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0  structures 0  species 0  sequences

Motif: Terminator1 (RM00022)

Description: Rho independent terminator 1

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 203 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 31 0.816 440.7 Match Image
3 RF00021 Spot 42 RNA 14 0.737 178.9 Match Image
3 RF00022 GcvB RNA 16 0.593 216.2 Match Image
3 RF00028 Group I catalytic intron 2 0.167 49.7 Match Image
3 RF00034 RprA RNA 2 0.154 25.0 Match Image
3 RF00079 OmrA-B family 22 0.957 289.3 Match Image
3 RF00082 SraG RNA 3 0.429 41.7 Match Image
3 RF00083 GlmZ RNA activator of glmS mRNA 15 0.714 209.4 Match Image
3 RF00084 CsrC RNA family 4 1.000 137.7 Match Image
3 RF00106 RNAI 10 1.000 164.9 Match Image
3 RF00112 CyaR/Rye RNA 3 0.176 34.4 Match Image
3 RF00121 MicC RNA 8 1.000 210.0 Match Image
3 RF00124 IS102 RNA 4 0.800 74.6 Match Image
3 RF00125 IS128 RNA 5 1.000 82.3 Match Image
3 RF00130 mir-192/215 microRNA precursor 11 0.268 130.0 Match Image
3 RF00195 RsmY RNA family 7 0.636 95.5 Match Image
3 RF00236 ctRNA 8 0.533 126.0 Match Image
3 RF00238 ctRNA 36 0.750 479.5 Match Image
3 RF00242 ctRNA 10 0.625 145.2 Match Image
3 RF00369 sroC RNA 4 0.667 44.6 Match Image
3 RF00372 sroH RNA 2 1.000 30.5 Match Image
3 RF00378 Qrr RNA 26 0.867 385.2 Match Image
3 RF00397 Small nucleolar RNA SNORA14 4 0.222 48.0 Match Image
3 RF00414 Small nucleolar RNA SNORA22 3 0.097 34.2 Match Image
3 RF00444 PrrF RNA 2 0.111 23.7 Match Image
3 RF00460 U1A polyadenylation inhibition element (PIE) 3 0.077 32.9 Match Image
3 RF00489 ctRNA 5 0.500 66.8 Match Image
3 RF00503 RNAIII 5 0.500 52.1 Match Image
3 RF00506 Threonine operon leader 25 1.000 667.3 Match Image
3 RF00512 Leucine operon leader 5 0.833 113.8 Match Image
3 RF00513 Tryptophan operon leader 13 0.591 184.1 Match Image
3 RF00514 Histidine operon leader 29 0.879 547.0 Match Image
3 RF00515 PyrR binding site 20 0.488 274.6 Match Image
3 RF00516 ylbH leader 3 1.000 50.3 Match Image
3 RF00519 Makes More Granules Regulator RNA (mmgR) 72 0.828 1153.1 Match Image
3 RF00534 SgrS RNA 3 0.375 35.4 Match Image
3 RF00557 Ribosomal protein L10 leader 61 0.629 1067.5 Match Image
3 RF00558 Ribosomal protein L20 leader 31 0.721 504.7 Match Image
3 RF00563 Small nucleolar RNA SNORA53 4 0.143 57.8 Match Image
3 RF00598 Small nucleolar RNA SNORA76 6 0.273 76.6 Match Image
3 RF00624 Pseudomonas sRNA P9 8 0.471 105.9 Match Image
3 RF00628 RgsA sRNA 8 0.296 86.7 Match Image
3 RF00630 Pseudomonas sRNA P26 3 0.111 33.0 Match Image
3 RF00639 microRNA mir-515 6 0.150 77.8 Match Image
3 RF00714 microRNA MIR535 2 0.500 21.7 Match Image
3 RF00722 microRNA mir-451 7 0.368 88.3 Match Image
3 RF00746 microRNA mir-454 2 0.118 25.0 Match Image
3 RF00768 microRNA MIR405 8 0.615 98.1 Match Image
3 RF00779 microRNA MIR474 3 0.273 38.4 Match Image
3 RF00840 microRNA mir-374 8 0.615 121.5 Match Image
3 RF00885 microRNA MIR821 3 0.600 43.6 Match Image
3 RF00887 microRNA mir-802 9 0.692 114.2 Match Image
3 RF00906 microRNA MIR1122 5 0.417 83.2 Match Image
3 RF00969 microRNA mir-556 2 1.000 32.4 Match Image
3 RF01045 microRNA mir-544 5 0.208 58.5 Match Image
3 RF01050 Saccharomyces telomerase 7 0.538 148.0 Match Image
3 RF01066 6C RNA 3 0.167 33.5 Match Image
3 RF01071 Ornate Large Extremophilic RNA 3 0.150 36.5 Match Image
3 RF01227 Small nucleolar RNA snoR83 2 0.286 23.7 Match Image
3 RF01241 Small nucleolar RNA SNORA81 8 0.286 91.1 Match Image
3 RF01253 Small nucleolar RNA snR46 3 0.500 33.2 Match Image
3 RF01264 Small nucleolar RNA snR83 5 1.000 86.9 Match Image
3 RF01270 Small nucleolar RNA snR84 3 0.500 35.9 Match Image
3 RF01291 Small nucleolar RNA SNORD97 7 0.350 91.5 Match Image
3 RF01400 istR Hfq binding RNA 3 0.429 43.7 Match Image
3 RF01405 STnc490 Hfq binding RNA 63 0.829 667.8 Match Image
3 RF01407 STnc560 Hfq binding RNA 12 1.000 179.9 Match Image
3 RF01411 BsrF 4 0.364 50.4 Match Image
3 RF01412 BsrG 3 0.500 38.3 Match Image
3 RF01419 Antisense RNA which regulates isiA expression 35 0.114 421.9 Match Image
3 RF01459 Listeria sRNA rliE 4 1.000 119.0 Match Image
3 RF01470 Listeria sRNA rli38 12 0.600 198.9 Match Image
3 RF01472 Listeria sRNA rli40 4 1.000 74.7 Match Image
3 RF01473 Listeria sRNA rli41 6 1.000 145.5 Match Image
3 RF01491 Listeria sRNA rli54 7 1.400 73.2 Match Image
3 RF01521 caulobacter sRNA CC1840 2 0.667 21.7 Match Image
3 RF01577 Plasmodium RNase_P 4 2.000 62.2 Match Image
3 RF01602 small nucleolar RNA snoR27 3 0.750 37.1 Match Image
3 RF01606 small nucleolar RNA snoR31 2 0.667 27.9 Match Image
3 RF01670 Pseudomonas sRNA P17 3 1.000 38.8 Match Image
3 RF01673 PhrS 2 0.154 21.0 Match Image
3 RF01675 Pseudomonas sRNA CrcZ 6 0.316 81.8 Match Image
3 RF01702 Cyano-2 RNA 11 0.193 156.0 Match Image
3 RF01705 Flavo-1 RNA 19 0.095 273.6 Match Image
3 RF01719 Pseudomon-1/ErsA RNA 19 1.000 308.1 Match Image
3 RF01723 Rhizobiales-2 RNA 8 0.533 85.3 Match Image
3 RF01730 Termite-leu RNA 14 0.700 268.3 Match Image
3 RF01743 leu/phe leader RNA from Lactococcus 6 0.667 93.5 Match Image
3 RF01766 cspA thermoregulator 10 0.667 166.2 Match Image
3 RF01770 Gammaprotebacteria rimP leader 46 1.000 1150.8 Match Image
3 RF01771 Enterobacteria rnk leader 13 1.000 218.3 Match Image
3 RF01772 Pseudomonas rnk leader 15 1.000 317.0 Match Image
3 RF01773 Pseudomonas rpsL leader 2 0.222 29.5 Match Image
3 RF01774 Rickettsia rpsL leader 7 1.000 92.5 Match Image
3 RF01796 Fumarate/nitrate reductase regulator sRNA 4 0.250 49.5 Match Image
3 RF01808 MicX Vibrio cholerae sRNA 10 1.000 256.9 Match Image
3 RF01816 RNA Staph. aureus A 2 0.286 24.2 Match Image
3 RF01819 RNA Staph. aureus D 8 1.000 99.8 Match Image
3 RF01820 RNA Staph. aureus E (RoxS) 10 0.667 161.4 Match Image
3 RF01859 Phenylalanine leader peptide 63 0.887 1242.3 Match Image
3 RF01867 caulobacter sRNA CC2171 5 0.385 60.3 Match Image
3 RF01882 Taurine upregulated gene 1 conserved region 1 17 0.810 215.7 Match Image
3 RF01946 KCNQ1 overlapping transcript 1 conserved region 1 6 0.750 95.1 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 16 0.186 196.1 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 13 0.143 228.4 Match Image
3 RF02029 sraA 14 0.700 233.2 Match Image
3 RF02031 tpke11 4 0.143 45.3 Match Image
3 RF02045 CDKN2B antisense RNA 1 convserved region 3 2 0.111 21.3 Match Image
3 RF02051 Enterobacterial sRNA STnc450 2 0.167 23.5 Match Image
3 RF02053 Enterobacterial sRNA STnc430 6 0.857 170.4 Match Image
3 RF02055 Enterobacterial sRNA STnc380 4 0.800 86.1 Match Image
3 RF02057 Salmonella enterica sRNA STnc40 17 1.000 335.8 Match Image
3 RF02058 Gammaproteobacterial sRNA STnc400 2 1.000 31.2 Match Image
3 RF02063 Salmonella enterica sRNA STnc350 2 1.000 24.2 Match Image
3 RF02064 Enterobacterial sRNA STnc370 10 1.000 174.6 Match Image
3 RF02065 Enterobacterial sRNA STnc340 3 0.750 73.5 Match Image
3 RF02067 Salmonella enterica sRNA STnc310 4 0.500 84.4 Match Image
3 RF02074 Enterobacterial sRNA STnc240 13 0.867 186.0 Match Image
3 RF02075 Enterobacterial sRNA STnc230 8 0.727 120.8 Match Image
3 RF02076 Gammaproteobacterial sRNA STnc100 10 0.417 155.5 Match Image
3 RF02079 Enterobacterial sRNA STnc180 4 0.400 81.8 Match Image
3 RF02082 Enterobacterial sRNA STnc540 3 1.000 89.2 Match Image
3 RF02083 OrzO-P RNA antitoxin family 6 0.857 63.0 Match Image
3 RF02084 Enterobacteria sRNA STnc130 10 0.769 142.2 Match Image
3 RF02101 Highly up-regulated in liver cancer conserved region 2 0.105 23.9 Match Image
3 RF02105 Deleted in lymphocytic leukemia 2 conserved region 1 7 0.259 77.6 Match Image
3 RF02110 Deleted in lymphocytic leukemia 2 conserved region 6 3 0.094 31.2 Match Image
3 RF02144 rsmX 12 0.750 185.1 Match Image
3 RF02190 ST7 overlapping transcript 4 conserved region 4 2 0.077 29.2 Match Image
3 RF02225 Proteobacterial sRNA sX6 8 1.000 117.9 Match Image
3 RF02230 Proteobacterial sRNA sX11 5 0.500 70.0 Match Image
3 RF02278 Betaproteobacteria toxic small RNA 40 0.784 604.1 Match Image
3 RF02342 Alphaproteobacterial sRNA ar7 28 0.966 372.9 Match Image
3 RF02343 Alphaproteobacterial sRNA ar9 13 0.464 218.2 Match Image
3 RF02344 Alphaproteobacterial ar14 83 0.703 1267.2 Match Image
3 RF02345 Alphaproteobacterial ar15 12 0.197 216.6 Match Image
3 RF02346 Alphaproteobacterial sRNA ar35 9 0.692 119.0 Match Image
3 RF02351 Proteobacteria sRNA psRNA14 2 0.667 47.5 Match Image
3 RF02353 Bradyrhizobiaceae sRNA BjrC68 4 0.333 49.0 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 23 0.920 335.8 Match Image
3 RF02362 Cyanobacterial functional RNA 10 5 0.833 87.3 Match Image
3 RF02366 Cyanobacterial functional RNA 19 6 1.000 132.5 Match Image
3 RF02368 Cyanobacterial functional RNA 21 2 1.000 24.6 Match Image
3 RF02370 Bacillus tryptophan operon leader 5 0.556 52.4 Match Image
3 RF02371 PyrG leader 9 0.900 114.3 Match Image
3 RF02375 Aar sRNA 13 1.000 203.7 Match Image
3 RF02376 SR1 sRNA 6 1.000 121.0 Match Image
3 RF02378 SurC sRNA 4 1.000 49.4 Match Image
3 RF02379 Cia-dependent small RNA csRNA1 28 0.583 394.5 Match Image
3 RF02384 FasX small RNA 7 0.875 85.5 Match Image
3 RF02385 Staphylococcus sRNA sau-13 3 0.500 40.8 Match Image
3 RF02399 Nitrogen stress-induced RNA 1 2 0.118 24.2 Match Image
3 RF02405 Pseudomonas sRNA P34 5 1.000 88.2 Match Image
3 RF02409 Small nucleolar RNA snoR125 4 0.800 51.0 Match Image
3 RF02411 Small nucleolar RNA snoR138 3 0.429 34.4 Match Image
3 RF02420 Burkholderia sRNA Bp1_Cand612_SIPHT 4 0.364 51.0 Match Image
3 RF02423 Burkholderia sRNA Bp1_Cand871_SIPHT 7 0.467 80.4 Match Image
3 RF02424 Burkholderia sRNA Bp2_Cand287_SIPHT 8 0.571 93.0 Match Image
3 RF02425 Streptococcus sRNA SpF01 8 0.615 129.8 Match Image
3 RF02430 Streptococcus sRNA SpF19 3 1.000 49.9 Match Image
3 RF02432 Streptococcus sRNA SpF25 18 0.900 340.7 Match Image
3 RF02433 Streptococcus sRNA SpF36 4 1.000 112.4 Match Image
3 RF02434 Streptococcus sRNA SpF39 8 0.615 107.0 Match Image
3 RF02435 Streptococcus sRNA SpF41 2 0.222 28.8 Match Image
3 RF02442 Streptococcus sRNA SpF66 9 1.000 175.2 Match Image
3 RF02445 Streptococcus sRNA SpR14 3 0.600 33.6 Match Image
3 RF02449 Bacillus sRNA ncr1015 16 1.000 300.6 Match Image
3 RF02450 Bacillus sRNA ncr1175 4 1.000 66.5 Match Image
3 RF02452 Bacillus sRNA ncr1575 7 0.241 96.4 Match Image
3 RF02470 Mycobacterium sRNA Ms_IGR-8 2 0.667 22.5 Match Image
3 RF02495 Oppression of Hydrophobic ORF by sRNA 19 0.559 208.1 Match Image
3 RF02502 Rhizobiales sRNA Atu_C8 27 1.000 451.2 Match Image
3 RF02503 Rhizobiales sRNA Atu_C9 9 1.000 136.0 Match Image
3 RF02524 Streptococcus sRNA sagA 5 0.833 58.8 Match Image
3 RF02526 Streptococcus sRNA SSRC34 8 0.500 94.8 Match Image
3 RF02528 Streptococcus sRNA SSRC41 2 0.250 23.9 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 24 0.273 531.2 Match Image
3 RF02545 Trypanosomatid mitochondrial small subunit ribosomal RNA 3 0.750 37.7 Match Image
3 RF02551 ABC transporter regulator 4 0.667 58.9 Match Image
3 RF02552 RcsR1 sRNA 10 1.000 141.6 Match Image
3 RF02569 IhtA sRNA 2 0.400 23.1 Match Image
3 RF02631 Hfq-regulated sRNA 13 2 1.000 24.8 Match Image
3 RF02657 Sense overlapping transcript RNA 2652 (sot) 2 1.000 27.6 Match Image
3 RF02713 Mycoplasma sRNA MCS4 5 1.000 114.3 Match Image
3 RF02728 Haemophilus regulatory RNA responsive to iron 6 0.857 113.7 Match Image
3 RF02732 Aggregatibacter sRNA JA04 5 0.833 81.1 Match Image
3 RF02737 Soft rot Enterobacteriaceae Rev 13 asRNA 3 1.000 51.5 Match Image
3 RF02742 Soft rot Enterobacteriaceae Rev 72 asRNA 3 1.000 42.6 Match Image
3 RF02744 Soft rot Enterobacteriaceae Rev 39 5'UTR 4 1.000 97.8 Match Image
3 RF02767 Yersinia sRNA 186/sR026/CsrC 4 1.000 85.0 Match Image
3 RF02790 sodF sRNA 5 0.833 76.1 Match Image
3 RF02837 Burkholderia RNA 7 (anti-hemB) 3 1.000 60.0 Match Image
3 RF02842 Enterococcus sRNA A1 4 1.000 94.1 Match Image
3 RF02844 Enterococcus sRNA A9 2 0.500 31.2 Match Image
3 RF02846 Enterococcus sRNA 84 2 0.400 21.8 Match Image
3 RF02859 Actinobacillus sRNA 11 2 1.000 43.7 Match Image
3 RF02860 Actinobacillus sRNA 14 4 1.000 56.9 Match Image
3 RF02863 Enterococcus sRNA 2410 2 0.667 35.5 Match Image
3 RF02865 Burkholderia sRNA 1 4 1.000 70.4 Match Image
3 RF02867 Burkholderia sRNA 11 4 1.000 80.4 Match Image
3 RF02880 Mesorhizobail RNA 15 2 1.000 30.1 Match Image
3 RF02883 Burkholderia sRNA 2 2 0.400 24.0 Match Image
3 RF02884 Burkholderia sRNA 7 5 1.000 69.8 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 1,012 39.97 46

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