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Encyclopedia results for Rfam

Rfam





Encyclopedia results for Rfam

  1. Rfam

    infobox biodatabase title Rfam logo File Rfam logo.png 120px description The Rfam database provides alignments ... standard format Stockholm format url http rfam.sanger.ac.uk Rfam download ftp ftp.sanger.ac.uk pub databases Rfam Rfam ftp webservice sql sparql webapp standalone license Public domain versioning frequency curation bookmark yes version Rfam is a database containing information about non coding RNA ... A, Eddy SR title Rfam an RNA family database journal Nucleic Acids Res. volume 31 issue 1 pages 439 ... journal author Griffiths Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A title Rfam annotating ... journal author Gardner PP, Daub J, Tate JG, et al. title Rfam updates to the RNA families database ... SR, Bateman A title Rfam Wikipedia, clans and the decimal release. journal Nucleic Acids Res volume ... Rfam is designed to be similar to the Pfam database for annotating protein families. Unlike proteins ... sequence . Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing ... of secondary structure information. Rfam researchers also contribute to Wikipedia s Wikipedia ... url pmc 2590952 ref Uses of Rfam The Rfam database can be used for a variety of functions. For each ... references and other RNA databases. Rfam also provides links to Wikipedia so that entries can be created or edited by users. The interface at the Rfam website allows users to search ncRNAs by keyword ... with Rfam to annotate sequences including complete genomes for homologues to known ncRNAs. Methods Image Rfam alignment2.PNG left thumb A theoretical ncRNA alignment from 6 species. Secondary structure ... information. This seed alignment is used to create the SCFG, which is used with the Rfam software ... threshold value is chosen to avoid false positives. Performing Rfam searches using profile SCFG ... full alignment. History Version 1.0 of Rfam was launched in 2003 and contained 25 ncRNA families and annotated ... the ref & ref tags and the Reflist template Reflist External links http rfam.sanger.ac.uk Rfam Web ...   more details



  1. Pseudomonas sRNA

    structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk ... rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01668 RF01668 Image P13 secondary structure.jpg P13 Secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family ... structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family ... Rfam database. Family http rfam.sanger.ac.uk family RF01670 RF01670 Image P18 secondary structure.jpg P18 Secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family http ... taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01673 ... Rfam database. Family http rfam.sanger.ac.uk family RF01674 RF01674 Image P29 secondary structure.jpg P29 Secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk ... from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01676 RF01676 Image P35 secondary structure.jpg P35 Secondary structure taken from the http rfam.sanger.ac.uk Rfam ...   more details



  1. Hfq binding sRNA

    Infobox rfam Name isrA Hfq binding RNA image RF01385.png width caption Predicted secondary structure of isrA Hfq binding RNA Symbol isrA AltSymbols Rfam RF01385 miRBase miRBase family RNA type gene , sRNA ... http rfam.sanger.ac.uk Rfam database Navbox name hidden title Gallery of secondary structure images ... RNA Predicted secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family ... structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk ... from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01387 RF01387 ... Rfam database. Family http rfam.sanger.ac.uk family RF01388 RF01388 . Image RF01389.png isrF Hfq binding RNA Predicted secondary structure taken from the http rfam.sanger.ac.uk Rfam database ... secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk ... taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01391 ... rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01392 RF01392 . Image RF01393.png isrJ Hfq binding RNA Predicted secondary structure taken from the http rfam.sanger.ac.uk Rfam ... RNA Predicted secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk ... structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family ... rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01396 RF01396 . Image ... Rfam database. Family http rfam.sanger.ac.uk family RF01397 RF01397 . Image RF01398.png isrP Hfq binding RNA Predicted secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family ... structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk ... taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01400 RF01400 ... Rfam database. Family http rfam.sanger.ac.uk family RF01401 RF01401 . Image RF01402.png ...   more details



  1. CtRNA

    lowercase Infobox rfam Name ctRNA image RF00489.jpg width caption Predicted secondary structure and sequence conservation of ctRNA p42d Symbol ctRNA p42d AltSymbols Rfam RF00489 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 In molecular biology ctRNA counter transcribed RNA is a plasmid encoded noncoding RNA that binds to the mRNA of repB and causes translation genetics translational inhibition. ref name Ven03 cite journal last Venkova Canova first T coauthors Patek M, Nesvera J year 2003 title Control of rep gene expression in plasmid pGA1 from Corynebacterium glutamicum journal J Bacteriol volume 185 pages 2402&ndash 2409 pmid 12670963 doi 10.1128 JB.185.8.2402 2409.2003 issue 8 pmc 152619 ref ctRNA is encoded by plasmids and functions in rolling circle replication to maintain a low copy number. In Corynebacterium Corynebacterium glutamicum , it achieves this by antisense pairing with the mRNA of RepB, a self replication replication initiation protein. ref name Ven03 In Enterococcus faecium the plasmid pJB01 contains three open reading frames, copA, repB, and repC. The pJB01 ctRNA is coded on the opposite strand from the copA repB intergenic region and partially overlaps an atypical ribosome binding site for repB. ref name pmid18511887 cite journal author Kim SW, Jeong IS, Jeong EJ, et al. title The terminal and internal hairpin loops of the ctRNA of plasmid pJB01 play critical roles in regulating copy number journal Mol. Cells volume 26 issue 1 pages 26 33 year 2008 month July pmid 18511887 doi url ref See also S element References references External links Rfam id RF00236 name ctRNA pGA1 Rfam id RF00489 name ctRNA p42d Rfam id RF00238 name ctRNA pND324 Rfam id RF00242 name ctRNA pT181 Category Antisense RNA molecular cell biology stub ...   more details



  1. Plasmodium RUF4 RNA

    Infobox rfam Name Plasmodium RNA of unknown function 4 image RUF4 SS.png width caption Predicted secondary structure of RUF4 Symbol RUF4 AltSymbols Rfam RF01578 miRBase miRBase family RNA type sRNA Tax domain Plasmodium GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData RUF4 is a non coding RNA ncRNA present within the plasmodium genome . bioinformatics Bioinformatic studies predicted that RUF4 was present within the plasmodium genome and the expression of this ncRNA was verified by Northern Blot . ref name pmid17901154 Cite pmid 17901154 ref The location of this ncRNAs was subsequently mapped within the P. falciparum strain 3DF genome by primer extension . RUF4 is a novel RNA of unknown function but has shown to contain some structural similarity with the H ACA box snoRNA but no known targets have been identified. References reflist External links Rfam id RF01582 name RNA of unknown function RUF4 Category Non coding RNA ...   more details



  1. Plasmodium RUF2 RNA

    Infobox rfam Name Plasmodium RNA of unknown function 2 image RUF2 SS.png width caption Predicted secondary structure of RUF2 Symbol RUF2 AltSymbols Rfam RF01579 miRBase miRBase family RNA type sRNA Tax domain Plasmodium GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData RUF2 is a non coding RNA ncRNA present within the plasmodium genome . bioinformatics Bioinformatic studies predicted that RUF2 was present within the plasmodium genome and the expression of this ncRNA was verified by Northern Blot . ref name pmid17901154 Cite pmid 17901154 ref The location of this ncRNAs was subsequently mapped within the P. falciparum strain 3DF genome by primer extension . RUF2 is a novel RNA of unknown function but has shown to contain some structural similarity with the H ACA box snoRNA but no known targets have been identified. References reflist External links Rfam id RF01579 name Plasmodium RNA of unknown function RUF2 Category Non coding RNA ...   more details



  1. Plasmodium RUF1 RNA

    Infobox rfam Name Plasmodium RNA of unknown function 1 image RUF1 SS.png width caption Secondary structure of RUF1 Symbol RUF1 AltSymbols Rfam RF01578 miRBase miRBase family RNA type sRNA Tax domain Plasmodium GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData RUF1 is a non coding RNA ncRNA present within the plasmodium genome . bioinformatics Bioinformatic studies predicted that RUF1 was present within the plasmodium genome and the expression of this ncRNA was verified by Northern Blot . ref name pmid17901154 Cite pmid 17901154 ref The location of this ncRNAs was subsequently mapped within the P. falciparum strain 3DF genome by primer extension . RUF1 is a novel RNA of unknown function but has shown to contain some structural similarity with the H ACA box snoRNA but no known targets have been identified. References reflist External links Rfam id RF01578 name Plasmodium RNA of unknown function RUF1 Category Non coding RNA ...   more details



  1. Regulatory region of repZ gene

    Orphan date October 2010 Infobox rfam Name Regulatory region of repZ gene image RF01087.png width 200 caption Secondary structure of the regulatory region of repZ gene Symbol repZ AltSymbols Rfam RF01087 miRBase miRBase family RNA type Cis reg Tax domain Proteobacteria CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The regulatory region of the repZ gene , which encodes the replication initiator of plasmid ColIb P9, contains a pseudoknot . This acts as a molecular switch controlling translation of repZ and repY. ref cite journal title An RNA pseudoknot as the molecular switch for translation of the repZ gene encoding the replication initiator of IncIalpha plasmid ColIb P9. journal J Biol Chem year 2003 first k last Asano K coauthors K Mizobuchi volume 273 pages 11815 25 pmid 9565606 issue 19 doi 10.1074 jbc.273.19.11815 ref References Reflist External links http rfam.sanger.ac.uk family RF01087 Rfam entry for Regulatory region of repZ gene Category Non coding RNA ...   more details



  1. Plasmodium RUF6 RNA

    Infobox rfam Name Plasmodium RNA of unknown function 6 image RUF6 SS.png width caption Predicted secondary structure of RUF6 Symbol RUF6 AltSymbols Rfam RF01581 miRBase miRBase family RNA type sRNA Tax domain Plasmodium GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData RUF6 is a non coding RNA ncRNA present within the plasmodium genome . bioinformatics Bioinformatic studies predicted that RUF6 was present within the plasmodium genome and the expression of this ncRNA was verified by Northern Blot . ref name pmid17901154 Cite pmid 17901154 ref The location of this ncRNAs was subsequently mapped within the P. falciparum strain 3DF genome by primer extension . This ncRNA was shown to be encoded for by multiple genes that are clustered together within the plasmodium genome. These clusters were located in regions that flanked the malaria surface antigens RIFIN and VAR genes or in locations that are known for being genetic recombination recombination hot spots. The function of RUF6 is still unknown but from knowing the location of RUF6 within the plasmodium genome it has been suggested that RUF6 may have a role in the expression or maintenance of the malaria surface antigens but this has yet to be determined. References reflist External links Rfam id RF01580 name Plasmodium RNA of unknown function RU6 F3 Rfam id RF01581 name Plasmodium RNA of unknown function RUF6 5 Category Non coding RNA ...   more details



  1. Listeria monocytogenes non-coding RNA

    Infobox rfam Name Listeria snRNA rli22 image RF01457.png width 200 caption Predicted secondary structure of Listeria snRNA rli22 Symbol rli22 AltSymbols Rfam RF01457 miRBase miRBase family RNA type gene ... Characteristic Rfam rli22 31997 32107 110 lmo0028 lmo0029 sRNA rli23 172171 172268 97 lmo0172 sRNA ... lmo1150 sRNA Annotated as a cobalamin riboswitch in Rfam rli40 1275810 1275547 264 lmo1251 lmo1252 ... ? lmo1190 cbiA 3 UTR derived Annotated as a cobalamin riboswitch in Rfam lmo1190 rli57 transcript ... ID Rfam ID Rfam SAM riboswitch S box leader SAM RF00162 PrfA thermoregulator UTR PrfA RF00038 Listeria ... reflist External links http rfam.sanger.ac.uk Rfam database Navbox name hidden title Gallery ... Rfam database. Family http rfam.sanger.ac.uk family RF01457 RF01457 . Image RF01458.png Listeria snRNA rli23 Predicted secondary structure taken from the http rfam.sanger.ac.uk Rfam database ... secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk ... taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01460 RF01460 ... Rfam database. Family http rfam.sanger.ac.uk family RF01461 RF01461 . Image RF01462.png Listeria snRNA rli26 Predicted secondary structure taken from the http rfam.sanger.ac.uk Rfam database ... Predicted secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk ... taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01464 ... rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01465 RF01465 . Image RF01466.png ... Rfam database. Family http rfam.sanger.ac.uk family RF01466 RF01466 . Image RF01467.png Listeria snRNA rli36 Predicted secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family http ... structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family ... the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01469 RF01469 . Image ...   more details



  1. Bxd (gene)

    Infobox rfam Name Bithoraxoid conserved region 1 image Bxd c1 SS.png width caption Conserved secondary structure of Bithoraxoid conserved region 1 Symbol bxd 1 AltSymbols Rfam RF01929 miRBase miRBase family RNA type Gene Tax domain Drosophila Bithoraxoid bxd is a long non coding RNA found in Drosophila . It silences the expression of the Ultrabithorax Ubx gene by Transcription genetics transcriptional interference. ref name pmid17174895 cite journal author Petruk S, Sedkov Y, Riley KM, et al. title Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference journal Cell volume 127 issue 6 pages 1209 21 year 2006 month December pmid 17174895 pmc 1866366 doi 10.1016 j.cell.2006.10.039 url ref ref name pmid17568198 cite journal author Petruk S, Sedkov Y, Brock HW, Mazo A title A model for initiation of mosaic HOX gene expression patterns by non coding RNAs in early embryos journal RNA Biol volume 4 issue 1 pages 1 6 year 2007 pmid 17568198 doi 10.4161 rna.4.1.4300 url ref References reflist 2 Further reading refbegin cite journal author Janssen R, Budd GE title Gene expression suggests conserved aspects of Hox gene regulation in arthropods and provides additional support for monophyletic Myriapoda journal Evodevo volume 1 issue 1 pages 4 year 2010 pmid 20849647 pmc 2938723 doi 10.1186 2041 9139 1 4 url cite journal author Kozma G, Bender W, Sipos L title Replacement of a Drosophila Polycomb response element core, and in situ analysis of its DNA motifs journal Mol. Genet. Genomics volume 279 issue 6 pages 595 603 year 2008 month ... MCB.21.14.4528 4543.2001 url External links Rfam id RF01930 name Bithoraxoid conserved region 2 Rfam id RF01931 name Bithoraxoid conserved region 3 Rfam id RF01933 name Bithoraxoid conserved region 5 Rfam id RF01929 name Bithoraxoid conserved region 1 Rfam id RF01935 name Bithoraxoid conserved region 7 Rfam id RF01934 name Bithoraxoid conserved region 6 Rfam id RF01932 name Bithoraxoid conserved ...   more details



  1. Alpha operon ribosome binding site

    Infobox rfam Name Alpha operon ribosome binding site image RF00140.jpg width caption Predicted secondary structure and sequence conservation of Alpha RBS Symbol Alpha RBS AltSymbols Rfam RF00140 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Bacteria GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The alpha operon ribosome binding site in bacteria is surrounded by this complex pseudoknot ted RNA structure. Translation of the mRNA produces 4 ribosomal protein products, one of which S4 acts as a translational repressor by binding to the nested pseudoknot region. The mechanism of repression is thought to involve a conformational switch in the pseudoknot region and ribosome entrapment. ref cite journal last Schlax first PJ coauthors Xavier KA, Gluick TC, Draper DE year 2001 title Translational repression of the Escherichia coli alpha operon mRNA importance of an mRNA conformational switch and a ternary entrapment complex journal J Biol Chem volume 276 pages 38494&ndash 38501 pmid 11504736 doi 10.1074 jbc.M106934200 issue 42 ref References reflist 1 External links Rfam id RF00140 name Alpha operon ribosome binding site Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. Apolipoprotein B (apoB) 5' UTR cis-regulatory element

    Infobox rfam Name Apolipoprotein B apoB 5 UTR cis regulatory element image RF00463.jpg width caption Predicted secondary structure and sequence conservation of ApoB 5 CRE Symbol ApoB 5 CRE AltSymbols Rfam RF00463 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Eukaryota GO SO SO 0000204 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The apolipoprotein B apoB 5 UTR cis regulatory element is an cis regulatory element RNA element located in the 5 UTR of the human apoB mRNA . This structured element increases translation of the apoB protein or a reporter gene. ref cite journal last Pontrelli first L coauthors Sidiropoulos KG, Adeli K year 2004 title Translational control of apolipoprotein B mRNA regulation via cis elements in the 5 and 3 untranslated regions journal Biochemistry volume 43 pages 6734&ndash 6744 pmid 15157107 doi 10.1021 bi049887s issue 21 ref References reflist 1 External links Rfam id RF00463 name Apolipoprotein B apoB 5 UTR cis regulatory element Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. Bovine leukaemia virus RNA packaging signal

    Infobox rfam Name Bovine leukaemia virus RNA packaging signal image RF00192.jpg width caption Predicted secondary structure and sequence conservation of BLV package Symbol BLV package AltSymbols Rfam RF00192 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Eukaryota Virus es GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData This family represents the bovine leukaemia virus RNA capsid encapsidation packaging signal which is essential for efficient viral replication . ref cite journal last Mansky first LM coauthors Gajary LC year 2002 title The primary nucleotide sequence of the bovine leukemia virus RNA packaging signal can influence efficient RNA packaging and virus replication journal Virology volume 301 pages 272&ndash 280 pmid 12359429 doi 10.1006 viro.2002.1578 issue 2 ref See also Mason Pfizer monkey virus packaging signal References reflist 1 External links Rfam id RF00192 name Bovine leukaemia virus RNA packaging signal Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. C0299 RNA

    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



  1. C0465 RNA

    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



  1. C0719 RNA

    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



  1. Cardiovirus cis-acting replication element

    Infobox rfam Name Cardiovirus cis acting replication element CRE image RF00453.jpg width caption Predicted secondary structure and sequence conservation of Cardiovirus CRE Symbol Cardiovirus CRE AltSymbols Rfam RF00453 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Virus es GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData This family represents a Cardiovirus cis acting replication element CRE which is located within the region encoding the capsid protein VP2 and is required for viral replication . ref cite journal last Lobert first PE coauthors Escriou N, Ruelle J, Michiels T year 1999 title A coding RNA sequence acts as a replication signal in cardioviruses journal Proc Natl Acad Sci USA volume 96 pages 11560&ndash 11565 pmid 10500216 doi 10.1073 pnas.96.20.11560 issue 20 pmc 18073 ref See also Citrus tristeza virus replication signal Coronavirus SL III cis acting replication element CRE Rubella virus 3 cis acting element References reflist 1 External links Rfam id RF00453 name Cardiovirus cis acting replication element CRE Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. Connexin-32 internal ribosome entry site (IRES)

    Infobox rfam Name Connexin 32 internal ribosome entry site IRES image RF00484.jpg width caption Predicted secondary structure and sequence conservation of IRES Cx32 Symbol IRES Cx32 AltSymbols Rfam RF00484 miRBase miRBase family RNA type Cis regulatory element Cis reg Internal ribosome entry site IRES Tax domain Eukaryota GO GO 0043022 SO SO 0000243 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The connexin 32 internal ribosome entry site IRES is an Cis regulatory element RNA element present in the Five prime untranslated region 5 UTR of the mRNA of connexin 32 and allows cap independent translation. This internal ribosome entry site IRES allows cap independent translation during conditions such as heat shock and stress. ref cite journal last Hudder first A coauthors Werner R year 2000 title Analysis of a Charcot Marie Tooth disease mutation reveals an essential internal ribosome entry site element in the connexin 32 gene journal J Biol Chem volume 275 pages 34586&ndash 34591 pmid 10931843 doi 10.1074 jbc.M005199200 issue 44 ref References reflist 1 External links Rfam id RF00484 name Connexin 32 internal ribosome entry site IRES Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. Connexin-43 internal ribosome entry site (IRES)

    Infobox rfam Name Connexin 43 internal ribosome entry site IRES image RF00487.jpg width caption Predicted secondary structure and sequence conservation of IRES Cx43 Symbol IRES Cx43 AltSymbols Rfam RF00487 miRBase miRBase family RNA type Cis regulatory element Cis reg Internal ribosome entry site IRES Tax domain Eukaryota GO GO 0043022 SO SO 0000243 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The connexin 43 internal ribosome entry site IRES is an Cis regulatory element RNA element present in the Five prime untranslated region 5 UTR of the mRNA of connexin 43 and allows cap independent translation. The connexin 43 internal ribosome entry site IRES allows cap independent translation during conditions such as heat shock and stress. ref cite journal last Schiavi first A coauthors Hudder A, Werner R year 1999 title Connexin43 mRNA contains a functional internal ribosome entry site journal FEBS Lett volume 464 pages 118&ndash 122 pmid 10618489 doi 10.1016 S0014 5793 99 01699 3 issue 3 ref References reflist 1 External links Rfam id RF00487 name Connexin 43 internal ribosome entry site IRES Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. Enterovirus 5' cloverleaf cis-acting replication element

    Infobox rfam Name Enterovirus 5 cloverleaf cis acting replication element image RF00386.jpg width caption Predicted secondary structure and sequence conservation of Entero 5 CRE Symbol Entero 5 CRE AltSymbols Rfam RF00386 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Virus es GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The Enterovirus 5 cloverleaf cis acting replication element is an cis regulatory element RNA element found in the 5 UTR of Enterovirus genomes . The element has a cloverleaf like secondary structure and is known to be a multifunctional cis acting replication element CRE , required for the initiation of negative strand RNA synthesis . ref cite journal last Barton first DJ coauthors O Donnell BJ, Flanegan JB year 2001 title 5 cloverleaf in poliovirus RNA is a cis acting replication element required for negative strand synthesis journal EMBO J volume 20 pages 1439&ndash 1448 pmid 11250909 doi 10.1093 emboj 20.6.1439 issue 6 pmc 145522 ref See also Enteroviral 3 UTR element Enterovirus cis acting replication element References reflist 1 External links Rfam id RF00386 name Enterovirus 5 cloverleaf cis acting replication element Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. Hairy RNA localisation element (HLE)

    Infobox rfam Name Hairy RNA localisation element HLE image RF00437.jpg width caption Predicted secondary structure and sequence conservation of HLE Symbol HLE AltSymbols Rfam RF00437 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Eukaryota GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The hairy localisation element HLE is an Cis regulatory element RNA element found in the Three prime untranslated region 3 UTR of the hairy gene. HLE contains two stem loop s. HLE is essential for the mediation of apical localisation and the two stem loop structures act to allow the recognition of hairy mRNA by the localisation machinery. ref cite journal last Bullock first SL coauthors Zicha D, Ish Horowicz D year 2003 title The Drosophila hairy RNA localization signal modulates the kinetics of cytoplasmic mRNA transport journal EMBO J volume 22 pages 2484&ndash 2494 pmid 12743042 doi 10.1093 emboj cdg230 issue 10 pmc 155988 ref HLE is found in Drosophila species. References reflist 1 External links Rfam id RF00437 name Hairy RNA localisation element HLE Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES)

    Infobox rfam Name Heat shock protein 70 Hsp70 internal ribosome entry site IRES image RF00495.jpg width caption Predicted secondary structure and sequence conservation of IRES Hsp70 Symbol IRES Hsp70 AltSymbols Rfam RF00495 miRBase miRBase family RNA type Cis regulatory element Cis reg Internal ribosome entry site IRES Tax domain Eukaryota GO GO 0043022 SO SO 0000243 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The heat shock protein 70 Hsp70 internal ribosome entry site IRES is an cis regulatory element RNA element that allows cap independent translation during conditions such as heat shock and stress. It has been shown that the 216 nucleotide long 5 UTR contains internal ribosome entry site activity. ref cite journal last Rubtsova first MP coauthors Sizova DV, Dmitriev SE, Ivanov DS, Prassolov VS, Shatsky IN year 2003 title Distinctive properties of the 5 untranslated region of human hsp70 mRNA journal J Biol Chem volume 278 pages 22350&ndash 22356 pmid 12682055 doi 10.1074 jbc.M303213200 issue 25 ref References reflist 1 External links Rfam id RF00495 name Heat shock protein 70 Hsp70 internal ribosome entry site IRES Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. Hepatitis E virus cis-reactive element

    Infobox rfam Name Hepatitis E virus cis reactive element image RF00550.jpg width caption Predicted secondary structure and sequence conservation of HepE CRE Symbol HepE CRE AltSymbols Rfam RF00550 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Virus es GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The Hepatitis E virus cis reactive element is a cis regulatory element RNA element that is thought to be essential for some step in gene expression . ref name Gra05 cite journal last Graff first J coauthors Nguyen H, Yu C, Elkins WR, St Claire M, Purcell RH, Emerson SU year 2005 title The open reading frame 3 gene of hepatitis E virus contains a cis reactive element and encodes a protein required for infection of macaques journal J Virol volume 79 pages 6680&ndash 6689 pmid 15890906 doi 10.1128 JVI.79.11.6680 6689.2005 issue 11 pmc 1112134 ref The mutation of this element resulted in Hepatitis E strains which were unable to infect Rhesus macaque s Macaca mulatta . ref name Gra05 References reflist 1 External links Rfam id RF00550 name Hepatitis E virus cis reactive element Category Cis regulatory RNA elements molecular cell biology stub ...   more details



  1. HgcF RNA

    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




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