA30/SNORA37 family 2 0.182 15.5 Match Image
3 RF00419 Small nucleolar RNA SNORA52 2 0.095 25.4 Match Image
3 RF00423 Small Cajal body specific RNA 4 2 0.083 16.4 Match Image
3 RF00427 Small Cajal body specific RNA 23 4 0.222 29.9 Match Image
3 RF00428 Small nucleolar RNA SNORA38 4 0.160 37.9 Match Image
3 RF00431 Small nucleolar RNA SNORA55 6 0.207 55.6 Match Image
3 RF00435 Repression of heat shock gene expression (ROSE) element 6 0.462 65.2 Match Image
3 RF00438 Small nucleolar RNA SNORA33 4 0.143 40.1 Match Image
3 RF00442 ykkC-yxkD leader 22 0.227 250.5 Match Image
3 RF00444 PrrF RNA 13 0.722 144.4 Match Image
3 RF00448 Epstein-Barr virus nuclear antigen (EBNA) IRES 2 0.333 23.4 Match Image
3 RF00449 HIF-1 alpha IRES 5 0.294 50.1 Match Image
3 RF00461 Vascular endothelial growth factor (VEGF) IRES A 7 1.000 110.9 Match Image
3 RF00480 HIV Ribosomal frameshift signal 93 0.641 763.5 Match Image
3 RF00485 Potassium channel RNA editing signal 23 0.271 218.9 Match Image
3 RF00489 ctRNA 8 0.800 87.8 Match Image
3 RF00490 S-element 8 0.276 83.5 Match Image
3 RF00504 Glycine riboswitch 7 0.159 66.9 Match Image
3 RF00506 Threonine operon leader 16 0.640 131.7 Match Image
3 RF00512 Leucine operon leader 5 0.833 37.1 Match Image
3 RF00514 Histidine operon leader 7 0.212 89.8 Match Image
3 RF00515 PyrR binding site 10 0.244 81.0 Match Image
3 RF00516 ylbH leader 2 0.667 23.5 Match Image
3 RF00517 serC leader 13 0.186 112.8 Match Image
3 RF00519 suhB 35 0.402 388.2 Match Image
3 RF00523 Prion pseudoknot 64 0.432 634.2 Match Image
3 RF00525 Flavivirus DB element 34 0.306 278.6 Match Image
3 RF00542 Small nucleolar RNA psi28S-1192 3 0.200 28.8 Match Image
3 RF00547 TrkB IRES 5 0.312 48.6 Match Image
3 RF00548 U11 spliceosomal RNA 12 0.167 98.1 Match Image
3 RF00549 c-sis internal ribosome entry site (IRES) 8 0.800 78.8 Match Image
3 RF00552 rncO 5 0.278 55.1 Match Image
3 RF00557 Ribosomal protein L10 leader 17 0.175 147.7 Match Image
3 RF00558 Ribosomal protein L20 leader 17 0.395 186.2 Match Image
3 RF00562 Small nucleolar RNA SNORA49 2 0.095 17.2 Match Image
3 RF00564 Small Cajal body specific RNA 11 2 0.083 16.4 Match Image
3 RF00567 Small nucleolar RNA SNORD17 3 0.158 24.0 Match Image
3 RF00598 Small nucleolar RNA SNORA76 14 0.636 119.2 Match Image
3 RF00602 Small Cajal body specific RNA 21 3 0.125 31.3 Match Image
3 RF00603 Small nucleolar RNA SNORD23 5 0.333 43.2 Match Image
3 RF00613 Small nucleolar RNA SNORD94 3 0.143 25.7 Match Image
3 RF00618 U4atac minor spliceosomal RNA 9 0.148 76.2 Match Image
3 RF00620 Hepatitis C alternative reading frame stem-loop 11 0.306 78.4 Match Image
3 RF00625 Pseudomonas sRNA P11 11 0.733 186.2 Match Image
3 RF00627 Pseudomonas sRNA P15 21 0.955 185.9 Match Image
3 RF00628 Pseudomonas sRNA P16 9 0.333 74.5 Match Image
3 RF00629 Pseudomonas sRNA P24 6 0.429 66.5 Match Image
3 RF00630 Pseudomonas sRNA P26 10 0.370 95.6 Match Image
3 RF00634 S-adenosyl methionine (SAM) riboswitch, 11 0.275 93.8 Match Image
3 RF00639 microRNA mir-515 4 0.100 33.9 Match Image
3 RF00644 microRNA mir-27 4 0.125 32.3 Match Image
3 RF00654 microRNA mir-216 5 0.152 42.8 Match Image
3 RF00686 microRNA mir-338 2 0.095 20.1 Match Image
3 RF00718 microRNA mir-431 9 1.000 136.8 Match Image
3 RF00746 microRNA mir-454 4 0.235 32.1 Match Image
3 RF00758 microRNA mir-346 5 1.000 39.9 Match Image
3 RF00770 microRNA mir-330 3 0.500 40.3 Match Image
3 RF00779 microRNA MIR474 5 0.455 44.5 Match Image
3 RF00784 microRNA mir-486 10 0.833 82.9 Match Image
3 RF00871 microRNA mir-689 6 0.462 56.8 Match Image
3 RF00957 microRNA mir-663 4 0.333 36.4 Match Image
3 RF00959 microRNA mir-612 3 0.500 26.4 Match Image
3 RF00960 microRNA mir-661 2 0.500 18.8 Match Image
3 RF01008 microRNA mir-636 4 0.800 43.2 Match Image
3 RF01010 microRNA mir-632 8 0.500 80.3 Match Image
3 RF01016 microRNA mir-584 2 0.125 14.7 Match Image
3 RF01036 microRNA mir-567 3 0.333 24.9 Match Image
3 RF01051 Cyclic di-GMP-I riboswitch 86 0.555 955.8 Match Image
3 RF01052 Arthropod 7SK RNA 6 0.316 42.4 Match Image
3 RF01055 Moco (molybdenum cofactor) riboswitch 126 0.787 1315.5 Match Image
3 RF01059 microRNA mir-598 3 0.125 29.0 Match Image
3 RF01066 6C RNA 8 0.444 68.9 Match Image
3 RF01069 purD RNA motif 8 0.381 83.9 Match Image
3 RF01070 SucA RNA motif 7 0.200 66.1 Match Image
3 RF01071 Ornate Large Extremophilic RNA 19 0.950 457.0 Match Image
3 RF01084 Pseudoknot of tRNA-like structure 4 0.500 50.0 Match Image
3 RF01116 Cyanobacterial functional RNA 1 7 0.189 69.8 Match Image
3 RF01196 Small nucleolar RNA Z30a 10 1.000 125.4 Match Image
3 RF01208 Small nucleolar RNA snoR99 2 0.222 14.7 Match Image
3 RF01225 Small nucleolar RNA ACA64 4 0.133 32.0 Match Image
3 RF01233 Small nucleolar RNA U109 3 0.115 23.6 Match Image
3 RF01234 Small nucleolar RNA SNORA47 9 0.450 66.9 Match Image
3 RF01252 Small nucleolar RNA snR5 2 0.182 17.2 Match Image
3 RF01255 Small nucleolar RNA snR35 3 0.273 26.9 Match Image
3 RF01263 Small nucleolar RNA snR191 2 0.182 23.4 Match Image
3 RF01268 Small Cajal body-specific RNA 2 10 0.500 101.7 Match Image
3 RF01294 Small nucleolar RNA U89 3 0.188 25.8 Match Image
3 RF01295 Small Cajal body-specific RNA 7 5 0.278 40.2 Match Image
3 RF01296 Small nucleolar RNA U85 5 0.238 48.4 Match Image
3 RF01322 CRISPR RNA direct repeat element 4 0.571 48.4 Match Image
3 RF01331 CRISPR RNA direct repeat element 6 1.000 63.0 Match Image
3 RF01347 CRISPR RNA direct repeat element 3 1.000 31.5 Match Image
3 RF01405 STnc490 Hfq binding RNA 67 0.882 491.2 Match Image
3 RF01411 BsrF 3 0.273 22.8 Match Image
3 RF01412 BsrG 4 0.667 45.0 Match Image
3 RF01492 Listeria sRNA rli28 3 0.143 25.2 Match Image
3 RF01502 Fungal signal recognition particle RNA 16 0.320 212.6 Match Image
3 RF01521 caulobacter sRNA CC1840 3 1.000 48.0 Match Image
3 RF01527 Caulobacter sRNA CrfA 4 2.000 35.8 Match Image
3 RF01529 Cauldobacter sRNA CC3552 2 1.000 58.4 Match Image
3 RF01541 Trypanosomatid snoRNA TB11Cs4H3 2 0.667 14.8 Match Image
3 RF01581 Plasmodium RNA of unknown function RUF6-5 12 0.600 86.9 Match Image
3 RF01610 Caenorhabditis snoRNA ceN104 2 0.400 16.5 Match Image
3 RF01653 Caenorhabditis snoRNA ceN80 2 0.400 21.6 Match Image
3 RF01670 Pseudomonas sRNA P17 3 1.000 25.1 Match Image
3 RF01673 PhrS 3 0.231 22.9 Match Image
3 RF01675 Pseudomonas sRNA CrcZ 9 0.474 85.4 Match Image
3 RF01686 Acido-1 RNA 4 1.000 55.0 Match Image
3 RF01687 Acido-Lenti-1 RNA 16 0.184 120.7 Match Image
3 RF01691 Bacillus-plasmid RNA 5 0.161 50.8 Match Image
3 RF01693 Bacteroidales-1 RNA 3 0.073 23.2 Match Image
3 RF01695 C4 antisense RNA 132 0.289 1741.0 Match Image
3 RF01696 Chlorobi-1 RNA 4 0.267 38.9 Match Image
3 RF01699 Clostridiales-1 RNA 94 0.485 1122.3 Match Image
3 RF01700 Collinsella-1 RNA 2 0.333 22.6 Match Image
3 RF01702 Cyano-2 RNA 30 0.526 288.2 Match Image
3 RF01703 Dictyoglomi-1 RNA 3 0.750 55.1 Match Image
3 RF01704 Downstream peptide RNA 61 0.097 703.5 Match Image
3 RF01708 L17 ribosomal protein downstream element 9 0.173 104.2 Match Image
3 RF01721 Pseudomon-groES RNA 11 0.611 143.9 Match Image
3 RF01722 Pyrobac-1 RNA 3 0.375 25.3 Match Image
3 RF01723 Rhizobiales-2 RNA 11 0.733 86.8 Match Image
3 RF01725 SAM-I/IV variant riboswitch 66 0.151 725.2 Match Image
3 RF01728 STAXI RNA 7 0.233 59.7 Match Image
3 RF01729 Termite-flg RNA 2 0.154 14.4 Match Image
3 RF01730 Termite-leu RNA 14 0.700 136.6 Match Image
3 RF01731 TwoAYGGAY RNA 55 0.262 465.0 Match Image
3 RF01732 asd RNA 4 0.129 46.5 Match Image
3 RF01733 atoC RNA 5 0.625 47.9 Match Image
3 RF01735 epsC RNA 3 0.100 24.8 Match Image
3 RF01736 flg-Rhizobiales RNA 12 0.923 191.0 Match Image
3 RF01739 glnA RNA 117 0.122 1304.8 Match Image
3 RF01740 gyrA RNA 4 0.222 29.6 Match Image
3 RF01742 lactis-plasmid RNA 5 0.357 38.6 Match Image
3 RF01745 manA RNA 120 0.635 1118.6 Match Image
3 RF01746 mraW RNA 7 0.156 60.0 Match Image
3 RF01748 nuoG RNA 9 0.290 85.1 Match Image
3 RF01750 pfl RNA 19 0.104 178.5 Match Image
3 RF01752 psaA RNA 7 0.226 53.0 Match Image
3 RF01753 psbNH RNA 7 0.179 60.2 Match Image
3 RF01754 radC RNA 24 0.185 359.9 Match Image
3 RF01755 rmf RNA 6 0.375 63.4 Match Image
3 RF01756 rne-II RNA 5 0.312 55.0 Match Image
3 RF01757 sbcD RNA 5 0.833 81.4 Match Image
3 RF01758 sucA-II RNA 7 0.412 59.4 Match Image
3 RF01761 wcaG RNA 13 0.110 118.5 Match Image
3 RF01762 Whalefall-1 RNA 5 0.357 65.2 Match Image
3 RF01766 cspA thermoregulator 6 0.400 46.8 Match Image
3 RF01772 Pseudomonas rnk leader 7 0.467 52.7 Match Image
3 RF01773 Pseudomonas rpsL leader 5 0.556 43.9 Match Image
3 RF01783 Mycobacterium B11 4 2.000 32.8 Match Image
3 RF01794 sok antitoxin 44 0.484 484.1 Match Image
3 RF01796 Fumarate/nitrate reductase regulator sRNA 13 0.812 148.0 Match Image
3 RF01807 GIR1 branching ribozyme 2 0.167 17.7 Match Image
3 RF01808 MicX Vibrio cholerae sRNA 7 0.700 93.3 Match Image
3 RF01809 SymR antitoxin 7 0.350 52.9 Match Image
3 RF01811 Plasmid transferred anti-sense RNA 14 0.875 113.2 Match Image
3 RF01820 RNA Staph. aureus E 2 0.133 19.0 Match Image
3 RF01830 Salmonella enterica Typhi npcRNA 44 10 0.294 145.8 Match Image
3 RF01835 ribosomal frameshift site 3 0.158 22.8 Match Image
3 RF01844 SmY spliceosomal RNA 11 0.180 94.1 Match Image
3 RF01846 Fungal small nucleolar RNA U3 21 0.318 295.2 Match Image
3 RF01848 ACEA small nucleolar RNA U3 12 0.429 132.0 Match Image
3 RF01849 Alphaproteobacteria transfer-messenger RNA 75 0.676 1655.1 Match Image
3 RF01850 Betaproteobacteria transfer-messenger RNA 3 0.429 40.3 Match Image
3 RF01852 Selenocysteine transfer RNA 27 0.248 283.7 Match Image
3 RF01854 Bacterial large signal recognition particle RNA 29 0.315 221.5 Match Image
3 RF01855 Plant signal recognition particle RNA 49 0.778 527.7 Match Image
3 RF01856 Protozoan signal recognition particle RNA 9 0.500 110.6 Match Image
3 RF01857 Archaeal signal recognition particle RNA 45 0.849 964.0 Match Image
3 RF01859 Phenylalanine leader peptide 30 0.423 258.6 Match Image
3 RF01867 caulobacter sRNA CC2171 12 0.923 227.1 Match Image
3 RF01874 Myocardial infarction associated transcript exon 1 6 0.600 55.7 Match Image
3 RF01877 Myocardial infarction associated transcript exon 5 conserved region 3 2 0.125 15.3 Match Image
3 RF01909 CDKN2B antisense RNA 1 intronic convserved region 5 0.200 42.7 Match Image
3 RF01946 KCNQ1 overlapping transcript 1 conserved region 1 3 0.375 25.7 Match Image
3 RF01947 KCNQ1 overlapping transcript 1 conserved region 2 2 0.111 14.5 Match Image
3 RF01953 SOX2 overlapping transcript exon 3 4 0.364 33.1 Match Image
3 RF01955 Nuclear enriched abundant transcript 1 conserved region 1 2 0.118 19.3 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 86 1.000 7662.3 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 86 0.945 2894.8 Match Image
3 RF01975 HOX antisense intergenic RNA myeloid 1 conserved region 1 6 0.429 53.5 Match Image
3 RF01998 Group II catalytic intron D1-D4-1 117 0.494 1523.7 Match Image
3 RF01999 Group II catalytic intron D1-D4-2 38 0.264 331.1 Match Image
3 RF02001 Group II catalytic intron D1-D4-3 50 0.123 402.9 Match Image
3 RF02003 Group II catalytic intron D1-D4-4 46 0.511 534.3 Match Image
3 RF02004 Group II catalytic intron D1-D4-5 60 0.432 733.9 Match Image
3 RF02005 Group II catalytic intron D1-D4-6 149 0.856 1920.6 Match Image
3 RF02012 Group II catalytic intron D1-D4-7 177 0.725 2436.2 Match Image
3 RF02025 microRNA mir-3017 12 0.333 104.6 Match Image
3 RF02027 microRNA MIR2907 14 0.269 127.3 Match Image
3 RF02030 tp2 4 0.167 30.2 Match Image
3 RF02031 tpke11 14 0.500 182.7 Match Image
3 RF02032 Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA 24 0.686 402.2 Match Image
3 RF02033 HNH endonuclease-associated RNA and ORF (HEARO) RNA 68 0.618 605.5 Match Image
3 RF02035 IMES-2 RNA motif 280 0.765 3015.6 Match Image
3 RF02037 IMES-4 RNA motif 23 0.767 217.4 Match Image
3 RF02041 HOXA transcript at the distal tip, conserved region 2 5 0.200 52.3 Match Image
3 RF02042 HOXA transcript at the distal tip, conserved region 3 7 0.304 61.7 Match Image
3 RF02057 Salmonella enterica sRNA STnc40 5 0.294 58.5 Match Image
3 RF02067 Salmonella enterica sRNA STnc310 4 0.500 32.5 Match Image
3 RF02081 Enterobacterial sRNA STnc550 3 0.273 22.9 Match Image
3 RF02089 CLRN1 antisense RNA 1 conserved region 2 0.105 17.2 Match Image
3 RF02093 mir-2968 microRNA precursor 4 0.333 29.7 Match Image
3 RF02096 mir-2973 microRNA precursor 5 0.714 43.4 Match Image
3 RF02100 Translational regulator of tfoXVC 4 0.400 48.9 Match Image
3 RF02103 Deleted in lymphocytic leukemia 1 conserved region 1 5 0.192 44.7 Match Image
3 RF02104 Deleted in lymphocytic leukemia 1 conserved region 2 8 0.500 62.7 Match Image
3 RF02109 Deleted in lymphocytic leukemia 2 conserved region 5 8 0.267 65.6 Match Image
3 RF02116 FAS antisense RNA 1 conserved region 2 0.105 16.6 Match Image
3 RF02118 FMR1 antisense RNA 1 conserved region 2 12 0.480 118.1 Match Image
3 RF02127 GNAS antisense RNA 1 conserved region 1 6 0.286 46.2 Match Image
3 RF02138 HOXA11 antisense RNA 1 conserved region 2 10 0.476 99.3 Match Image
3 RF02141 HOXA11 antisense RNA 1 conserved region 5 3 0.107 27.2 Match Image
3 RF02143 Hydatidiform mole associated and imprinted conserved region 1 6 0.375 72.2 Match Image
3 RF02145 Maternally expressed 8 exon 1 5 0.217 45.0 Match Image
3 RF02151 MER1 repeat containing imprinted transcript 1 conserved region 1 2 0.095 18.3 Match Image
3 RF02160 Prostate androgen-regulated transcript 1 conserved region 2 5 0.172 49.6 Match Image
3 RF02164 Pvt1 oncogene conserved region 1 7 0.412 81.7 Match Image
3 RF02165 Pvt1 oncogene conserved region 2 3 0.176 25.7 Match Image
3 RF02187 ST7 overlapping transcript 4 conserved region 1 2 0.083 18.1 Match Image
3 RF02189 ST7 overlapping transcript 4 conserved region 3 3 0.150 27.1 Match Image
3 RF02198 TTC28 antisense RNA 1 conserved region 1 5 0.357 43.1 Match Image
3 RF02200 TTC28 antisense RNA 1 conserved region 3 3 0.500 32.4 Match Image
3 RF02201 TTC28 antisense RNA 1 conserved region 4 3 0.167 25.1 Match Image
3 RF02205 WT1 antisense RNA conserved region 3 10 0.526 105.0 Match Image
3 RF02208 WT1 antisense RNA conserved region 6 3 0.158 23.2 Match Image
3 RF02215 ZNFX1 antisense RNA 1 conserved region 1 11 0.733 88.4 Match Image
3 RF02220 ZNRD1 antisense RNA 1 conserved region 3 6 0.667 45.5 Match Image
3 RF02221 sRNA-Xcc1 31 0.419 261.6 Match Image
3 RF02225 Proteobacterial sRNA sX6 8 1.000 70.5 Match Image
3 RF02234 Xanthomonadaceae sRNA sX15 7 0.500 67.6 Match Image
3 RF02235 Xanthomonadaceae sRNA asX1 11 0.733 159.6 Match Image
3 RF02238 Xanthomonas sRNA asX4/Xoo4 4 0.500 31.3 Match Image
3 RF02243 Proteobacterial sRNA Xoo8 4 1.000 79.4 Match Image
3 RF02247 Six3os1 conserved region 2 4 0.267 30.4 Match Image
3 RF02249 Six3os1 conserved region 4 3 0.429 23.2 Match Image
3 RF02251 Six3os1 conserved region 6 4 1.000 53.6 Match Image
3 RF02276 Hammerhead ribozyme (type II) 11 0.458 127.4 Match Image
3 RF02278 Betaproteobacteria toxic small RNA 15 0.294 169.1 Match Image
3 RF02343 Alphaproteobacterial sRNA ar9 20 0.714 270.5 Match Image
3 RF02344 Alphaproteobacterial ar14 72 0.610 573.3 Match Image
3 RF02345 Alphaproteobacterial ar15 5 0.082 64.1 Match Image
3 RF02349 Proteobacterial sRNA psRNA2 2 0.286 14.5 Match Image
3 RF02351 Proteobacteria sRNA psRNA14 2 0.667 21.8 Match Image
3 RF02353 Bradyrhizobiaceae sRNA BjrC68 12 1.000 221.4 Match Image
3 RF02354 Bradyrhizobiaceae sRNA BjrC80 11 0.733 107.7 Match Image
3 RF02355 Bradyrhizobiaceae sRNA BjrC174 11 0.733 172.4 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 20 0.800 290.3 Match Image
3 RF02357 RNaseP truncated form 9 1.000 260.5 Match Image
3 RF02363 Cyanobacterial functional RNA 11 2 0.500 15.7 Match Image
3 RF02371 PyrG leader 5 0.500 76.0 Match Image
3 RF02384 FasX small RNA 2 0.250 20.1 Match Image
3 RF02399 Nitrogen stress-induced RNA 1 2 0.118 18.8 Match Image
3 RF02401 ClpQY promoter 9 0.231 85.1 Match Image
3 RF02405 Pseudomonas sRNA P34 6 1.200 57.3 Match Image
3 RF02413 Small nucleolar RNA snoR145 3 0.158 28.0 Match Image
3 RF02421 Burkholderia sRNA Bp1_Cand684_SIPHT 13 0.929 140.4 Match Image
3 RF02422 Burkholderia sRNA Bp1_Cand738_SIPHT 9 0.429 83.5 Match Image
3 RF02423 Burkholderia sRNA Bp1_Cand871_SIPHT 2 0.133 15.0 Match Image
3 RF02424 Burkholderia sRNA Bp2_Cand287_SIPHT 3 0.214 32.9 Match Image
3 RF02435 Streptococcus sRNA SpF41 3 0.333 51.9 Match Image
3 RF02446 Streptococcus sRNA SpR18 5 0.217 37.7 Match Image
3 RF02448 Streptococcus sRNA SpR20 5 0.714 42.9 Match Image
3 RF02453 Bacillus sRNA ncr952 4 0.667 31.1 Match Image
3 RF02457 Tombusvirus 3' cap-independent translation element 8 0.889 67.2 Match Image
3 RF02461 Blackcurrant reversion virus cap-independent translation element 3 1.000 29.3 Match Image
3 RF02462 Ascomycota telomerase RNA 4 1.000 128.5 Match Image
3 RF02471 Actinobacteria sRNA Ms_IGR-5 16 0.762 189.0 Match Image
3 RF02483 Small nucleolar RNA GlsR20 2 0.667 18.8 Match Image
3 RF02488 Small nucleolar RNA GlsR25 3 1.000 23.8 Match Image
3 RF02502 Rhizobiales sRNA Atu_C8 2 0.074 14.4 Match Image
3 RF02506 Rhizobiales sRNA Atu_Ti1 2 0.143 17.4 Match Image
3 RF02523 Repression of heat shock gene expression (ROSE) element 4 0.250 30.5 Match Image
3 RF02531 Nrf2 internal ribosome entry site (IRES) 2 0.100 19.2 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 91 1.000 14392.9 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 102 1.000 9153.3 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 39 0.848 796.4 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 87 0.989 5123.0 Match Image
3 RF02566 Mycobacterium smegmatis small RNA 1 3 0.750 29.3 Match Image
3 RF02605 Streptomyces sRNA scr5239 4 0.667 40.3 Match Image
3 RF02645 Ruegeria cis2 sRNA 2 1.000 16.1 Match Image
3 RF02649 Ruegeria trans44 sRNA 2 1.000 15.1 Match Image
3 RF02673 Streptomyces sRNA 4677 5 0.417 51.9 Match Image
3 RF02679 Pistol ribozyme 7 0.156 71.3 Match Image
3 RF02680 PreQ1-III riboswitch 2 0.071 17.4 Match Image
3 RF02682 HDV ribozyme from F. prausnitzii 4 0.083 31.5 Match Image
3 RF02683 NiCo riboswitch 11 0.134 110.5 Match Image
3 RF02684 Type-P5 twister ribozyme 4 0.267 51.1 Match Image
3 RF02690 Burkholderia sRNA 1 5 1.000 64.4 Match Image
3 RF02728 Haemophilus regulatory RNA responsive to iron 3 0.429 32.0 Match Image
3 RF02743 Saccharopolyspora sRNA 389 2 1.000 33.5 Match Image
3 RF02744 Soft rot Enterobacteriaceae Rev 39 5'UTR 4 1.000 68.4 Match Image
3 RF02745 Soft rot Enterobacteriaceae Rev 42 5'UTR 2 0.667 18.8 Match Image
3 RF02746 antisense RNA of rseC mRNA 6 0.857 64.8 Match Image
3 RF02748 Francisella sRNA B 4 0.800 46.5 Match Image
3 RF02778 FdoG-1 5' UTR thermometer 2 0.667 20.1 Match Image

References

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

Literature references

  1. Jaeger L, Michel F, Westhof E J Mol Biol. 1994;236:1271-6. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. PUBMED:7510342

  2. Abramovitz DL, Pyle AM J Mol Biol. 1997;266:493-506. Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction. PUBMED:9067606

  3. 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

  4. Jucker FM, Heus HA, Yip PF, Moors EH, Pardi A J Mol Biol. 1996;264:968-80. A network of heterogeneous hydrogen bonds in GNRA tetraloops. PUBMED:9000624

  5. 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

  6. 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

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 112 17.59 47

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 7.0
Covariance model Download the Infernal CM for the motif here