0  structures 0  species 0  sequences

Motif: CsrA_binding (RM00005)

Description: CsrA/RsmA binding motif

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 CsrA protein 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

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Alignment format:
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Family matches

There are 190 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 RF00003 U1 spliceosomal RNA 30 0.300 246.2 Match Image
3 RF00009 Nuclear RNase P 23 0.198 194.0 Match Image
3 RF00010 Bacterial RNase P class A 147 0.321 1410.3 Match Image
3 RF00011 Bacterial RNase P class B 19 0.167 163.3 Match Image
3 RF00017 Metazoan signal recognition particle RNA 44 0.484 412.3 Match Image
3 RF00018 CsrB/RsmB RNA family 38 1.000 4480.4 Match Image
3 RF00023 transfer-messenger RNA 113 0.237 983.3 Match Image
3 RF00024 Vertebrate telomerase RNA 12 0.324 115.4 Match Image
3 RF00030 RNase MRP 10 0.152 73.7 Match Image
3 RF00057 RyhB RNA 8 0.308 72.3 Match Image
3 RF00078 MicA sRNA 5 0.294 40.4 Match Image
3 RF00079 OmrA-B family 5 0.217 36.0 Match Image
3 RF00084 CsrC RNA family 4 1.000 134.6 Match Image
3 RF00100 7SK RNA 24 0.533 187.5 Match Image
3 RF00101 SraC/RyeA RNA 13 1.000 101.0 Match Image
3 RF00102 VA RNA 19 0.352 172.8 Match Image
3 RF00113 Short Intergenic Abundant RNA 4 0.235 32.2 Match Image
3 RF00166 PrrB/RsmZ RNA family 37 1.000 1495.1 Match Image
3 RF00174 Cobalamin riboswitch 60 0.140 531.7 Match Image
3 RF00177 Bacterial small subunit ribosomal RNA 94 0.949 1739.0 Match Image
3 RF00178 mir-24 microRNA precursor family 17 1.000 130.9 Match Image
3 RF00195 RsmY RNA family 11 1.000 294.3 Match Image
3 RF00222 Bag-1 internal ribosome entry site (IRES) 2 0.133 18.0 Match Image
3 RF00224 FGF-2 internal ribosome entry site (IRES) 5 0.833 47.7 Match Image
3 RF00322 Small nucleolar RNA SNORA31 3 0.600 30.6 Match Image
3 RF00335 Small nucleolar RNA Z13/snr52 3 0.071 23.5 Match Image
3 RF00353 Small nucleolar RNA snoR31/Z110/Z27 3 0.375 22.5 Match Image
3 RF00373 Archaeal RNase P 19 0.271 165.2 Match Image
3 RF00374 Gammaretrovirus core encapsidation signal 5 0.227 37.8 Match Image
3 RF00409 Small nucleolar RNA SNORA7 3 0.097 25.0 Match Image
3 RF00411 Small nucleolar RNA SNORA9 4 0.111 35.3 Match Image
3 RF00425 Small nucleolar RNA SNORA18 2 0.069 14.9 Match Image
3 RF00435 Repression of heat shock gene expression (ROSE) element 6 0.462 47.7 Match Image
3 RF00436 UnaL2 LINE 3' element 8 0.267 56.0 Match Image
3 RF00442 ykkC-yxkD leader 11 0.113 102.8 Match Image
3 RF00448 Epstein-Barr virus nuclear antigen (EBNA) IRES 2 0.333 16.4 Match Image
3 RF00449 HIF-1 alpha IRES 5 0.294 41.6 Match Image
3 RF00468 Hepatitis C virus stem-loop VII 33 0.300 309.7 Match Image
3 RF00470 Togavirus 5' plus strand cis-regulatory element 2 0.061 17.4 Match Image
3 RF00503 RNAIII 4 0.400 36.8 Match Image
3 RF00517 serC leader 14 0.200 132.7 Match Image
3 RF00545 Small nucleolar RNA psi18S-841/snoR66 2 0.083 18.5 Match Image
3 RF00547 TrkB IRES 3 0.188 25.7 Match Image
3 RF00564 Small Cajal body specific RNA 11 4 0.167 29.2 Match Image
3 RF00573 Small nucleolar RNA SNORD67 7 0.467 53.1 Match Image
3 RF00584 Small nucleolar RNA SNORD105 2 0.133 18.8 Match Image
3 RF00593 Small nucleolar RNA U83B 3 0.143 25.7 Match Image
3 RF00602 Small Cajal body specific RNA 21 2 0.083 15.8 Match Image
3 RF00604 Small nucleolar RNA SNORD88 7 0.200 57.1 Match Image
3 RF00608 Small nucleolar RNA SNORD99 4 0.174 38.2 Match Image
3 RF00613 Small nucleolar RNA SNORD94 3 0.143 32.8 Match Image
3 RF00614 Small nucleolar RNA SNORA11 8 0.229 63.3 Match Image
3 RF00624 Pseudomonas sRNA P9 10 0.588 96.3 Match Image
3 RF00625 Pseudomonas sRNA P11 8 0.533 65.3 Match Image
3 RF00656 microRNA mir-205 6 0.207 47.8 Match Image
3 RF00665 microRNA mir-290 3 0.111 25.0 Match Image
3 RF00673 microRNA mir-217 5 0.185 42.8 Match Image
3 RF00679 microRNA mir-210 2 0.077 17.2 Match Image
3 RF00758 microRNA mir-346 4 0.800 29.2 Match Image
3 RF00773 microRNA mir-298 4 0.800 40.2 Match Image
3 RF00775 microRNA mir-432 4 0.667 30.4 Match Image
3 RF00875 microRNA mir-692 2 0.182 16.5 Match Image
3 RF00886 microRNA MIR807 5 0.167 38.0 Match Image
3 RF01016 microRNA mir-584 3 0.188 29.5 Match Image
3 RF01050 Saccharomyces telomerase 7 0.538 50.9 Match Image
3 RF01070 SucA RNA motif 4 0.114 32.0 Match Image
3 RF01071 Ornate Large Extremophilic RNA 2 0.100 17.3 Match Image
3 RF01211 Small nucleolar RNA SNORD124 9 0.500 72.8 Match Image
3 RF01231 Small nucleolar RNA snoR74 2 0.222 15.6 Match Image
3 RF01233 Small nucleolar RNA U109 2 0.077 15.2 Match Image
3 RF01234 Small nucleolar RNA SNORA47 5 0.250 44.7 Match Image
3 RF01254 Small nucleolar RNA snR34 4 1.000 29.6 Match Image
3 RF01263 Small nucleolar RNA snR191 2 0.182 16.5 Match Image
3 RF01294 Small nucleolar RNA U89 2 0.125 18.7 Match Image
3 RF01296 Small nucleolar RNA U85 4 0.190 29.6 Match Image
3 RF01486 Listeria sRNA rli62 2 1.000 18.5 Match Image
3 RF01502 Fungal signal recognition particle RNA 16 0.320 148.9 Match Image
3 RF01512 A. fumigatus sRNA Afu_309 2 0.200 17.0 Match Image
3 RF01532 Trypanosomatid snoRNA TB10Cs3H2 4 0.667 35.8 Match Image
3 RF01673 PhrS 3 0.231 22.8 Match Image
3 RF01675 Pseudomonas sRNA CrcZ 3 0.158 22.9 Match Image
3 RF01684 MALAT1-associated small cytoplasmic RNA/MEN beta RNA 7 0.132 63.2 Match Image
3 RF01702 Cyano-2 RNA 10 0.175 120.0 Match Image
3 RF01712 Methylobacterium-1 RNA 3 0.088 27.9 Match Image
3 RF01717 PhotoRC-II RNA 51 0.115 441.1 Match Image
3 RF01729 Termite-flg RNA 12 0.923 118.0 Match Image
3 RF01731 TwoAYGGAY RNA 193 0.919 3179.0 Match Image
3 RF01736 flg-Rhizobiales RNA 4 0.308 29.9 Match Image
3 RF01740 gyrA RNA 6 0.333 72.5 Match Image
3 RF01745 manA RNA 20 0.106 167.1 Match Image
3 RF01755 rmf RNA 6 0.375 71.3 Match Image
3 RF01756 rne-II RNA 2 0.125 14.4 Match Image
3 RF01757 sbcD RNA 5 0.833 61.0 Match Image
3 RF01760 traJ-II RNA 10 0.213 85.5 Match Image
3 RF01762 Whalefall-1 RNA 4 0.286 39.6 Match Image
3 RF01763 ykkC-III RNA 10 0.256 91.8 Match Image
3 RF01794 sok antitoxin 12 0.132 94.0 Match Image
3 RF01803 Editing element of GABA-3 exon 9 6 0.115 44.8 Match Image
3 RF01841 venezuelan equine encephalitis virus ribosomal frameshift element 5 0.500 39.5 Match Image
3 RF01844 SmY spliceosomal RNA 7 0.115 56.4 Match Image
3 RF01845 Early nodulin 40 5 0.143 46.0 Match Image
3 RF01846 Fungal small nucleolar RNA U3 9 0.136 87.9 Match Image
3 RF01847 Plant small nucleolar RNA U3 4 0.167 40.0 Match Image
3 RF01851 Cyanobacteria transfer-messenger RNA 17 0.630 169.7 Match Image
3 RF01857 Archaeal signal recognition particle RNA 22 0.415 206.7 Match Image
3 RF01867 caulobacter sRNA CC2171 2 0.154 24.8 Match Image
3 RF01872 Maternally expressed 3 conserved region 2 16 1.000 261.7 Match Image
3 RF01874 Myocardial infarction associated transcript exon 1 4 0.400 41.3 Match Image
3 RF01875 Myocardial infarction associated transcript exon 5 conserved region 1 2 0.222 17.8 Match Image
3 RF01897 microRNA mir-188 3 0.214 34.8 Match Image
3 RF01909 CDKN2B antisense RNA 1 intronic convserved region 2 0.080 18.5 Match Image
3 RF01942 microRNA mir-1937 27 0.158 289.1 Match Image
3 RF01946 KCNQ1 overlapping transcript 1 conserved region 1 6 0.750 57.9 Match Image
3 RF01947 KCNQ1 overlapping transcript 1 conserved region 2 13 0.722 117.3 Match Image
3 RF01951 SOX2 overlapping transcript exon 1 4 0.138 31.6 Match Image
3 RF01953 SOX2 overlapping transcript exon 3 9 0.818 93.6 Match Image
3 RF01957 Nuclear enriched abundant transcript 1 conserved region 3 13 0.722 117.2 Match Image
3 RF01959 Archaeal small subunit ribosomal RNA 80 0.930 1596.2 Match Image
3 RF01960 Eukaryotic small subunit ribosomal RNA 38 0.418 419.4 Match Image
3 RF01963 Rhabdomyosarcoma 2 associated transcript conserved region 2 3 0.188 25.5 Match Image
3 RF01969 Rhabdomyosarcoma 2 associated transcript conserved region 8 2 0.091 17.8 Match Image
3 RF02032 Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA 7 0.200 76.4 Match Image
3 RF02041 HOXA transcript at the distal tip, conserved region 2 3 0.120 27.0 Match Image
3 RF02047 Sphinx conserved region 2 2 0.054 15.9 Match Image
3 RF02057 Salmonella enterica sRNA STnc40 9 0.529 78.0 Match Image
3 RF02071 Salmonella enterica sRNA STnc280 3 1.000 22.0 Match Image
3 RF02084 Enterobacteria sRNA STnc130 3 0.231 28.1 Match Image
3 RF02094 mir-1803 microRNA precursor 2 0.333 14.5 Match Image
3 RF02101 Highly up-regulated in liver cancer conserved region 6 0.316 62.1 Match Image
3 RF02103 Deleted in lymphocytic leukemia 1 conserved region 1 2 0.077 14.6 Match Image
3 RF02104 Deleted in lymphocytic leukemia 1 conserved region 2 2 0.125 16.1 Match Image
3 RF02111 IS009 7 0.636 70.2 Match Image
3 RF02113 DLG2 antisense RNA 1 conserved region 2 3 0.130 24.2 Match Image
3 RF02116 FAS antisense RNA 1 conserved region 2 0.105 19.0 Match Image
3 RF02117 FMR1 antisense RNA 1 conserved region 1 4 0.200 32.8 Match Image
3 RF02121 FTX transcript, XIST regulator conserved region 3 10 0.714 103.6 Match Image
3 RF02122 FTX transcript, XIST regulator conserved region 5 3 0.214 24.3 Match Image
3 RF02123 FTX transcript, XIST regulator conserved region 4 4 0.308 32.3 Match Image
3 RF02124 JPX transcript, XIST activator conserved region 1 2 0.143 14.6 Match Image
3 RF02127 GNAS antisense RNA 1 conserved region 1 6 0.286 44.1 Match Image
3 RF02138 HOXA11 antisense RNA 1 conserved region 2 6 0.286 51.0 Match Image
3 RF02143 Hydatidiform mole associated and imprinted conserved region 1 10 0.625 93.9 Match Image
3 RF02144 rsmX 16 1.000 510.4 Match Image
3 RF02145 Maternally expressed 8 exon 1 8 0.348 70.3 Match Image
3 RF02151 MER1 repeat containing imprinted transcript 1 conserved region 1 2 0.095 22.2 Match Image
3 RF02164 Pvt1 oncogene conserved region 1 4 0.235 41.8 Match Image
3 RF02165 Pvt1 oncogene conserved region 2 15 0.882 142.2 Match Image
3 RF02170 Pvt1 oncogene conserved region 7 5 0.625 40.0 Match Image
3 RF02188 ST7 overlapping transcript 4 conserved region 2 5 0.172 45.4 Match Image
3 RF02189 ST7 overlapping transcript 4 conserved region 3 5 0.250 41.7 Match Image
3 RF02195 TP53 target 1 conserved region 1 2 0.125 15.2 Match Image
3 RF02196 TP53 target 1 conserved region 2 7 0.583 55.2 Match Image
3 RF02197 TP73 antisense RNA 1 conserved region 3 0.750 33.7 Match Image
3 RF02198 TTC28 antisense RNA 1 conserved region 1 2 0.143 16.8 Match Image
3 RF02201 TTC28 antisense RNA 1 conserved region 4 2 0.111 15.9 Match Image
3 RF02204 WT1 antisense RNA conserved region 2 2 0.111 18.0 Match Image
3 RF02205 WT1 antisense RNA conserved region 3 11 0.579 116.5 Match Image
3 RF02212 ZFAT antisense RNA 1 conserved region 2 2 0.182 14.4 Match Image
3 RF02213 ZFAT antisense RNA 1 conserved region 3 4 0.800 32.3 Match Image
3 RF02225 Proteobacterial sRNA sX6 4 0.500 35.0 Match Image
3 RF02226 Xanthomonas sRNA sX7 16 2.000 146.0 Match Image
3 RF02234 Xanthomonadaceae sRNA sX15 11 0.786 107.5 Match Image
3 RF02238 Xanthomonas sRNA asX4/Xoo4 8 1.000 151.3 Match Image
3 RF02243 Proteobacterial sRNA Xoo8 3 0.750 28.4 Match Image
3 RF02247 Six3os1 conserved region 2 8 0.533 68.3 Match Image
3 RF02270 Neisseria sigma-E sRNA 6 0.857 43.8 Match Image
3 RF02276 Hammerhead ribozyme (type II) 2 0.083 14.3 Match Image
3 RF02342 Alphaproteobacterial sRNA ar7 2 0.069 14.8 Match Image
3 RF02355 Bradyrhizobiaceae sRNA BjrC174 3 0.200 21.8 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 7 0.280 61.6 Match Image
3 RF02377 SurA sRNA 7 1.750 57.1 Match Image
3 RF02405 Pseudomonas sRNA P34 9 1.800 83.5 Match Image
3 RF02422 Burkholderia sRNA Bp1_Cand738_SIPHT 9 0.429 67.1 Match Image
3 RF02424 Burkholderia sRNA Bp2_Cand287_SIPHT 2 0.143 16.7 Match Image
3 RF02430 Streptococcus sRNA SpF19 2 0.667 17.4 Match Image
3 RF02433 Streptococcus sRNA SpF36 4 1.000 29.6 Match Image
3 RF02462 Ascomycota telomerase RNA 4 1.000 56.2 Match Image
3 RF02463 Mycobacterium sRNA Ms_AS-1 4 0.800 36.4 Match Image
3 RF02514 5' ureB small RNA 2 0.154 14.8 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 83 0.912 1779.4 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 90 0.882 1771.2 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 21 0.457 355.6 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 65 0.739 940.9 Match Image
3 RF02545 Trypanosomatid mitochondrial small subunit ribosomal RNA 3 0.750 22.8 Match Image
3 RF02605 Streptomyces sRNA scr5239 4 0.667 33.2 Match Image
3 RF02683 NiCo riboswitch 10 0.122 123.0 Match Image
3 RF02687 RAGATH-8 RNA 3 1.000 25.2 Match Image
3 RF02689 hilD 3'UTR 4 0.800 46.4 Match Image
3 RF02757 Erse small RNA 4 0.667 43.3 Match Image
3 RF02767 Yersinia sRNA 186/sR026/CsrC 4 1.000 107.1 Match Image

References

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

Literature references

  1. Liu MY, Gui G, Wei B, Preston JF 3rd, Oakford L, Yuksel U, Giedroc DP, Romeo T J Biol Chem 1997;272:17502-17510. The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. PUBMED:97362239

  2. Cui Y, Chatterjee A, Liu Y, Dumenyo CK, Chatterjee AK J Bacteriol 1995;177:5108-5115. Identification of a global repressor gene, rsmA, of Erwinia carotovora subsp. carotovora that controls extracellular enzymes, N-(3-oxohexanoyl)-L-homoserine lactone, and pathogenicity in soft-rotting Erwinia spp. PUBMED:7665490

  3. Weilbacher T, Suzuki K, Dubey AK, Wang X, Gudapaty S, Morozov I, Baker CS, Georgellis D, Babitzke P, Romeo T Mol Microbiol 2003;48:657-670. A novel sRNA component of the carbon storage regulatory system of Escherichia coli. PUBMED:12694612

  4. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S; Curr Biol 2001;11:941-950. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. PUBMED:11448770

  5. Aarons S, Abbas A, Adams C, Fenton A, O'Gara F J Bacteriol 2000;182:3913-3919. A regulatory RNA (PrrB RNA) modulates expression of secondary metabolite genes in Pseudomonas fluorescens F113. PUBMED:10869066

  6. Valverde C, Heeb S, Keel C, Haas D Mol Microbiol 2003;50:1361-1379. RsmY, a small regulatory RNA, is required in concert with RsmZ for GacA-dependent expression of biocontrol traits in Pseudomonas fluorescens CHA0. PUBMED:14622422

  7. Moll S, Schneider DJ, Stodghill P, Myers CR, Cartinhour SW, Filiatrault MJ RNA Biol. 2010;7:508-516. Construction of an rsmX co-variance model and identification of five rsmX non-coding RNAs in Pseudomonas syringae pv. tomato DC3000. PUBMED:21060253

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 Gardner PP
Structure source N/A
Type Specific Recognition Motif
Author Gardner PP
Alignment details
Alignment Number of
sequences
Average length Sequence
identity (%)
seed 1,247 13.19 54

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 11.0
Covariance model Download the Infernal CM for the motif here