Infobox rfam Name rydB RNA image RF00118.jpg width caption Predicted secondary structure and sequence conservation of rydB Symbol rydB AltSymbols Rfam RF00118 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The RydB RNA is a non coding RNA originally identified in E. coli in an RNA screen. ref name Was01 cite journal last Wassarman first KM coauthors Repoila F, Rosenow C, Storz G, Gottesman S year 2001 title Identification of novel small RNAs using comparative genomics and microarrays journal Genes Dev volume 15 pages 1637&ndash 1651 pmid 11445539 doi 10.1101 gad.901001 issue 13 pmc 312727 ref This gene is only 67 nucleotide s in length and is composed of a stem loop hairpin like structure. RydB lies between the ydiC and ydiH in E. coli . Homologous RNA genes have been found in other species such as Shigella flexneri and Salmonella species. The molecular function of this RNA is unknown. ref name Was01 See also RyhB RNA RyeB RNA RyeE RNA References reflist 1 External links Rfam id RF00118 name rydB RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name RyeB RNA image RF00111.jpg width caption Predicted secondary structure and sequence conservation of RyeB Symbol RyeB AltSymbols Rfam RF00111 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The RyeB RNA is a non coding RNA that was identified in a large scale screen of E. coli . ref cite journal last Wassarman first KM coauthors Repoila F, Rosenow C, Storz G, Gottesman S year 2001 title Identification of novel small RNAs using comparative genomics and microarrays journal Genes Dev volume 15 pages 1637&ndash 1651 pmid 11445539 doi 10.1101 gad.901001 issue 13 pmc 312727 ref The exact 5 and 3 ends of this RNA are uncertain. This RNA overlaps the SraC RyeA RNA on the opposite strand suggesting that the two may act in a concerted manner. See also RydB RNA RyhB RNA RyeE RNA References reflist 1 External links Rfam id RF00111 name RyeB RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name C0719 RNA image RF00117.jpg width caption Predicted secondary structure and sequence conservation of C0719 Symbol C0719 AltSymbols Rfam RF00117 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The C0719 RNA is a bacterial non coding RNA of 222 nucleotides in length that is found between the yghK and glcB gene s in the genomes of Escherichia coli and Shigella flexneri . This non coding RNA was originally identified in E.coli using microarray high density oligonucleotide probe arrays microarray. ref name pmid12202758 cite journal author Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res. volume 30 issue 17 pages 3732 8 year 2002 pmid 12202758 doi 10.1093 nar gkf505 pmc 137427 ref The function of this ncRNA is unknown. See also C0299 RNA C0343 RNA C0465 RNA References references External links Rfam id RF00117 name C0719 RNA DEFAULTSORT C0719 Rna Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name IS102 RNA image RF00124.jpg width caption Predicted secondary structure and sequence conservation of IS102 Symbol IS102 AltSymbols Rfam RF00124 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The IS102 RNA is a non coding RNA that is found in bacteria such as Shigella flexneri and Escherichia coli . The RNA is 208 nucleotide s in length and found between the yeeP and flu genes . This RNA was identified in a computational screen of E. coli . ref cite journal last Tjaden first B coauthors Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C year 2002 title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res volume 30 pages 3732&ndash 3738 pmid 12202758 doi 10.1093 nar gkf505 issue 17 pmc 137427 ref The function of this RNA is unknown. See also IS061 RNA IS128 RNA References reflist 1 External links Rfam id RF00124 name IS102 RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name IS128 RNA image RF00125.jpg width caption Predicted secondary structure and sequence conservation of IS128 Symbol IS128 AltSymbols Rfam RF00125 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0001263 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The IS128 RNA is a non coding RNA found in bacteria such as Escherichia coli and Shigella flexneri . The RNA is 209 nucleotides in length. It is found between the sseA and sseB genes . The IS128 RNA was initially identified in a computational screen of the E. coli genome. ref cite journal last Tjaden first B coauthors Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C year 2002 title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res volume 30 pages 3732&ndash 3738 pmid 12202758 doi 10.1093 nar gkf505 issue 17 pmc 137427 ref The function of this RNA is unknown. See also IS061 RNA IS102 RNA References reflist 1 External links Rfam id RF00125 name IS128 RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name RydC RNA image RF00505.jpg width caption Predicted secondary structure and sequence conservation of RydC Symbol RydC AltSymbols Rfam RF00505 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData RydC is a bacteria l non coding RNA . RydC is thought to regulate a messenger RNA mRNA , yejABEF , which encodes an ABC transporter protein . RydC is known to bind the Hfq protein , which causes a conformational change in the RNA molecule. The Hfq RydC complex is then thought to bind to the target mRNA and induce its degradation. ref name antal 2005 cite journal last Antal first M coauthors Bordeau V, Douchin V, Felden B year 2005 title A small bacterial RNA regulates a putative ABC transporter journal J Biol Chem. volume 280 pages 7901&ndash 7908 pmid 15618228 doi 10.1074 jbc.M413071200 issue 9 ref See also RyfA RNA RydB RNA RybB RNA References reflist 1 External links Rfam id RF00505 name RydC RNA Category Non coding RNA molecular cell biology stub ... more details
Orphan date February 2009 Infobox rfam Name sar RNA image RF00262.jpg width caption Predicted secondary structure and sequence conservation of sar Symbol sar AltSymbols Rfam RF00262 miRBase miRBase family RNA type Gene Antisense RNA antisense Tax domain Bacteria Virus es GO GO 0003729 SO SO 0000644 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Sar RNA is an antisense non coding RNA that is partly responsible for the negative regulation of antirepressor synthesis during development of bacteriophage P22 phage P22 . ref name Sch97 cite journal last Schaefer first KL coauthors McClure WR year 1997 title Antisense RNA control of gene expression in bacteriophage P22. I. Structures of sar RNA and its target, ant mRNA journal RNA volume 3 pages 141&ndash 156 pmid 9042942 issue 2 pmc 1369469 ref The target of Sar RNA is ant mRNA. Structurally, Sar RNA forms two stem loop s. ref name Sch97 References reflist 1 External links Rfam id RF00262 name sar RNA Category Antisense RNA molecular cell biology stub ... more details
Orphan date February 2009 Infobox rfam Name RNA OUT image RF00240.jpg width caption Predicted secondary structure and sequence conservation of RNA OUT Symbol RNA OUT AltSymbols Rfam RF00240 miRBase miRBase family RNA type Gene Antisense RNA antisense Tax domain Bacteria GO SO SO 0000644 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData RNA OUT is a non coding RNA that is antisense to the RNA IN non coding RNA. Transposable element Transposition of insertion sequence IS10 is regulated by an anti sense RNA which inhibits transposase expression when IS10 is present in multiple copies per cell. RNA OUT consists of a stem loop domain topped by a flexibly paired loop the 5 end of the target molecule, RNA IN, is complementary to the top of the loop, and complementarity extends for 35 nucleotides down one side of RNA OUT. ref cite journal last Kittle first JD coauthors Simons RW, Lee J, Kleckner N year 1989 title Insertion sequence IS10 anti sense pairing initiates by an interaction between the 5 end of the target RNA and a loop in the anti sense RNA journal J Mol Biol volume 210 pages 561&ndash 572 pmid 2482367 doi 10.1016 0022 2836 89 90132 0 issue 3 ref References reflist 1 External links Rfam id RF00240 name RNA OUT Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name CyaR Rye RNA image RF00112.jpg width caption Predicted secondary structure and sequence conservation of CyaR RyeE Symbol CyaR RyeE AltSymbols RyeE Rfam RF00112 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The CyaR RNA formerly known as RyeE RNA non coding RNA was identified in a large scale screen of E. coli and was called candidate 14. ref cite journal last Wassarman first KM coauthors Repoila F, Rosenow C, Storz G, Gottesman S year 2001 title Identification of novel small RNAs using comparative genomics and microarrays journal Genes Dev volume 15 pages 1637&ndash 1651 pmid 11445539 doi 10.1101 gad.901001 issue 13 pmc 312727 ref The exact 5 and 3 ends of this RNA are uncertain. This gene lies between yegQ and orgK in E. coli . This small RNA was shown to be bound by the Hfq protein . This RNA has been renamed as CyaR for cyclic AMP activated RNA . It has recently been shown that CyaR RNA acts as a repressor of the porin OmpX. ref name pmid18399940 cite journal author Papenfort K, Pfeiffer V, Lucchini S, Sonawane A, Hinton JC, Vogel J title Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP dependent riboregulator of OmpX synthesis journal Mol. Microbiol. volume 68 issue 4 pages 890 906 year 2008 month May pmid 18399940 doi 10.1111 j.1365 2958.2008.06189.x url ref It has also been shown that cyaR expression is tightly controlled by the cyclic AMP receptor protein, CRP . ref name pmid18399940 See also RydB RNA RyhB RNA RyeB RNA References reflist 1 External links Rfam id RF00112 name RyeE RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name C0299 RNA image RF00119.jpg width caption Predicted secondary structure and sequence conservation of C0299 Symbol C0299 AltSymbols Rfam RF00119 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0001263 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The C0299 RNA family consists of a group of Shigella flexneri and Escherichia coli RNA genes which are 78 bases in length and are found between the hlyE and umuD gene s. The function of this RNA is unknown. ref cite journal last Tjaden first B coauthors Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C year 2002 title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res volume 30 pages 3732&ndash 3738 pmid 12202758 doi 10.1093 nar gkf505 issue 17 pmc 137427 ref See also C0343 RNA C0465 RNA C0719 RNA References reflist 1 External links Rfam id RF00119 name C0299 RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name C0465 RNA image RF00116.jpg width caption Predicted secondary structure and sequence conservation of C0465 Symbol C0465 AltSymbols Rfam RF00116 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The C0465 RNA is a bacterial non coding RNA of 78 nucleotides in length that is found between the tar and cheW gene s in the genomes of Escherichia coli and Shigella flexneri . This ncRNA was originally identified in E.coli using microarray high density oligonucleotide probe arrays microarray ref name pmid12202758 cite journal author Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res. volume 30 issue 17 pages 3732 8 year 2002 pmid 12202758 doi 10.1093 nar gkf505 pmc 137427 ref . The function of this ncRNA is unknown. See also C0299 RNA C0343 RNA C0719 RNA References references External links Rfam id RF00116 name C0465 RNA DEFAULTSORT C0465 Rna Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name HgcF RNA image RF00058.jpg width caption Predicted secondary structure and sequence conservation of HgcF Symbol HgcF AltSymbols Rfam RF00058 miRBase miRBase family RNA type Gene Tax domain Archaea GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The HgcF RNA gene is a non coding RNA identified computationally and experimentally verified in AT rich hyperthermophiles. ref cite journal last Klein first RJ coauthors Misulovin Z, Eddy SR year 2002 title Noncoding RNA genes identified in AT rich hyperthermophiles journal Proc Natl Acad Sci USA volume 99 pages 7542&ndash 7547 pmid 12032319 doi 10.1073 pnas.112063799 issue 11 pmc 124278 ref The genes were named hgcA through hgcG high GC . The molecular function of HgcF is unknown. See also HgcC family RNA HgcE RNA HgcG RNA SscA RNA References reflist 1 External links Rfam id RF00058 name HgcF RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name IS061 RNA image RF00115.jpg width caption Predicted secondary structure and sequence conservation of IS061 Symbol IS061 AltSymbols Rfam RF00115 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0001263 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The ISO61 RNA is a bacterial non coding RNA of 181 nucleotides in length that is found between the abgR and ydaL genes in Escherichia coli and Shigella flexneri . It was discovered using a computational screen of the E. coli genome . ref cite journal last Chen first S coauthors Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB year 2002 title A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome journal Biosystems volume 65 pages 157&ndash 177 pmid 12069726 doi 10.1016 S0303 2647 02 00013 8 issue 2 3 ref The function of this RNA is unknown. See also IS102 RNA IS128 RNA References reflist 1 External links Rfam id RF00115 name IS061 RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name SscA RNA image RF00063.jpg width caption Predicted secondary structure and sequence conservation of SscA Symbol SscA AltSymbols Rfam RF00063 miRBase miRBase family RNA type Gene Tax domain Archaea GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The SscA RNA Secondary Structure Conserved A gene was identified computationally in AT rich hyperthermophile s using QRNA bioinformatics software. ref name Kle02 cite journal last Klein first RJ coauthors Misulovin Z, Eddy SR year 2002 title Noncoding RNA genes identified in AT rich hyperthermophiles journal Proc Natl Acad Sci USA volume 99 pages 7542&ndash 7547 pmid 12032319 doi 10.1073 pnas.112063799 issue 11 pmc 124278 ref SscA is 97 nucleotide s in length and is of unknown function. The predicted distribution of SscA RNA is currently restricted to the pyrococcus genus. ref name Kle02 Other RNAs identified with SscA include HgcC family RNA HgcC , HgcE RNA HgcE , HgcF RNA HgcF and HgcG RNA HgcG . ref name Kle02 References reflist 1 External links Rfam id RF00063 name SscA RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name SraG RNA image RF00082.jpg width caption Predicted secondary structure and sequence conservation of SraG Symbol SraG AltSymbols Rfam RF00082 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData SraG small RNA G is a is a small non coding RNA ncRNA . It is the functional product of a gene which is not translated into protein . This ncRNA was discovered in the bacteria Escherichia coli during a large scale computational screen for transcription signals and genomic features of known small RNA encoding genes. ref name pmid11448770 cite journal author Argaman L, Hershberg R, Vogel J, et al. title Novel small RNA encoding genes in the intergenic regions of Escherichia coli journal Curr. Biol. volume 11 issue 12 pages 941 50 year 2001 pmid 11448770 doi 10.1016 S0960 9822 01 00270 6 ref During this screen 14 novel ncRNA genes were identified, including GlmZ RNA GlmZ , SraB RNA SraB , SraC RyeA RNA SraC and SraD RNA SraD . ref name pmid11448770 The expression of SraG was experimentally confirmed by Northern blotting which also indicated this RNA undergoes specific cleavage processing. ref name pmid11448770 The function of this RNA is unknown. References references External links Rfam id RF00082 name SraG RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name HgcG RNA image RF00064.jpg width caption Predicted secondary structure and sequence conservation of HgcG Symbol HgcG AltSymbols Rfam RF00064 miRBase miRBase family RNA type Gene Tax domain Archaea GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The HgcG RNA gene is a non coding RNA that was identified bioinformatics computationally and experimentally verified in AT rich hyperthermophile s. ref cite journal last Klein first RJ coauthors Misulovin Z, Eddy SR year 2002 title Noncoding RNA genes identified in AT rich hyperthermophiles journal Proc Natl Acad Sci USA volume 99 pages 7542&ndash 7547 pmid 12032319 doi 10.1073 pnas.112063799 issue 11 pmc 124278 ref The genes from this screen were named hgcA through hgcG high GC . HgcG is of unknown function. hgcG is significantly similar to a region of the Archaeoglobus Archaeoglobus fulgidus genome. See also HgcC family RNA HgcE RNA HgcF RNA References reflist 1 External links Rfam id RF00064 name HgcG RNA Category Non coding RNA molecular cell biology stub ... more details
RNA extraction is the purification of RNA from biological samples. This procedure is complicated by the ubiquitous presence of ribonuclease enzymes in cells and tissues, which can rapidly degrade RNA. ref cite journal author Peirson SN, Butler JN title RNA extraction from mammalian tissues journal Methods Mol. Biol. volume 362 issue pages 315 27 year 2007 pmid 17417019 doi 10.1007 978 1 59745 257 1 22 series Methods in Molecular Biology isbn 978 1 58829 417 3 ref Several methods are used in molecular biology to isolate RNA from samples, the most common of these is Guanidinium thiocyanate phenol chloroform extraction . ref cite journal author Chomczynski P, Sacchi N title The single step method of RNA isolation by acid guanidinium thiocyanate phenol chloroform extraction twenty something years on journal Nat Protoc volume 1 issue 2 pages 581 5 year 2006 pmid 17406285 doi 10.1038 nprot.2006.83 ref ref cite journal author Bird IM title Extraction of RNA from cells and tissue journal Methods Mol. Med. volume 108 issue pages 139 48 year 2005 pmid 16028681 ref See also RNA quality control see the following page http RNA integrity.gene quantification.info DNA extraction Phenol chloroform extraction Ethanol precipitation Column purification References reflist Molecular Biology Category Biochemistry methods de RNA Isolation ... more details
Infobox rfam Name HgcE RNA image RF00060.jpg width caption Predicted secondary structure and sequence conservation of HgcE Symbol HgcE AltSymbols Rfam RF00060 miRBase miRBase family RNA type Gene Tax domain Archaea GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The HgcE RNA also known as Pf3 RNA gene is a non coding RNA that was identified computationally and experimentally verified in AT rich hyperthermophiles . ref cite journal last Klein first RJ coauthors Misulovin Z, Eddy SR year 2002 title Noncoding RNA genes identified in AT rich hyperthermophiles journal Proc Natl Acad Sci USA volume 99 pages 7542&ndash 7547 pmid 12032319 doi 10.1073 pnas.112063799 issue 11 pmc 124278 ref The genes in the screen were named hgcA through hgcG high GC . The HgcE has been renamed as Pf3 and identified as an H ACA snoRNA that is suggested to target 23S rRNA for pseudouridylation. ref name pmid12560482 cite journal author Rozhdestvensky TS, Tang TH, Tchirkova IV, Brosius J, Bachellerie JP, H ttenhofer A title Binding of L7Ae protein to the K turn of archaeal snoRNAs a shared RNA binding motif for C D and H ACA box snoRNAs in Archaea journal Nucleic Acids Res. volume 31 issue 3 pages 869 77 year 2003 month February pmid 12560482 pmc 149196 doi 10.1093 nar gkg175 url http nar.oxfordjournals.org cgi pmidlookup?view long&pmid 12560482 ref This RNA contains two K turn motif s. ref name pmid12560482 See also HgcC family RNA HgcF RNA HgcG RNA SscA RNA References reflist 1 External links Rfam id RF00060 name HgcE RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name sroD RNA image RF00370.jpg width caption Predicted secondary structure and sequence conservation of sroD Symbol sroD AltSymbols Rfam RF00370 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The bacterial sroD RNA gene is a non coding RNA of 90 nucleotides in length. sroD is found in several Enterobacterial species but its function is unknown. ref name Vog03 cite journal last Vogel first J coauthors Bartels V, Tang TH, Churakov G, Slagter Jager JG, Huttenhofer A, Wagner EG year 2003 title RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria journal Nucleic Acids Res volume 31 pages 6435&ndash 6443 pmid 14602901 doi 10.1093 nar gkg867 issue 22 pmc 275561 ref SroE RNA SroE and SroH RNA SroH were identified in the same bioinformatics search. ref name Vog03 References reflist 1 External links Rfam id RF00370 name sroD RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name sroE RNA image RF00371.jpg width caption Predicted secondary structure and sequence conservation of sroE Symbol sroE AltSymbols Rfam RF00371 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The bacterial sroE RNA gene is a non coding RNA molecule of 90 nucleotides in length. sroE is found in several Enterobacterial species but its function is unknown. ref name Vog03 cite journal last Vogel first J coauthors Bartels V, Tang TH, Churakov G, Slagter Jager JG, Huttenhofer A, Wagner EG year 2003 title RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria journal Nucleic Acids Res volume 31 pages 6435&ndash 6443 pmid 14602901 doi 10.1093 nar gkg867 issue 22 pmc 275561 ref SroD RNA SroD and SroH RNA SroH were identified in the same bioinformatics search. ref name Vog03 References reflist 1 External links Rfam id RF00371 name sroE RNA Category Non coding RNA molecular cell biology stub ... more details
infobox enzyme Name DNA Directed RNA Polymerase EC number 2.7.7.6 CAS number 9014 24 8 IUBMB EC number 2 7 7 6 GO code 0034062 image width 260px caption Check the EC number again RNA polymerase RNAP or RNApol , also known as DNA dependent RNA polymerase , is an enzyme that produces RNA . In cell biology cell s, RNAP is necessary for constructing RNA chains using DNA gene s as templates, a process called Transcription genetics transcription . RNA polymerase enzymes are essential to life and are found ... polymerizes ribonucleotide s at the 3 end of an RNA transcript. History RNAP was discovered ... author Jerard Hurwitz year 2005 month December title The Discovery of RNA Polymerase journal Journal ... Prize in Chemistry was awarded to Roger D. Kornberg for creating detailed molecular images of RNA ... of RNAP molecules too small to be resolved. Each RNAP is transcribing an RNARNA strand , which can ... End indicates the 5 end , where the longer RNA molecules are almost completely transcribed ... coli RNA polymerase year 2000 volume 54 pages 499 518 pmid 11018136 doi 10.1146 annurev.micro.54.1.499 ... biology promoter s. It then produces an RNA chain, which is Complementarity molecular biology complementary to the template DNA strand. The process of adding nucleotide s to the RNA strand is known ... length of the dystrophin gene . RNAP will preferentially release its RNA transcript at specific DNA ... include Messenger RNA mRNA &mdash template for the Translation biology synthesis of proteins by ribosome s. Non coding RNA or RNA genes &mdash a broad class of genes that encode RNA that is not translated into protein. The most prominent examples of RNA genes are transfer RNA tRNA and ribosomal RNA ... the late 1990s, many new RNA genes have been found, and thus RNA genes may play a much more significant role than previously thought. Transfer RNA tRNA &mdash transfers specific amino acid s to growing ... Ribosomal RNA rRNA &mdash a component of ribosomes Micro RNA &mdash regulates gene activity Catalytic ... more details
RNA silencing also called as post transcriptional gene silencing PTGS refers to a family of gene silencing effects by which the gene expression expression of one or more genes is downregulated or entirely suppressed by the introduction of an antisense RNA molecule. The most common and well studied example is RNA interference , in which endogenously expressed microRNA or exogenously derived small interfering RNA induces the degradation of complementarity molecular biology complementary messenger RNA . It also plays an important role in defending plants against viruses. Enzymes detect double stranded RNA that is not normally found in cells and digest it into small pieces that are not able to cause disease. ref name pmid10753772 cite journal author Ding SW title RNA silencing. journal Curr Opin Biotechnol volume 11 issue 2 pages 152 6 year 2000 pmid 10753772 ref ref name pmid15159620 cite journal author Susi P, Hohkuri M, Wahlroos T, Kilby NJ title Characteristics of RNA silencing in plants similarities and differences across kingdoms. journal Plant Mol Biol volume 54 issue 2 pages 157 74 year 2004 pmid 15159620 ref ref name pmid15372043 cite journal author Baulcombe D title RNA silencing in plants. journal Nature volume 431 issue 7006 pages 356 63 year 2004 pmid 15372043 doi 10.1038 nature02874 ref ref name pmid15950871 cite journal author Baulcombe D title RNA silencing. journal Trends Biochem Sci volume 30 issue 6 pages 290 3 year 2005 pmid 15950871 doi 10.1016 j.tibs.2005.04.012 ref ref Citation title PDF from blatny.com url http www.blatny.com Epigenetika2007 2007 12 04 papers Meister 202004.pdf year 2004 journal Nature pages 343 349 volume 431 issue 7006 last1 Meister first1 G. last2 Tuschl first2 T. accessdate 2011 02 08 ref See also miRNA RNAi References reflist DEFAULTSORT Rna Silencing Category RNA Category Gene expression Cell biology stub ... more details
Rfam box acc RF00120 description C0343 RNA abbreviation C0343 avg length 74.80 avg identity 88.00 type Gene sRNA se Hershberg R ss Predicted PFOLD release 10.0 The C0343 RNA is a bacterial non coding RNA of 74 nucleotides in length that is found between the ydaN and dbpA gene s in the genomes of Escherichia coli and Shigella flexneri , Salmonella enterica and Salmonella typhimurium . This ncRNA was originally identified in E.coli using microarray high density oligonucleotide probe arrays microarray ref name pmid12202758 cite journal author Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C title Transcriptome analysis of Escherichia coli using high density oligonucleotide probe arrays journal Nucleic Acids Res. volume 30 issue 17 pages 3732 8 year 2002 pmid 12202758 doi 10.1093 nar gkf505 pmc 137427 ref . The function of this ncRNA is unknown. FnrS RNA was later found to be transcription genetics transcribed from the same intergenic region as C0343 RNA. ref cite journal author Durand S, Storz G title Reprogramming of anaerobic metabolism by the FnrS small RNA journal Mol. Microbiol. volume 75 issue 5 pages 1215 31 year 2010 month March pmid 20070527 pmc 2941437 doi 10.1111 j.1365 2958.2010.07044.x url http www3.interscience.wiley.com resolve openurl?genre article&sid nlm pubmed&issn 0950 382X&date 2010&volume 75&issue 5&spage 1215 accessdate 2010 08 04 ref See also C0299 RNA C0465 RNA C0719 RNA References references External links Rfam id RF00120 name C0343 RNA DEFAULTSORT C0343 Rna Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name ryfA RNA image RF00126.jpg width caption Predicted secondary structure and sequence conservation of ryfA Symbol ryfA AltSymbols Rfam RF00126 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The ryfA RNA gene is a non coding RNA present in E. coli , Shigella flexneri and Salmonella species where it is found between the ydaN and dbpA genes. These RNA genes are about 300 nucleotide s in length. The function of this RNA is unknown. ref cite journal last Wassarman first KM coauthors Repoila F, Rosenow C, Storz G, Gottesman S year 2001 title Identification of novel small RNAs using comparative genomics and microarrays journal Genes Dev volume 15 pages 1637&ndash 1651 pmid 11445539 doi 10.1101 gad.901001 issue 13 pmc 312727 ref ref cite journal last Rivas first E coauthors Klein RJ, Jones TA, Eddy SR year 2001 title Computational identification of noncoding RNAs in E. coli by comparative genomics journal Curr Biol volume 11 pages 1369&ndash 1373 pmid 11553332 doi 10.1016 S0960 9822 01 00401 8 issue 17 ref See also RydB RNA RybB RNA RydC RNA References reflist 1 External links Rfam id RF00126 name ryfA RNA Category Non coding RNA molecular cell biology stub ... more details
Infobox rfam Name SraB RNA image RF00077.jpg width caption Predicted secondary structure and sequence conservation of SraB Symbol SraB AltSymbols sraB Rfam RF00077 miRBase miRBase family RNA type Gene Bacterial small RNA sRNA Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The SraB RNA is a small non coding RNA discovered in E. coli during a large scale experimental screen ref name ref1 cite journal last Argaman first L coauthors Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S year 2001 title Novel small RNA encoding genes in the intergenic regions of Escherichia coli journal Curr Biol volume 11 pages 941&ndash 950 pmid 11448770 doi 10.1016 S0960 9822 01 00270 6 issue 12 ref . The 14 novel RNAs discovered were named sra for s mall R N A , examples include SraC RyeA RNA SraC , SraD RNA SraD and SraG RNA SraG . ref name ref1 This ncRNA was found to be expressed only in stationary phase ref name ref1 . The exact function of this RNA is unknown but it has been shown to affect survival of Salmonella enterica to antibiotic administration in egg albumin . ref name pmid21268901 cite journal author Jiang H, Cao M, Cao X, Gu H, Zeng K title sRNA sraB regulate the resistant ability of Salmonella enterica serovar enteritidis to egg albumen language Chinese journal Wei Sheng Wu Xue Bao volume 50 issue 11 pages 1537 44 year 2010 month November pmid 21268901 doi url ref The authors suggest this may be due to SraB regulating a response to components in albumin. See Also Escherichia coli sRNA References reflist 1 External links Rfam id RF00077 name SraB RNA Category Non coding RNA molecular cell biology stub ... more details
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