28SribosomalRNA is the eukaryotic nuclear homologue of the prokaryotic 23S ribosomalRNA this is the structural RNA for the large component of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells. General references Lodish, H. Molecular Cell Biology 3rd ed. Freeman, 1995. Ribosome subunits DEFAULTSORT 28sRibosomalRna Category RibosomalRNA ... more details
ribosomes can be broken down into two subunits the S in 16S ribosomalRNA 16S represents Svedberg units class wikitable Type Size Large subunit Small subunit prokaryotic 70S 50S 5S ribosomalRNA 5S , 23S ribosomalRNA 23S 30S 16S ribosomalRNA 16S eukaryotic 80S 60S 5S ribosomalRNA 5S , 5.8S ribosomalRNA 5.8S , 28SribosomalRNA28S 40S 18S ribosomalRNA 18S Note that the S units of the subunits ... RNA 5S , 5.8S ribosomalRNA 5.8S and 28SribosomalRNA28S rRNAs . Mammalian cells have 2 mitochondrial 12S ribosomalRNA 12S and 16S rRNA molecules and 4 types of cytoplasmic rRNA 28S, 5.8S, 5S large ... 18S and LSU 23S 28S http www.psb.ugent.be rRNA European database on small subunit ribosomalRNA http ...Ribosomal ribonucleic acid rRNA is the RNA component of the ribosome , the organelle that is the site of protein synthesis in all living biological cell cells . RibosomalRNA provides a mechanism for decoding ... In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomalRNA 16S rRNA. The large 50S ribosomal subunit contains two rRNA species the 5S and 23S ribosomalRNA 23S rRNAs . Bacterial 16S ribosomalRNA 16S , 23S ribosomalRNA 23S , and 5S rRNA genes are typically organized as a co .... The 3 end of the 16S ribosomalRNA 16S rRNA in a ribosome binds to a sequence on the 5 ... subunit ribosomalRNA, 5 domain taken from the Rfam database. This example is http www.sanger.ac.uk ... clusters on chromosomes 13, 14, 15, 21 and 22 . The 18S ribosomalRNA 18S rRNA in most eukaryotes is in the small ... by RNA polymerase III . The tertiary structure of the small subunit ribosomalRNA SSU rRNA has ... RNA 16S rRNA, BioMineWiki Rfam id RF00177 name Small subunit ribosomalRNA, 5 domain MeshName RibosomalRNA Nucleic acids Ribosome subunits Category Protein biosynthesis Category RNA Category Non coding RNA Category RibosomalRNA Category Ribozymes ar br Trenkenn ribonukleek ribosom ... ribonucleico ribos mico eo RRNA fr Acide ribonucl ique ribosomique ko RNA id RibosomalRNA it RNA ... more details
Rfam box acc RF00002 description 5.8S ribosomalRNA abbreviation 5 8S rRNA avg length 153.80 avg identity 81.00 type Gene rRNA se Wuyts et al, European LSU rRNA database, PMID 11125083 ss Published PMID 11125083 release 10.0 In molecular biology the 5.8S ribosomalRNA 5.8S rRNA is a non coding RNA component of the large subunit of the Eukaryote eukaryotic ribosome and so plays an important role in translation genetics protein translation . It is Transcription genetics transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA . Its function is thought to be in 5.8S rRNA ribosome translocation. ref name Abou 1997 cite journal last Abou first Elela S coauthors Nazar RN year 1997 title Role of the 5.8S rRNA in ribosome translocation journal Nucleic Acids Res volume 25 pages 1788&ndash 1794 pmid 9108162 doi 10.1093 nar 25.9.1788 issue 9 pmc 146658 ref It is also known to form covalent linkage to the p53 tumour suppressor protein. ref name Fontoura 197 cite journal last Fontoura first BM coauthors Atienza CA, Sorokina EA, Morimoto T, Carroll RB year 1997 title Cytoplasmic p53 polypeptide is associated with ribosomes journal Mol Cell Biol volume 17 pages 3146&ndash 3154 pmid 9154813 issue 6 pmc 232167 ref 5.8S rRNA is also found in archaea . 5.8S rRNA can be used as a reference gene for miRNA detection. ref name s58 real cite journal author Shi R, Chiang VL title Facile means for quantifying microRNA expression by real time PCR journal BioTechniques volume 39 issue 4 pages 519 25 year 2005 month October pmid 16235564 doi 10.2144 000112010 url http www.biotechniques.com article 000112010 accessdate 2010 09 15 ref References reflist 1 External links Rfam id RF00002 name 5.8S ribosomalRNA http rrna.uia.ac.be lsu index.html LSU http www.ncbi.nlm.nih.gov nuccore 186498419 Arabidopsis 5.8S rRNA sequence http www.ncbi.nlm.nih.gov nuccore 169814 Rice 5.8S rRNA sequence Ribosome subunits Category RibosomalRNA molecular cell biology stub ... more details
Rfam box acc RF00001 description 5S ribosomalRNA abbreviation 5S rRNA avg length 114.50 avg identity 59.00 type Gene rRNA se Szymanski et al, 5S ribosomal database, PMID 11752286 ss Published PMID 11283358 release 10.0 Image PDB 1c2x EBI.png thumb 200px left A 3D representation of a 5S rRNA molecule. This structure is of the 5S rRNA from the Escherichia coli 50S ribosomal subunit and is based on a Transmission electron microscopy cryo electron microscopic reconstruction . ref name pmid10756104 cite journal author Mueller F, Sommer I, Baranov P, Matadeen R, Stoldt M, W hnert J, G rlach M, van Heel M, Brimacombe R title The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo electron microscopic reconstruction at 7.5 A resolution. journal J ... by SecM via a cascade of ribosomalRNA rearrangements. journal Mol Cell volume 22 issue 4 pages 533 43 year 2006 pmid 16713583 doi 10.1016 j.molcel.2006.05.003 ref 5S ribosomalRNA 5 Svedberg S rRNA is a component of the large Ribosome ribosomal subunit in both prokaryote s and eukaryote s. In prokaryotes, it is part of the 50S subunit. In eukaryotes, it is synthesised by RNA polymerase III the other eukaryotic rRNAs are cleaved from a 45S precursor synthesized by RNA polymerase I . In Xenopus oocyte ... reflist 1 External links Rfam id RF00001 name 5S ribosomalRNA http rose.man.poznan.pl 5SData 5SData MeshName 5S RibosomalRNA Ribosome subunits Category RibosomalRNA molecular cell biology stub zh 5S RNA ... bind to the central region of 5S RNA. ref name Searles 2000 cite journal last Searles first MA coauthors ... in binding to 5 S RNA journal J Mol Biol volume 301 pages 47&ndash 60 pmid 10926492 doi 10.1006 jmbi.2000.3946 ... of the 5S RNA gene and stabilize the 5S RNA transcript until it is required for ribosome assembly ... transcription factor that can bind either the 5S RNA gene or 5S RNA journal Proc Natl Acad Sci volume ... more details
links Rfam id RF01118 name 23S ribosomalRNA http www.ekevanbatenburg.nl PKBASE PKB00148.HTML Pseudobase entry for pseudoknot of the 23S ribosomalRNA PKB00148 Ribosome subunits Category RibosomalRNA molecular cell biology stub es ARN ribosomal 23S ...Rfam box acc PK G12rRNA secondary structure description Pseudoknot of the domain G G12 of 23S ribosomalRNA abbreviation PK G12rRNA avg length 108.00 avg identity 72.00 type Gene rRNA se Pseudobase ss Pseudobase release 9.1 Image PDB 1c2w EBI.png thumb 200px left A 3D representation of the ribosome. This is a view of the 3D arrangement of the 23S and 5S rRNA in the Escherichia coli 50S ribosomal subunit based on a Transmission electron microscopy cryo electron microscopic reconstruction . ref name pmid10756104 cite journal author Mueller F, Sommer I, Baranov P, Matadeen R, Stoldt M, W hnert J, G rlach M, van Heel M, Brimacombe R title The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo electron microscopic reconstruction at 7.5 A resolution. journal J Mol Biol volume 298 issue 1 pages 35 59 year 2000 pmid 10756104 doi 10.1006 jmbi.2000.3635 ref Image PDB 2j28 EBI.jpg thumb 200px left A 3D representation of the ribosome. ref name pmid17086193 cite journal author Halic M, Blau M, Becker T, Mielke T, Pool MR, Wild K, Sinning I, Beckmann R title Following the signal sequence from ribosomal tunnel exit to signal recognition particle. journal Nature volume 444 issue 7118 pages 507 11 year 2006 pmid 17086193 doi 10.1038 nature05326 ref The 23S rRNA is a 2904 Nucleotide nt long E. coli component of the large prokaryotic subunit 50S The ribosomal peptidyl transferase activity resides in this rRNA. This is achieved by a base A2486 which the nitrogen at position 3 acts as a base and accepts the H from the amino group of the aa tRNA in the A site, the aa tRNA with its free electron nucleophile Nucleophilic acyl substitution reacts ... more details
18 Svedberg S ribosomalRNA abbreviated 18S rRNA is a part of the ribosomalRNA . The S in 18S represents Svedberg units. 18S rRNA is a component of the small eukaryotic ribosomal subunit 40S . 18S rRNA is the structural RNA for the small component of eukaryotic cytoplasmic ribosome s, and thus one of the basic components of all eukaryotic cells. It is the eukaryotic nuclear homologue of 16S ribosomalRNA , which exists only in Prokaryote s. 18S rRNA data is widely used in molecular analysis to reconstruct the evolutionary history of organisms, especially invertebrates, as its slow evolutionary rate makes it suitable to reconstruct ancient divergences. Uses in phylogeny The small subunit SSU 18S rRNA gene is one of the most frequently used genes in phylogenetic studies and an important marker for random target polymerase chain reaction PCR in environmental biodiversity screening. ref name Meyer 2010 In general, rRNA gene sequences are easy to access due to highly conserved flanking regions allowing for the use of universal primer s. ref name Meyer 2010 Their repetitive arrangement within the genome provides excessive amounts of template DNA for PCR, even in smallest organisms. The 18S gene is part of the ribosomal functional core and is exposed to similar selective forces in all living beings. Thus, when the first large scale phylogenetic studies based on 18S sequences were published first and foremost phylogeny of the animal kingdom by Field et al. 1988 ref Field K. G., Olsen G. J., Lane D. J., Giovannoni S. J., Ghiselin M. T., Raff E. C., Pace N. R. & Raff R. A. 1988 . Molecular phylogeny of the animal kingdom . Science journal Science 239 4841 748 753. doi 10.1126 science.3277277 . ref the gene was celebrated as the prime candidate for reconstructing the metazoa n tree of life . ref name Meyer 2010 And in fact, 18S sequences later provided evidence for the splitting ... RibosomalRna Category RibosomalRNA cs 18S rRNA ... more details
It has several functions Like the 23S ribosomalRNA large 23S ribosomalRNA , it has a structural role, acting as a scaffold defining the positions of the ribosomal protein The 3 end contains the anti ... ribosomalRNA operons in sequenced bacterial genomes journal FEMS Microbiol. Lett. volume 228 issue ... subunits Category RibosomalRNA ca ARN ribos mic 16S fr ARN ribosomique 16S ko 16S rRNA ja 16S rRNA ru 16S uk 16S zh 16S RNA ..., aiding in the binding of the two ribosomal subunits 50S 30S Stabilizes correct codon anticodon ... studies ref name Weisburg http jb.asm.org cgi content abstract 173 2 697 16S ribosomal DNA amplification ... Laboratory Medicine Molecular Diagnosis Bacterial Sequencing http rdp.cme.msu.edu The Ribosomal ... more details
homologies in mammalian 5.8S ribosomalRNA. Biochemistry 15 3 505 508, PMID 1252408. ref In cases for sibling ... MT 1991 . Ribosomal DNA molecular evolution and phylogenetic inference. Quart Rev Biol 66 4 411 453, PMID 1784710. ref See also RibosomalRNA Ribosome Notes reflist DEFAULTSORT Ribosomal Dna Category ...Image Eucaryot rdna.png thumb 400px right The gene segment of eukaryotic rDNA contains 18S, 5.8S, and 28S tracts and forms a tandem repetitive cluster the 5S rDNA is coded separately. NTS , nontranscribed spacer, ETS , external transcribed spacer, ITS , internal transcribed spacers 1 and 2, numbered from 5 end. Ribosomal DNA rDNA codes for RRNA ribosomalRNA . These sequences regulate amplification and Transcription genetics transcription initiation and contain transcribed and nontranscribed spacer segments. The ribosome is an intracellular macromolecule that produces proteins or polypeptide chains. The ribosome itself consists of a composite of proteins and rRNA. As shown in the figure, rDNA consists of a tandem repeat of a unit segment, an operon, composed of NTS, ETS, 18S, ITS1, 5.8S, ITS2, and 28S tracts. rDNA has another gene, coding for 5S rRNA, located elsewhere in the genome in most eukaryotes. ref name Richard Richard GF, Kerrest A, Dujon B 2008 . Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 72 4 686 727, PMID 19052325, PMC 2593564 , DOI 10.1128 MMBR.00011 08 . ref 5S rDNA is also present in tandem repeats as in Drosophila . ref name Richard In the nucleus, the rDNA region of the chromosome is visualized as a nucleolus which forms expanded chromosomal loops with rDNA. The ribosomalRNA transcriptional units are clustered in tandem repeats. These rDNA regions are also called nucleolus organizer region s, as they give ... M 1995 . Structural evolution of the Drosophila 5S ribosomal genes. J Mol Evol 41 5 615 621, PMID ... spacers ITSs and coding regions in the EcoR I fragment of the ribosomal DNA of the Japanese pond ... more details
Ribosomal translocation is a step in both Eukaryotic translation Elongation Eukaryotic elongation and Prokaryotic translation Elongation Prokaryotic elongation , during Translation genetics translation of messenger RNA into proteins disambig ... more details
A ribosomal protein is any of the protein s that, in conjunction with RibosomalRNA rRNA , make up the ribosomal subunits involved in the cellular process of translation genetics translation . A large part of the knowledge about these organic molecules has come from the study of Escherichia coli E. coli ribosomes. Most ribosomic proteins have been isolated and specific anti bodies have been produced. These, together with electron microscope electronic microscopy and the use of certain reactives, have allowed for the determination of the topography of the proteins in the ribosome. Proteins in E. coli ribosomes The ribosome of E. coli has about 22 proteins in the small subunit labelled S1 to S22 and 34 proteins in the large subunit L1 to L36 . All of them are different with three exceptions one protein is found in both subunits S20 and L26 , L7 and L12 are acetylated and methylated forms of the same protein, and L8 is a complex of L7 L12 and L10. In addition, L31 is known to exist in two forms, the full length at 7.9 kiloDaltons kDa and fragmented at 7.0 kDa. This is why the number of proteins ... coli ribosomal proteins and their posttranslational modifications by mass spectrometry. Anal Biochem. v269 1 pp 105 12. PMID 10094780 ref Disposition in the small ribosomal subunit In the small 30S ... of RNA and to organize the overall structure. Nearly all the proteins contain one or more globular domains. Moreover, nearly all contain long extensions that can contact the RNA in far reaching regions ... repulsion of the RNA backbone. Protein protein interactions also exist to hold structure together by electrostatic ... J, McCammon JA. 2006 Dependency Map of Proteins in the Small Ribosomal Subunit. PLoS Comput. Biol ... messenger RNA. doi 10.1038 nature07117, First paragraph Full Text PDF External links http www.biochem.umd.edu biochem kahn bchm465 01 ribosome proteins.html 30S Ribosomal proteins at biochem.umd.edu MeshName Ribosomal Protein GeneticTranslation Category Proteins Category Protein biosynthesis ... more details
A ribosomal frameshift allows alternative translation biology translation of a mRNA sequence by changing the open reading frame . It is commonly found in viruses including barley yellow dwarf virus ref name pmid1840612 cite journal author Vincent JR, Lister RM, Larkins BA title Nucleotide sequence analysis and genomic organization of the NY RPV isolate of barley yellow dwarf virus journal J. Gen. Virol. volume 72 Pt 10 issue pages 2347 55 year 1991 month October pmid 1840612 doi url http vir.sgmjournals.org cgi pmidlookup?view long&pmid 1840612 ref , potato leafroll virus ref name pmid8502558 cite journal author Kujawa AB, Drugeon G, Hulanicka D, Haenni AL title Structural requirements for efficient translational frameshifting in the synthesis of the putative viral RNA dependent RNA polymerase of potato leafroll virus journal Nucleic Acids Res. volume 21 issue 9 pages 2165 71 year 1993 month May pmid 8502558 pmc 309480 doi 10.1093 nar 21.9.2165 url http nar.oxfordjournals.org cgi pmidlookup?view long&pmid 8502558 ref and simian retrovirus 1 ref name pmid9490779 cite journal author Sung D, Kang H title Mutational analysis of the RNA pseudoknot involved in efficient ribosomal frameshifting in simian retrovirus 1 journal Nucleic Acids Res. volume 26 issue 6 pages 1369 72 year 1998 month March pmid 9490779 pmc 147434 doi 10.1093 nar 26.6.1369 url http nar.oxfordjournals.org cgi pmidlookup?view long&pmid 9490779 ref . Ribosomal frameshifting is promoted by a pseudoknot structure and slippery Nucleotide sequence sequence usually UUUAAAC ref name pmid8517032 cite journal author Meulenberg ... required for translation of putative RNA dependent RNA polymerase . See also Translational frameshift HIV Ribosomal frameshift signal Navbox name hide the gallery title Gallery of secondary structure ... links http www.ekevanbatenburg.nl PKBASE Pseudobase http recode.ucc.ie Recode Category RNA Category Gene expression Category Cis regulatory RNA elements genetics stub ... more details
. However, it is notable that, in ribosomalRNA, many of the post transcriptional modifications occur ... and ribosomalRNA rRNA , both of which are involved in the process of translation. ref name Biochemistry ... bonding. ref name transcriptome RibosomalRNA rRNA is the catalytic component of the ribosomes. Eukaryotic ... RNA is one of the three major macromolecule s along with DNA and protein s that are essential for all known forms of life. Like DNA, RNA is made up of a long chain of components called nucleotide ... group. The sequence of nucleotides allows RNA to encode genetic information. For example, some virus es use RNA instead of DNA as their genetic material, and all organisms use messenger RNA mRNA to carry the genetic information that directs the synthesis of proteins. Like proteins, some RNA molecules play an active role in cells by catalyzing biological reactions, controlling gene expression ... of proteins on ribosome s. This process uses transfer RNA tRNA molecules to deliver amino acids to the ribosome, where ribosomalRNA rRNA links amino acids together to form proteins. The chemical structure of RNA is very similar to that of DNA , with two differences a RNA contains the sugar ... oxygen atom , and b RNA has the nucleobase uracil while DNA contains thymine uracil and thymine have similar base pairing properties . Unlike DNA, most RNA molecules are single stranded. Single stranded RNA molecules adopt very complex three dimensional structures, since they are not restricted to the repetitive double helical form of double stranded DNA. RNA is made within living cells by RNA polymerase s, enzyme s that act to copy a DNA or RNA template into a new RNA strand through processes known as Transcription genetics transcription or RNA replication , respectively. Comparison with DNA File 50S subunit of the ribosome 3CC2.png thumb Three dimensional representation of the 50S ribosomal subunit. RNA is in ochre, protein in blue. The active site is in the middle red . RNA and DNA are both ... more details
protein Name ribosomal protein S6 caption image width HGNCid 10429 Symbol RPS6 AltSymbols EntrezGene 6194 OMIM 180460 RefSeq NM 001010 UniProt P62753 PDB ECnumber Chromosome 9 Arm p Band 21 LocusSupplementaryData Ribosomal protein s6 is a ribosomal protein involved in Translation biology translation . A ribosomal protein that may play a role in controlling cell growth and proliferation. It is a major substrate of ribosomal protein S6 kinase and plays a role in regulating translation of RNAs that contain an RNA 5 terminal oligopyrimidine sequence. It is regulated by ribosomal s6 kinase . External links MeshName Ribosomal Protein S6 GeneticTranslation ... more details
A ribosomal protein leader is a mechanism used in Cell biology cells to control the cellular concentraction of a protein that forms a part of the ribosome , and to make sure that the concentration is neither too high nor too low. ref cite journal author Zengel JM, Lindahl L title Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli journal Prog. Nucleic Acid Res. Mol. Biol. volume 47 issue pages 331 70 year 1994 pmid 7517053 doi 10.1016 S0079 6603 08 60256 1 url ref Ribosomal protein leaders are RNA sequences that are a part of the 5 UTR of mRNA s encoding a ribosomal protein. When cellular concentrations of the ribosomal protein are high, excess protein will bind to the mRNA leader. This binding event can lower gene expression via a number of mechanisms for example, in the protein bound state, the RNA could form an intrinsic termination intrinsic transcription termination stem loop . When cellular concentrations of the ribosomal protein are not high, they are occupied in the ribosome, and are not available in significant quantities to bind the mRNA leader. This leads to increased expression of the gene, which leads to the synthesis of more copies of the ribosomal protein. Many examples of ribosomal protein leaders are known in bacteria . References references Category ribosomal protein leader ... more details
MH, Bachellerie JP title U21, a novel small nucleolar RNA with a 13 nt. complementarity to 28S rRNA, is encoded in an intron of ribosomal protein L5 gene in chicken and mammals journal Nucleic ...PBB geneid 6125 60S ribosomal protein L5 is a protein that in humans is encoded by the RPL5 gene . ref ... Cloning, sequencing and expression of the L5, L21, L27a, L28, S5, S9, S10 and S29 human ribosomal protein ... 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L18P family of ribosomal proteins. It is located ... of casein kinase II. As is typical for genes encoding ribosomal proteins, there are multiple processed ... has been found. This gene is co transcribed with the small nucleolar RNA gene U21, which is located in its fifth intron. As is typical for genes encoding ribosomal proteins, there are multiple processed ... RPL5 ribosomal protein L5 url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 6125 accessdate ref Interactions Ribosomal protein L5 has been shown to Protein protein interaction ... month Feb. title Interaction of the HIV 1 rev cofactor eukaryotic initiation factor 5A with ribosomal ... 1996 month Sep. title Interaction of the beta subunit of casein kinase II with the ribosomal protein ... Theresa, Burkhart William A, Xiong Yue year 2003 month Dec. title Ribosomal protein L11 negatively regulates oncoprotein MDM2 and mediates a p53 dependent ribosomal stress checkpoint pathway journal ... The ribosomal L5 protein is associated with mdm 2 and mdm 2 p53 complexes journal Mol. Cell. Biol. volume ... journal author Wool IG, Chan YL, Gl ck A title Structure and evolution of mammalian ribosomal proteins ... o95 101 cite journal author Pogue Geile K, Geiser JR, Shu M, et al. title Ribosomal protein genes are overexpressed in colorectal cancer isolation of a cDNA clone encoding the human S3 ribosomal ... more details
Rfam box acc RF00480 description HIV Ribosomal frameshift signal abbreviation HIV FE avg length 51.90 avg identity 90.00 type Cis reg frameshift element se PMID 14747573 ss Published PMID 14747573 release 10.0 The HIV Ribosomal frameshift signal is an cis regulatory element RNA element . HIV uses a system called 1 ribosomal Translational frameshift frameshifting to produce the required ratio of Gag and Gag Pol polyproteins. The stem loop structure of the frameshift signal is thought to impede the ribosome and cause slippage in the 5 direction, this causes the 1 frameshift and translation then continues in the new frame. ref cite journal last Biswas first P coauthors Jiang X, Pacchia AL, Dougherty JP, Peltz SW year 2004 title The human immunodeficiency virus type 1 ribosomal frameshifting site is an invariant sequence determinant and an important target for antiviral therapy journal J Virol volume 78 pages 2082&ndash 2087 pmid 14747573 doi 10.1128 JVI.78.4.2082 2087.2004 issue 4 pmc 369415 ref References reflist 1 External links Rfam id RF00480 name HIV Ribosomal frameshift signal Category Cis regulatory RNA elements molecular cell biology stub ... more details
Orphan date February 2009 Rfam box acc RF00114 description Ribosomal S15 leader abbreviation S15 avg length 116.50 avg identity 62.00 type Cis reg leader se Ji Y ss Published PMID 8955900 release 10.0 The E. coli ribosomal S15 leader is an cis regulatory element RNA element that can form two alternative structures found in the ribosomal S15 protein. One of the two alternate structures is a series of three stem loop hairpins , the other includes a pseudoknot . ref cite journal last Benard first L coauthors Philippe C, Ehresmann B, Ehresmann C, Portier C year 1996 title Pseudoknot and translational control in the expression of the S15 ribosomal protein journal Biochimie volume 78 pages 568&ndash 576 pmid 8955900 doi 10.1016 S0300 9084 96 80003 4 issue 7 ref This structure causes translational regulation of the S15 protein . Only the final two hairpins are conserved in other species. References reflist 1 External links Rfam id RF00114 name Ribosomal S15 leader Category ribosomal protein leader molecular cell biology stub ... more details
Rfam box acc RF00382 description DnaX ribosomal frameshifting element abbreviation DnaX avg length 64.70 avg identity 87.00 type Cis reg frameshift element se PMID 9300054 ss Published PMID 9300054 release 10.0 The DnaX ribosomal frameshifting element is a cis regulatory element RNA element found in the mRNA of the dnaX gene in E. coli . The dnaX gene has two encoded products tau and gamma which are produced in a 1 1 ratio. The gamma protein is synthesised due to programmed reading frame frameshifting and is shorter than tau. The two products of the dnaX gene are DNA polymerase III holoenzyme DNA polymerase III subunits. ref cite journal last Larsen first B coauthors Gesteland RF, Atkins JF year 1997 title Structural probing and mutagenic analysis of the stem loop required for Escherichia coli dnaX ribosomal frameshifting programmed efficiency of 50 journal J Mol Biol volume 271 pages 47&ndash 60 pmid 9300054 doi 10.1006 jmbi.1997.1162 issue 1 ref ref cite journal last Blinkova first A coauthors Burkart MF, Owens TD, Walker JR year 1997 title Conservation of the Escherichia coli dnaX programmed ribosomal frameshift signal in Salmonella typhimurium journal J Bacteriol volume 179 pages 4438&ndash 4442 pmid 9209069 issue 13 pmc 179275 ref References reflist 1 External links Rfam id RF00382 name DnaX ribosomal frameshifting element Category Cis regulatory RNA elements molecular cell biology stub ... more details
PBB geneid 6223 40S ribosomal protein S19 is a protein that in humans is encoded by the RPS19 gene . ref ... TJ, Tanaka T, Page DC title A map of 75 human ribosomal protein genes journal Genome Res volume 8 ... cite web title Entrez Gene RPS19 ribosomal protein S19 url http www.ncbi.nlm.nih.gov sites entrez?Db ... are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S19E family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal ... of patients. This suggests a possible extra ribosomal function for this gene in erythropoietic differentiation and proliferation, in addition to its ribosomal function. Higher expression levels of this gene .... ref name entrez Interactions Ribosomal protein S19 has been shown to Protein protein interaction ... growth factor 2 interacts with free ribosomal protein S19 journal Biochem. Biophys. Res. Commun. volume ... Structure and evolution of mammalian ribosomal proteins. journal Biochem. Cell Biol. volume 73 issue ... cite journal author Yamamoto T title Roles of the ribosomal protein S19 dimer and the C5a ... author Kondoh N, Schweinfest CW, Henderson KW, Papas TS title Differential expression of S19 ribosomal ... Characterization of the human small ribosomal subunit proteins by N terminal and internal sequencing ... B, et al. title The gene encoding ribosomal protein S19 is mutated in Diamond Blackfan anaemia ... author Willig TN, Draptchinskaia N, Dianzani I, et al. title Mutations in ribosomal protein S19 ... N, et al. title Truncating ribosomal protein S19 mutations and variable clinical expression in Diamond ... line, AsPC 1, release monocyte chemotactic S19 ribosomal protein dimer. journal J. Biochem. volume ... S, et al. title Fibroblast growth factor 2 interacts with free ribosomal protein S19. journal Biochem ... binding sites of monocyte chemotactic S19 ribosomal protein dimer. journal Am. J. Pathol. volume ... more details
A ribosomal binding site RBS is a sequence on mRNA that is bound by the ribosome when initiating translation biology protein translation . It can be either the 5 cap of a messenger RNA in eukaryotes , a region 6 7 nucleotides upstream of the start codon AUG in prokaryotes called the Shine Dalgarno sequence , or an internal ribosome entry site IRES in viruses. The sequence is complementary to the 3 end of the rRNA. The ribosome searches for this site and binds to it through base pairing of nucleotides. Then, the ribosome begins the translation process and recruits initiation factors. After finding the ribosome binding site in eukaryotes, the ribosome recognizes the Kozak consensus sequence and begins translation at the 1 AUG codon. genetics stub GeneticTranslation Category Protein biosynthesis Category Molecular biology category drug interaction Category Cell biology ... more details
PBB geneid 6124 60S ribosomal protein L4 is a protein that in humans is encoded by the RPL4 gene . ref name pmid9582194 cite journal author Kenmochi N, Kawaguchi T, Rozen S, Davis E, Goodman N, Hudson TJ, Tanaka T, Page DC title A map of 75 human ribosomal protein genes journal Genome Res volume 8 issue 5 pages 509 23 year 1998 month Aug pmid 9582194 pmc doi 10.1101 gr.8.5.509 ref ref name pmid8268230 cite journal author Bagni C, Mariottini P, Annesi F, Amaldi F title Human ribosomal protein L4 cloning and sequencing of the cDNA and primary structure of the protein journal Biochim Biophys Acta volume 1216 issue 3 pages 475 8 year 1994 month Feb pmid 8268230 pmc doi ref ref name entrez cite web title Entrez Gene RPL4 ribosomal protein L4 url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 6124 accessdate ref The PBB Summary template is automatically maintained by Protein Box Bot. See Template PBB Controls to Stop updates. PBB Summary section title summary text Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L4E family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene ... of mammalian ribosomal proteins. journal Biochem. Cell Biol. volume 73 issue 11 12 pages 933 47 year ... structures of rat ribosomal proteins L4 and L41. journal Biochem. Biophys. Res. Commun. volume ... 3 cite journal author Twiss JL, Smith DS, Chang B, Shooter EM title Translational control of ribosomal ... T, Kenmochi N title A complete map of the human ribosomal protein genes assignment of 80 genes ... M, Uechi T, Asakawa S, et al. title The human ribosomal protein genes sequencing and comparative ... more details
PBB geneid 9045 60S ribosomal protein L14 is a protein that in humans is encoded by the RPL14 gene . ref name pmid9480843 cite journal author Tanaka M, Tanaka T, Harata M, Suzuki T, Mitsui Y title Triplet repeat containing ribosomal protein L14 gene in immortalized human endothelial cell line t HUE4 journal Biochem Biophys Res Commun volume 243 issue 2 pages 531 7 year 1998 month Mar pmid 9480843 pmc doi 10.1006 bbrc.1998.8125 ref ref name entrez cite web title Entrez Gene RPL14 ribosomal protein L14 url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 9045 accessdate ref The PBB Summary template is automatically maintained by Protein Box Bot. See Template PBB Controls to Stop updates. PBB Summary section title summary text Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L14E family of ribosomal proteins. It contains a basic region leucine zipper bZIP like domain. The protein is located in the cytoplasm. This gene contains a trinucleotide GCT repeat tract whose length is highly polymorphic these triplet repeats result in a stretch of alanine residues in the encoded protein. Transcript variants utilizing alternative polyA signals and alternative 5 terminal exons exist but all encode the same protein. As is typical for genes encoding ribosomal proteins, there are multiple processed ... cite journal author Wool IG, Chan YL, Gl ck A title Structure and evolution of mammalian ribosomal ... ribosomal protein genes assignment of 80 genes to the cytogenetic map and implications for human ... The human ribosomal protein genes sequencing and comparative analysis of 73 genes. journal Genome ... modifications of the human large cytoplasmic ribosomal subunit proteins by mass ... more details
RRNA RibosomalRNA rRNA intergenic spacer analysis RISA is a method of microbial community analysis that provides a means of comparing differing environments or treatment impacts without the bias imposed by culture dependent approaches. RISA involves PCR amplification of a region of the rRNA gene operon between the small 16S and large 23S subunits called the intergenic spacer region ISR. By using oligonucleotide primers targeted to conserved regions in the 16S and 23S genes, RISA fragments can be generated from most of the dominant bacteria in an environmental sample. While the majority of the rRNA operon serves a structural function, portions of the 16S 23S intergenic region can encode tRNAs depending on the bacterial species. However the taxonomic value of the ISR lies in the significant heterogeneity in both length and nucleotide sequence. In RISA, we attempt to exploit the length heterogeneity of the ISR, which has been shown to range between 150 and 1500 bp with the majority of the ISR lengths being between 150 and 500 bp. The resulting PCR product will be a mixture of fragments contributed by several dominant community members. This product is electrophoresed in a polyacrylamide gel, and the DNA is visualized following staining. The result is a complex banding pattern that provides a community specific profile, with each DNA band corresponding to a bacterial population on the original assemblage. References references Borneman, J. and E.W. Triplett. 1997. Molecular microbial diversity in soils from eastern Amazonia evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63 2647 2653. Sigler, W.V. and J. Zeyer. 2002. Microbial diversity and activity along the forefields of two receding glaciers Microb. Ecol. 43 397 407. Sigler, W.V., S. Crivii, and J. Zeyer. 2002. Bacterial succession in glacial forefield soils characterized by community structure, activity and opportunistic growth dynamics. Microb ... more details
Orphan date February 2009 Rfam box acc RF00559 description Ribosomal protein L21 leader abbreviation L21 leader avg length 80.50 avg identity 62.00 type Cis reg leader se Predicted CMFinder, Barrick JE, Moy RH ss Predicted CMFinder, Barrick JE, Moy RH release 10.0 This family is a putative ribosomal protein leader autoregulatory structure ref cite journal last Zengel first JM coauthors Lindahl L year 1994 title Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli journal Prog Nucleic Acid Res Mol Biol. volume 47 pages 331&ndash 370 pmid 7517053 doi 10.1016 S0079 6603 08 60256 1 ref found in B. subtilis and other low GC Gram positive bacteria . It is located in the 5 untranslated regions of mRNA s encoding ribosomal protein L21, a protein of unknown function, and ribosomal protein L27 rplU ysxB rpmA . References reflist 1 External links Rfam id RF00559 name Ribosomal protein L21 leader Category ribosomal protein leader molecular cell biology stub ... more details
Orphan date February 2009 Rfam box acc RF00557 description Ribosomal protein L10 leader abbreviation L10 leader avg length 137.80 avg identity 48.00 type Cis reg leader se Predicted CMFinder, Barrick JE, Moy RH ss Predicted CMFinder, Barrick JE, Moy RH release 10.0 This family is a putative ribosomal protein leader autoregulatory structure ref cite journal last Zengel first JM coauthors Lindahl L year 1994 title Diverse mechanisms for regulating ribosomal protein synthesis in Escherichia coli journal Prog Nucleic Acid Res Mol Biol. volume 47 pages 331&ndash 370 pmid 7517053 doi 10.1016 S0079 6603 08 60256 1 ref found in B. subtilis and other low GC Gram positive bacteria . It is located in the 5 untranslated regions of mRNA s encoding ribosomal proteins L10 and L12 rplJ rplL . A Rho GTP binding protein Rho independent transcription terminator structure that is probably involved in regulation is included at the 3 end. References reflist 1 External links Rfam id RF00557 name Ribosomal protein L10 leader Category ribosomal protein leader molecular cell biology stub ... more details
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