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0  structures 0  species 0  sequences

Motif: Terminator2 (RM00023)

Description: Rho independent terminator 2

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 Terminator (genetics). More...

In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. This sequence mediates transcriptional termination by providing signals in the newly synthesized transcript RNA that trigger processes which release the transcript RNA from the transcriptional complex. These processes include the direct interaction of the mRNA secondary structure with the complex and/or the indirect activities of recruited termination factors. Release of the transcriptional complex frees RNA polymerase and related transcriptional machinery to begin transcription of new mRNAs.

In prokaryotes

Simplified schematics of the mechanisms of prokaryotic transcriptional termination. In Rho-independent termination, a terminating hairpin forms on the nascent mRNA interacting with the NusA protein to stimulate release of the transcript from the RNA polymerase complex (top). In Rho-dependent termination, the Rho protein binds at the upstream rut site, translocates down the mRNA, and interacts with the RNA polymerase complex to stimulate release of the transcript.

Two classes of transcription terminators, Rho-dependent and Rho-independent, have been identified throughout prokaryotic genomes. These widely distributed sequences are responsible for triggering the end of transcription upon normal completion of gene or operon transcription, mediating early termination of transcripts as a means of regulation such as that observed in transcriptional attenuation, and to ensure the termination of runaway transcriptional complexes that manage to escape earlier terminators by chance, which prevents unnecessary energy expenditure for the cell.

Rho-dependent terminators

Rho-dependent transcription terminators require a protein called Rho factor, which exhibits RNA helicase activity, to disrupt the mRNA-DNA-RNA polymerase transcriptional complex. Rho-dependent terminators are found in bacteria and phage. The Rho-dependent terminator occurs downstream of translational stop codons and consists of an unstructured, cytosine-rich sequence on the mRNA known as a Rho utilization site (rut) for which a consensus sequence has not been identified, and a downstream transcription stop point (tsp). The rut serves as a mRNA loading site and as an activator for Rho; activation enables Rho to efficiently hydrolyze ATP and translocate down the mRNA while it maintains contact with the rut site. Rho is able to catch up with the RNA polymerase, which is stalled at the downstream tsp sites.[1] Contact between Rho and the RNA polymerase complex stimulates dissociation of the transcriptional complex through a mechanism involving allosteric effects of Rho on RNA polymerase.[2][3]

Rho-independent terminators

Intrinsic transcription terminators or Rho-independent terminators require the formation of a self-annealing hairpin structure on the elongating transcript, which results in the disruption of the mRNA-DNA-RNA polymerase ternary complex. The terminator sequence in DNA contains a 20 basepair GC-rich region of dyad symmetry followed by a short poly-T tract or "T stretch" which is transcribed to form the terminating hairpin and a 7–9 nucleotide "U tract" respectively. The mechanism of termination is hypothesized to occur through a combination of direct promotion of dissociation through allosteric effects of hairpin binding interactions with the RNA polymerase and "competitive kinetics". The hairpin formation causes RNA polymerase stalling and destabilization, leading to a greater likelihood that dissociation of the complex will occur at that location due to an increased time spent paused at that site and reduced stability of the complex.[4][5] Additionally, the elongation protein factor NusA interacts with the RNA polymerase and the hairpin structure to stimulate transcriptional termination.[6]

In eukaryotes

In eukaryotic transcription of mRNAs, terminator signals are recognized by protein factors that are associated with the RNA polymerase II and which trigger the termination process. Once the poly-A signals are transcribed into the mRNA, the proteins cleavage and polyadenylation specificity factor (CPSF) and cleavage stimulation factor (CstF) transfer from the carboxyl terminal domain of RNA polymerase II to the poly-A signal. These two factors then recruit other proteins to the site to cleave the transcript, freeing the mRNA from the transcription complex, and add a string of about 200 A-repeats to the 3' end of the mRNA in a process known as polyadenylation. During these processing steps, the RNA polymerase continues to transcribe for several hundred to a few thousand bases and eventually dissociates from the DNA and downstream transcript through an unclear mechanism; there are two basic models for this event known as the torpedo and allosteric models.[7][8]

Torpedo model

After the mRNA is completed and cleaved off at the poly-A signal sequence, the left-over (residual) RNA strand remains bound to the DNA template and the RNA polymerase II unit, continuing to be transcribed. After this cleavage, a so-called exonuclease binds to the residual RNA strand and removes the freshly transcribed nucleotides one at a time (also called 'degrading' the RNA), moving towards the bound RNA polymerase II. This exonuclease is XRN2 (5'-3' Exoribonuclease 2) in humans. This model proposes that XRN2 proceeds to degrade the uncapped residual RNA from 5' to 3' until it reaches the RNA pol II unit. This causes the exonuclease to 'push off' the RNA pol II unit as it moves past it, terminating the transcription while also cleaning up the residual RNA strand.

Similar to Rho-dependent termination, XRN2 triggers the dissociation of RNA polymerase II by either pushing the polymerase off of the DNA template or pulling the template out of the RNA polymerase.[9] The mechanism by which this happens remains unclear, however, and has been challenged not to be the sole cause of the dissociation.[10]

In order to protect the transcribed mRNA from degradation by the exonuclease, a 5' cap is added to the strand. This is a modified guanine added to the front of mRNA, which prevents the exonuclease from binding and degrading the RNA strand. A 3' poly(A) tail is added to the end of a mRNA strand for protection from other exonucleases as well.

Allosteric model

The allosteric model suggests that termination occurs due to the structural change of the RNA polymerase unit after binding to or losing some of its associated proteins, making it detach from the DNA strand after the signal.[8] This would occur after the RNA pol II unit has transcribed the poly-A signal sequence, which acts as a terminator signal.

RNA polymerase is normally capable of transcribing DNA into single-stranded mRNA efficiently. However, upon transcribing over the poly-A signals on the DNA template, a conformational shift is induced in the RNA polymerase from the proposed loss of associated proteins from its carboxyl terminal domain. This change of conformation reduces RNA polymerase's processivity making the enzyme more prone to dissociating from its DNA-RNA substrate. In this case, termination is not completed by degradation of mRNA but instead is mediated by limiting the elongation efficiency of RNA polymerase and thus increasing the likelihood that the polymerase will dissociate and end its current cycle of transcription.[7]

See also

References

  1. ^ Richardson, J. P. (1996). "Rho-dependent Termination of Transcription Is Governed Primarily by the Upstream Rho Utilization (rut) Sequences of a Terminator". Journal of Biological Chemistry. 271 (35): 21597–21603. doi:10.1074/jbc.271.35.21597. ISSN 0021-9258.
  2. ^ Ciampi, MS. (Sep 2006). "Rho-dependent terminators and transcription termination". Microbiology. 152 (Pt 9): 2515–28. doi:10.1099/mic.0.28982-0. PMID 16946247.
  3. ^ Epshtein, V; Dutta, D; Wade, J; Nudler, E (Jan 14, 2010). "An allosteric mechanism of Rho-dependent transcription termination". Nature. 463 (7278): 245–9. doi:10.1038/nature08669. PMC 2929367. PMID 20075920.
  4. ^ von Hippel, P. H. (1998). "An Integrated Model of the Transcription Complex in Elongation, Termination, and Editing". Science. 281 (5377): 660–665. doi:10.1126/science.281.5377.660.
  5. ^ Gusarov, Ivan; Nudler, Evgeny (1999). "The Mechanism of Intrinsic Transcription Termination". Molecular Cell. 3 (4): 495–504. doi:10.1016/S1097-2765(00)80477-3. ISSN 1097-2765.
  6. ^ Santangelo, TJ.; Artsimovitch, I. (May 2011). "Termination and antitermination: RNA polymerase runs a stop sign". Nat Rev Microbiol. 9 (5): 319–29. doi:10.1038/nrmicro2560. PMC 3125153. PMID 21478900.
  7. ^ a b Watson, J. (2008). Molecular Biology of the Gene. Cold Spring Harbor Laboratory Press. pp. 410–411. ISBN 978-0-8053-9592-1.
  8. ^ a b Rosonina, Emanuel; Kaneko, Syuzo; Manley, James L. (2006-05-01). "Terminating the transcript: breaking up is hard to do". Genes & Development. 20 (9): 1050–1056. doi:10.1101/gad.1431606. ISSN 0890-9369. PMID 16651651.
  9. ^ Luo, W.; Bartley D. (2004). "A ribonucleolytic rat torpedoes RNA polymerase II". Cell. 119 (7): 911–914. doi:10.1016/j.cell.2004.11.041. PMID 15620350.
  10. ^ Luo, Weifei; Johnson, Arlen W.; Bentley, David L. (2006-04-15). "The role of Rat1 in coupling mRNA 3′-end processing to transcription termination: implications for a unified allosteric–torpedo model". Genes & Development. 20 (8): 954–965. doi:10.1101/gad.1409106. ISSN 0890-9369. PMC 1472303. PMID 16598041.

External links

This page is based on a wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

Alignments

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Family matches

There are 247 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 RF00018 CsrB/RsmB RNA family 35 0.921 660.3 Match Image
3 RF00021 Spot 42 RNA 19 1.000 334.1 Match Image
3 RF00022 GcvB RNA 26 0.963 451.2 Match Image
3 RF00028 Group I catalytic intron 2 0.167 58.9 Match Image
3 RF00034 RprA RNA 4 0.308 45.7 Match Image
3 RF00042 CopA-like RNA 12 0.324 138.1 Match Image
3 RF00057 RyhB RNA 6 0.231 64.3 Match Image
3 RF00079 OmrA-B family 14 0.609 150.3 Match Image
3 RF00080 yybP-ykoY manganese riboswitch 5 0.172 66.4 Match Image
3 RF00082 SraG RNA 2 0.286 25.9 Match Image
3 RF00083 GlmZ RNA activator of glmS mRNA 18 0.857 248.8 Match Image
3 RF00084 CsrC RNA family 4 1.000 110.1 Match Image
3 RF00106 RNAI 8 0.800 94.0 Match Image
3 RF00110 RybB RNA 6 0.750 77.1 Match Image
3 RF00111 SdsR_RyeB RNA 12 0.706 151.7 Match Image
3 RF00115 McaS/IsrA RNA 4 1.000 60.8 Match Image
3 RF00121 MicC RNA 8 1.000 178.7 Match Image
3 RF00124 IS102 RNA 4 0.800 64.6 Match Image
3 RF00125 IS128 RNA 5 1.000 64.7 Match Image
3 RF00126 ryfA RNA 3 0.333 32.1 Match Image
3 RF00130 mir-192/215 microRNA precursor 19 0.463 297.5 Match Image
3 RF00140 Alpha operon ribosome binding site 7 0.179 79.0 Match Image
3 RF00143 mir-6 microRNA precursor 9 0.375 109.1 Match Image
3 RF00166 PrrB/RsmZ RNA family 11 0.297 144.9 Match Image
3 RF00229 Picornavirus internal ribosome entry site (IRES) 23 0.250 247.0 Match Image
3 RF00236 ctRNA 13 0.867 194.4 Match Image
3 RF00238 ctRNA 47 0.979 751.7 Match Image
3 RF00242 ctRNA 13 0.812 174.3 Match Image
3 RF00257 mir-194 microRNA precursor family 12 0.414 133.2 Match Image
3 RF00280 Small nucleolar RNA SNORD51 4 0.286 52.4 Match Image
3 RF00304 Small nucleolar RNA Z279/snoR105/snoR108 2 0.100 24.8 Match Image
3 RF00345 Small nucleolar RNA snoR1 2 0.154 23.0 Match Image
3 RF00368 sroB RNA 5 0.312 57.4 Match Image
3 RF00369 sroC RNA 6 1.000 84.3 Match Image
3 RF00370 sroD RNA 5 1.000 60.0 Match Image
3 RF00378 Qrr RNA 30 1.000 508.8 Match Image
3 RF00397 Small nucleolar RNA SNORA14 3 0.167 38.7 Match Image
3 RF00424 Small Cajal body specific RNA 16 5 0.135 61.7 Match Image
3 RF00444 PrrF RNA 18 1.000 240.9 Match Image
3 RF00488 Yeast U1 spliceosomal RNA 3 0.600 31.9 Match Image
3 RF00489 ctRNA 6 0.600 70.5 Match Image
3 RF00503 RNAIII 3 0.300 37.6 Match Image
3 RF00506 Threonine operon leader 25 1.000 565.0 Match Image
3 RF00512 Leucine operon leader 6 1.000 94.4 Match Image
3 RF00513 Tryptophan operon leader 9 0.409 117.7 Match Image
3 RF00514 Histidine operon leader 33 1.000 587.4 Match Image
3 RF00515 PyrR binding site 26 0.634 373.2 Match Image
3 RF00516 ylbH leader 3 1.000 43.3 Match Image
3 RF00519 Makes More Granules Regulator RNA (mmgR) 81 0.931 1185.2 Match Image
3 RF00534 SgrS RNA 4 0.500 49.8 Match Image
3 RF00540 Small nucleolar RNA psi18S-1854 4 0.250 48.9 Match Image
3 RF00552 rncO 2 0.111 21.7 Match Image
3 RF00557 Ribosomal protein L10 leader 77 0.794 1238.8 Match Image
3 RF00558 Ribosomal protein L20 leader 35 0.814 526.0 Match Image
3 RF00563 Small nucleolar RNA SNORA53 4 0.143 53.6 Match Image
3 RF00586 Small nucleolar RNA SNORA12 2 0.087 27.8 Match Image
3 RF00598 Small nucleolar RNA SNORA76 4 0.182 48.7 Match Image
3 RF00599 Small nucleolar RNA SNORA77 9 0.474 116.7 Match Image
3 RF00600 Small nucleolar RNA SNORA79 4 0.160 49.0 Match Image
3 RF00616 Listeria LhrC 10 0.833 112.4 Match Image
3 RF00628 RgsA sRNA 7 0.259 82.6 Match Image
3 RF00639 microRNA mir-515 18 0.450 225.7 Match Image
3 RF00643 microRNA MIR171_1 5 0.088 61.8 Match Image
3 RF00645 microRNA MIR169_2 11 0.110 133.3 Match Image
3 RF00661 microRNA mir-31 3 0.107 32.8 Match Image
3 RF00665 microRNA mir-290 4 0.148 44.5 Match Image
3 RF00668 microRNA mir-302 32 0.727 478.8 Match Image
3 RF00689 microRNA MIR390 3 0.188 31.4 Match Image
3 RF00691 microRNA mir-146 3 0.091 33.7 Match Image
3 RF00708 microRNA mir-450 10 0.476 116.2 Match Image
3 RF00714 microRNA MIR535 3 0.750 34.0 Match Image
3 RF00722 microRNA mir-451 12 0.632 151.0 Match Image
3 RF00727 microRNA bantam 3 0.273 35.5 Match Image
3 RF00746 microRNA mir-454 3 0.176 41.1 Match Image
3 RF00747 microRNA mir-283 5 0.455 59.4 Match Image
3 RF00751 microRNA mir-12 2 0.286 21.2 Match Image
3 RF00756 microRNA mir-299 5 0.833 59.3 Match Image
3 RF00768 microRNA MIR405 11 0.846 144.4 Match Image
3 RF00779 microRNA MIR474 2 0.182 24.7 Match Image
3 RF00834 microRNA mir-268 3 0.750 44.8 Match Image
3 RF00840 microRNA mir-374 12 0.923 204.1 Match Image
3 RF00854 microRNA mir-5 6 1.000 71.5 Match Image
3 RF00885 microRNA MIR821 3 0.600 52.5 Match Image
3 RF00886 microRNA MIR807 3 0.100 34.8 Match Image
3 RF00906 microRNA MIR1122 7 0.583 118.9 Match Image
3 RF00928 microRNA mir-590 2 0.200 22.8 Match Image
3 RF00951 microRNA mir-1302 6 0.250 70.4 Match Image
3 RF01042 microRNA mir-891 2 0.286 28.3 Match Image
3 RF01045 microRNA mir-544 9 0.375 111.3 Match Image
3 RF01050 Saccharomyces telomerase 13 1.000 301.8 Match Image
3 RF01059 microRNA mir-598 7 0.292 89.4 Match Image
3 RF01065 23S methyl RNA motif 7 0.368 99.0 Match Image
3 RF01071 Ornate Large Extremophilic RNA 3 0.150 41.5 Match Image
3 RF01227 Small nucleolar RNA snoR83 4 0.571 49.0 Match Image
3 RF01231 Small nucleolar RNA snoR74 2 0.222 23.3 Match Image
3 RF01241 Small nucleolar RNA SNORA81 12 0.429 136.6 Match Image
3 RF01249 Small nucleolar RNA snR190 5 0.500 66.7 Match Image
3 RF01264 Small nucleolar RNA snR83 4 0.800 65.6 Match Image
3 RF01267 Small nucleolar RNA snR37 5 0.556 62.3 Match Image
3 RF01270 Small nucleolar RNA snR84 2 0.333 21.0 Match Image
3 RF01272 Small nucleolar RNA snR86 3 0.600 51.5 Match Image
3 RF01395 isrL Hfq binding RNA 4 1.000 52.9 Match Image
3 RF01401 rseX Hfq binding RNA 5 0.417 58.6 Match Image
3 RF01402 STnc150 Hfq binding RNA 9 1.000 151.5 Match Image
3 RF01407 STnc560 Hfq binding RNA 12 1.000 169.0 Match Image
3 RF01408 sraL Hfq binding RNA 5 0.833 54.1 Match Image
3 RF01411 BsrF 2 0.182 21.7 Match Image
3 RF01412 BsrG 2 0.333 31.6 Match Image
3 RF01419 Antisense RNA which regulates isiA expression 64 0.208 797.7 Match Image
3 RF01456 Vibrio regulatory RNA of OmpA 11 1.000 163.7 Match Image
3 RF01459 Listeria sRNA rliE 4 1.000 88.0 Match Image
3 RF01470 Listeria sRNA rli38 15 0.750 271.4 Match Image
3 RF01472 Listeria sRNA rli40 4 1.000 77.0 Match Image
3 RF01473 Listeria sRNA rli41 6 1.000 66.3 Match Image
3 RF01491 Listeria sRNA rli54 10 2.000 114.8 Match Image
3 RF01577 Plasmodium RNase_P 5 2.500 76.8 Match Image
3 RF01670 Pseudomonas sRNA P17 3 1.000 35.5 Match Image
3 RF01673 PhrS 4 0.308 48.3 Match Image
3 RF01675 Pseudomonas sRNA CrcZ 5 0.263 60.6 Match Image
3 RF01698 Chloroflexi-1 RNA 3 1.000 31.1 Match Image
3 RF01701 Cyano-1 RNA 20 0.075 271.5 Match Image
3 RF01702 Cyano-2 RNA 9 0.158 119.7 Match Image
3 RF01705 Flavo-1 RNA 27 0.134 357.0 Match Image
3 RF01715 Pedo-repair RNA 2 0.333 23.5 Match Image
3 RF01719 Pseudomon-1/ErsA RNA 19 1.000 281.8 Match Image
3 RF01730 Termite-leu RNA 14 0.700 242.9 Match Image
3 RF01743 leu/phe leader RNA from Lactococcus 6 0.667 138.2 Match Image
3 RF01758 sucA-II RNA 6 0.353 84.6 Match Image
3 RF01766 cspA thermoregulator 12 0.800 171.2 Match Image
3 RF01769 Enterobacteria greA leader 3 0.120 32.2 Match Image
3 RF01770 Gammaprotebacteria rimP leader 46 1.000 879.8 Match Image
3 RF01771 Enterobacteria rnk leader 13 1.000 189.6 Match Image
3 RF01772 Pseudomonas rnk leader 15 1.000 233.0 Match Image
3 RF01773 Pseudomonas rpsL leader 9 1.000 122.7 Match Image
3 RF01774 Rickettsia rpsL leader 7 1.000 108.9 Match Image
3 RF01775 RNA S.aureus Orsay G 3 0.429 34.5 Match Image
3 RF01796 Fumarate/nitrate reductase regulator sRNA 9 0.562 111.5 Match Image
3 RF01808 MicX Vibrio cholerae sRNA 10 1.000 279.2 Match Image
3 RF01816 RNA Staph. aureus A 3 0.429 37.6 Match Image
3 RF01819 RNA Staph. aureus D 8 1.000 111.4 Match Image
3 RF01820 RNA Staph. aureus E (RoxS) 11 0.733 148.6 Match Image
3 RF01848 ACEA small nucleolar RNA U3 5 0.179 60.0 Match Image
3 RF01859 Phenylalanine leader peptide 65 0.915 974.4 Match Image
3 RF01882 Taurine upregulated gene 1 conserved region 1 15 0.714 182.1 Match Image
3 RF01899 microRNA mir-2241 2 0.200 24.1 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 30 0.349 401.4 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 31 0.341 574.8 Match Image
3 RF02029 sraA 15 0.750 221.3 Match Image
3 RF02031 tpke11 9 0.321 148.0 Match Image
3 RF02045 CDKN2B antisense RNA 1 convserved region 3 2 0.111 21.7 Match Image
3 RF02053 Enterobacterial sRNA STnc430 6 0.857 127.8 Match Image
3 RF02055 Enterobacterial sRNA STnc380 4 0.800 80.7 Match Image
3 RF02057 Salmonella enterica sRNA STnc40 17 1.000 240.2 Match Image
3 RF02060 Enterobacterial sRNA STnc410 3 0.214 36.5 Match Image
3 RF02064 Enterobacterial sRNA STnc370 10 1.000 135.2 Match Image
3 RF02065 Enterobacterial sRNA STnc340 3 0.750 57.8 Match Image
3 RF02067 Salmonella enterica sRNA STnc310 4 0.500 74.0 Match Image
3 RF02074 Enterobacterial sRNA STnc240 15 1.000 257.8 Match Image
3 RF02075 Enterobacterial sRNA STnc230 4 0.364 47.3 Match Image
3 RF02076 Gammaproteobacterial sRNA STnc100 8 0.333 106.8 Match Image
3 RF02079 Enterobacterial sRNA STnc180 4 0.400 65.3 Match Image
3 RF02082 Enterobacterial sRNA STnc540 3 1.000 69.6 Match Image
3 RF02084 Enterobacteria sRNA STnc130 5 0.385 58.6 Match Image
3 RF02096 mir-2973 microRNA precursor 2 0.286 21.9 Match Image
3 RF02142 HOXA11 antisense RNA 1 conserved region 6 6 0.286 72.5 Match Image
3 RF02143 Hydatidiform mole associated and imprinted conserved region 1 3 0.188 34.2 Match Image
3 RF02190 ST7 overlapping transcript 4 conserved region 4 4 0.154 51.6 Match Image
3 RF02225 Proteobacterial sRNA sX6 8 1.000 109.6 Match Image
3 RF02230 Proteobacterial sRNA sX11 10 1.000 135.7 Match Image
3 RF02241 Xanthomonadaceae sRNA Xoo2 3 1.000 46.7 Match Image
3 RF02243 Proteobacterial sRNA Xoo8 4 1.000 49.6 Match Image
3 RF02278 Betaproteobacteria toxic small RNA 47 0.922 747.2 Match Image
3 RF02330 Tetrahymena snoRNA TtnuHACA23 2 1.000 23.8 Match Image
3 RF02342 Alphaproteobacterial sRNA ar7 18 0.621 255.0 Match Image
3 RF02343 Alphaproteobacterial sRNA ar9 16 0.571 256.3 Match Image
3 RF02344 Alphaproteobacterial ar14 107 0.907 1510.6 Match Image
3 RF02346 Alphaproteobacterial sRNA ar35 12 0.923 164.3 Match Image
3 RF02351 Proteobacteria sRNA psRNA14 2 0.667 39.7 Match Image
3 RF02353 Bradyrhizobiaceae sRNA BjrC68 11 0.917 146.3 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 23 0.920 319.0 Match Image
3 RF02362 Cyanobacterial functional RNA 10 5 0.833 81.3 Match Image
3 RF02363 Cyanobacterial functional RNA 11 4 1.000 51.7 Match Image
3 RF02366 Cyanobacterial functional RNA 19 6 1.000 140.5 Match Image
3 RF02370 Bacillus tryptophan operon leader 5 0.556 57.4 Match Image
3 RF02371 PyrG leader 10 1.000 140.3 Match Image
3 RF02375 Aar sRNA 13 1.000 268.8 Match Image
3 RF02376 SR1 sRNA 6 1.000 108.7 Match Image
3 RF02378 SurC sRNA 4 1.000 50.0 Match Image
3 RF02379 Cia-dependent small RNA csRNA1 12 0.250 131.1 Match Image
3 RF02384 FasX small RNA 3 0.375 31.1 Match Image
3 RF02399 Nitrogen stress-induced RNA 1 6 0.353 76.6 Match Image
3 RF02405 Pseudomonas sRNA P34 5 1.000 99.9 Match Image
3 RF02409 Small nucleolar RNA snoR125 5 1.000 75.2 Match Image
3 RF02410 Small nucleolar RNA snoR136 3 0.375 36.8 Match Image
3 RF02411 Small nucleolar RNA snoR138 3 0.429 38.2 Match Image
3 RF02419 Streptococcus sRNA Spd-sr37 3 0.120 31.5 Match Image
3 RF02423 Burkholderia sRNA Bp1_Cand871_SIPHT 9 0.600 103.7 Match Image
3 RF02424 Burkholderia sRNA Bp2_Cand287_SIPHT 9 0.643 99.6 Match Image
3 RF02425 Streptococcus sRNA SpF01 10 0.769 156.4 Match Image
3 RF02430 Streptococcus sRNA SpF19 3 1.000 42.3 Match Image
3 RF02431 Streptococcus sRNA SpF22 3 0.136 35.7 Match Image
3 RF02432 Streptococcus sRNA SpF25 18 0.900 300.1 Match Image
3 RF02433 Streptococcus sRNA SpF36 4 1.000 101.4 Match Image
3 RF02434 Streptococcus sRNA SpF39 13 1.000 278.9 Match Image
3 RF02435 Streptococcus sRNA SpF41 2 0.222 33.9 Match Image
3 RF02442 Streptococcus sRNA SpF66 9 1.000 144.4 Match Image
3 RF02445 Streptococcus sRNA SpR14 3 0.600 32.6 Match Image
3 RF02449 Bacillus sRNA ncr1015 16 1.000 300.4 Match Image
3 RF02450 Bacillus sRNA ncr1175 4 1.000 78.3 Match Image
3 RF02451 Bacillus sRNA ncr1241 4 0.500 53.3 Match Image
3 RF02452 Bacillus sRNA ncr1575 20 0.690 257.6 Match Image
3 RF02454 Bacillus sRNA ncr982 6 1.000 94.6 Match Image
3 RF02495 Oppression of Hydrophobic ORF by sRNA 23 0.676 274.8 Match Image
3 RF02502 Rhizobiales sRNA Atu_C8 26 0.963 339.2 Match Image
3 RF02503 Rhizobiales sRNA Atu_C9 9 1.000 137.2 Match Image
3 RF02524 Streptococcus sRNA sagA 6 1.000 101.0 Match Image
3 RF02526 Streptococcus sRNA SSRC34 8 0.500 95.3 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 37 0.420 871.6 Match Image
3 RF02551 ABC transporter regulator 6 1.000 98.3 Match Image
3 RF02569 IhtA sRNA 2 0.400 23.3 Match Image
3 RF02574 Rickettsia sRNA 10 3 1.000 31.7 Match Image
3 RF02630 Hfq-regulated sRNA 12 2 1.000 30.2 Match Image
3 RF02631 Hfq-regulated sRNA 13 2 1.000 27.5 Match Image
3 RF02713 Mycoplasma sRNA MCS4 5 1.000 90.5 Match Image
3 RF02728 Haemophilus regulatory RNA responsive to iron 7 1.000 109.4 Match Image
3 RF02732 Aggregatibacter sRNA JA04 5 0.833 90.1 Match Image
3 RF02737 Soft rot Enterobacteriaceae Rev 13 asRNA 3 1.000 38.6 Match Image
3 RF02744 Soft rot Enterobacteriaceae Rev 39 5'UTR 4 1.000 75.3 Match Image
3 RF02767 Yersinia sRNA 186/sR026/CsrC 4 1.000 79.6 Match Image
3 RF02790 sodF sRNA 5 0.833 66.0 Match Image
3 RF02834 Vibrio RNA VqmR 3 0.750 39.3 Match Image
3 RF02837 Burkholderia RNA 7 (anti-hemB) 3 1.000 60.6 Match Image
3 RF02838 Enterococcus sRNA 55 2 0.500 23.3 Match Image
3 RF02842 Enterococcus sRNA A1 4 1.000 50.6 Match Image
3 RF02844 Enterococcus sRNA A9 2 0.500 27.0 Match Image
3 RF02845 Enterococcus sRNA 1C 2 1.000 51.0 Match Image
3 RF02858 Actinobacillus sRNA 08 2 0.667 36.2 Match Image
3 RF02859 Actinobacillus sRNA 11 2 1.000 36.8 Match Image
3 RF02860 Actinobacillus sRNA 14 4 1.000 54.3 Match Image
3 RF02863 Enterococcus sRNA 2410 2 0.667 45.7 Match Image
3 RF02865 Burkholderia sRNA 1 4 1.000 53.8 Match Image
3 RF02866 Burkholderia sRNA 16 (Bc_KC_sr1) 3 0.750 35.1 Match Image
3 RF02867 Burkholderia sRNA 11 4 1.000 64.0 Match Image
3 RF02868 Burkholderia sRNA 37 3 1.000 41.7 Match Image
3 RF02870 Burkholderia sRNA 35 2 0.667 24.9 Match Image
3 RF02875 Antisense to pHK01_035 3 1.000 31.4 Match Image
3 RF02876 Antisense to pHK01_099 2 0.500 20.6 Match Image

References

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

Literature references

  1. Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z Nucleic Acids Res. 2011;39:5845-52. RNIE: genome-wide prediction of bacterial intrinsic terminators. PUBMED:21478170

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:21478170
Structure source N/A
Type Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 105 43.51 34

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 10.0
Covariance model Download the Infernal CM for the motif here