User:WillowW/Rfam commentary

miR-19 has now been predicted or experimentally SraE (also known as RygB) is highly abundant in stationary This family also contains snos R70 and R12 from Arabidopsis 18S G-1358. 18S U-1356. ACA11 belongs to the H/ACA box class of guide RNAs as it has Although evidence has been presented for an existence A similar role has been suggested for the H/ACA snoRNAs U17a -1 frameshift and translation then continues in the new frame 1-nt different from published. The classical swine virus UTR described in appears to This family also contains several other annotated snoRNAs including This family is predicted to direct a highly conserved Two independent studies have found that 7SK RNA binds the 201-nucleotide sequence just upstream of the polyadenylation Many Gram-positive species have two copies of 6S RNA. In miR-194 appears to be a vertebrate specific miRNA and has now 2'-O-ribose methylation guide for pre-rRNA. 2'O-ribose methylation of snRNA U6 at residue C60. 2'O-ribose methylation of the large 28S rRNA at residue U4590. 2'O-ribose methylation of the small 18S rRNA on position A512. It 2'-O-ribose residues on 18S ribosomal RNA. The function of these RNAs is unknown. This mirna appears to be specific to the vertebrates and has U106 contains conserved antisense elements which would U25 is thought to as a 2'-O-ribose methylation guide for 300-nucleotide 7S RNA (RF00017 RF00017]) and six proteins: SRPs 72, 3rd anti-codon position. 3' tails by UnaL2-encoded reverse transcriptase. The solution 3'-terminal 4 bases of the RNA(GCCC-OH). ~55nt pseudoknot structure which has been shown to be necessary 5.8S ribosomal RNA (5.8S rRNA) is a component of the large 5.8S rRNA is also found in archaea. (5'-ACAGG and CUCUUCC-5') in PSTVd, is thought to bind with the tomato 5' arm of the hairpin. 5 of ribosomal protein S8 in human and in homologous genes in (5-ribosyluracil) a constituent of structural RNAs (transfer, ribosomal, 5S ribosomal RNA (5S rRNA) is a component of the large ribosomal 5' UTRs. 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and 68-nucleotide element within the FIE3. ~70nt precursors and subsequently processed by the Dicer enzyme 7SK was discovered as an abundant small nuclear RNA in the 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. a 50-fold acceleration in transcript degradation. a biosensor for intracellular free polyamines. absent in PWS patients.  HBII-52 lacks any significant a bulged adenosine in domain VI attacks the 5' splice site, abundant snoRNAs in human cells and is essential for the cleavage ACA13 is a member of the H/ACA class of snoRNA that guide the sites of ACA27 is found in the same host gene within a different intron ACA28 is a member of the H/ACA class of snoRNA that guide the sites of ACA35 belong to the H/ACA box class of guide RNAs as it has the accession number for 'Homo sapiens snoRNA ACA53 gene' (AJ609478) access to the ribosome-binding site of ypaA mRNA. accumulation of gadX (a transcriptional regulator of the acid response) and achieves this by mediating the internal initiation of translation acid cycle, acnA and fumA, two ferritin genes, ftnA and bfr, acid transporter gene, and members of the yuaA-yubG operon which a complex secondary structure featuring multiple putative a conserved secondary structure containing three stem acquisition of a spliced leader from a SL RNA is a intra-molecular act as guides in the the modification of uridines to pseudouridines. activate PKR which is known to be a translational inhibitor. Mutations in activation of macrophages. activity in the absence of the protein subunit, i.e. it is a activity is strictly controlled and highly tissue specific. It is thought activity is supposed to reside in one of the protein components activity of poly(A) polymerase (PAP), and inhibits its activity activity. This rne 5' UTR element acts as a sensor of cellular acts as a translational repressor by binding to the nested acts to regulate renin production. REN-SRE is thought to destabilise the additional hairpin. This family includes a significant adenosylcobalamin (Ado-CBL) is known to repress expression of genes for Agrobacterium tumefaciens, and other methionine and SAM Agrobacterium tumefaciens and related alpha-proteobacteria. The a large number of new candidate thiamin-regulated genes, mostly alignment also includes a portion of the antiterminator alignment (Bateman A pers obs). Allosteric rearrangement of mRNA structure is mediated by ligand almost identical mature sequences. The extents of the hairpin alpha-proteobacteria that binds S-adenosyl methionine (SAM). Its alpha-proteobacteria. The final stem of the structure overlaps (Alpharetroviruses and Avian type C retroviruses). dr1 is required for also be involved in the regulation of viral replication. also contains the 26 amino acid delta-haemolysin gene (hld). also encode essential splicing proteins in intronic ORFs. The also interacts with a CsrA-like protein. also in the case of monocytes and macrophages, in response to also present in mice. U79 is a member of the C/D class of snoRNA which also present in this family. The hairpin precursors (represented alternative method of translation via internal ribosome entry where alternative structures. One that is a series although it has been suggested that it may function to switch on Although the U12 sequence is very divergent from that of U2 a methylation guide for 18S ribosomal RNA in plants.Although amino acid biosynthetic genes usually in Gram-positive bacteria. aminoacyl-tRNA synthetases). tRNAs cope with the degeneracy of and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be and a 5'-cap) are known to enhance translation. and ACA10 and mouse MBI-29. and a gene for superoxide dismutase, sodB. and are estimated based on hairpin prediction. The products are thought and a side-by-side helical alignment. and be expressed during different stages of growth. In many and create the active site for splicing catalysis. A recycling and  D (CUGA) box motifs. Most of the members of the box C/D family and equine rhinovirus genomes.  Its function is unknown, but and experimentally confirmed in Drosophila. miR-219 homologs and Fugu.  snoR75 from Arabidopsis  and homologues in rice and GTL2.  snoRNAs 14q(I) and 14q(II) differ from previously and highly tissue specific. and hY5.  These small RNAs are predicted to fold into and is critical for leader TRS function. and is encoded together with HBII-436, HBII-437, HBII-438A/B and and is known to be a multifunctional cis-acting replication element (CRE), and is predicted to guide the 2'O-ribose methylation of U4 snRNA and is specifically expressed in the brain, specifically in the and is thought to be needed for the formation of a "replication complex" and it is thought the IRES may initiate translation of vFLIP from this and L20 (infC-rpmI-rplT). A Rho-independent transcription and mir107. Animal miRNAs are transcribed as ~70nt precursors and and mir-200 (MI0000243 MI0000243], MI0000342 MI0000342]) are expressed from and other plants are alternatively known as U15, and, despite and plant Z100 snoRNA. and R59. Members of this family belong to the C/D box class of and regulates ompF expression by inhibiting translation and inducing and related bacteria that post-transcriptionally controls expression and ribosomal protein L27 (rplU-ysxB-rpmA). and several small untranslated RNA molecules. It has been and singlet (U4-8) forms of this snRNA have been purified from and snoZ131 in rice. and snRNAs. The precise target of this family is unknown. and so enhance secondary metabolism and biocontrol traits. and the branchpoint sequence (BPS) of the intron results in and the H/ACA box snoRNA ACA51 share the same host gene (NOL5A) and the rpoS-encoded sigma(s) subunit of RNA polymerase. and thiazole moieties in bacteria. The previously detected and translation of the tmRNA leads to addition of a proteolysis and U12 snRNAs and associated proteins, forms a spliceosome that and U1920 in Drosophila 18S rRNA to pseudouridine. and U76 snoRNAs show clear similarity to U24. and was named SraF. The family was later found to exist upstream of and when deleted leads to a 50% drop in regulation. The element is thought and ykoK genes in B. subtilis. The specific functions of these proteins are Animal histone pre-mRNAs are spliced by a different mechanism Animal miRNAs are transcribed as ~70nt precursors and an important role in the initiation of minus-strand RNA synthesis and may an internal loop of the RRE leading, encouraging further Rev-RRE an intron of the gene for ribosomal protein L5 in mammals , another C/D box domain U12-22 (RF00492 RF00492]). Both the doublet anterior/posterior patterning in the Drosophila embryo. anti-sense RNA which inhibits transposase expression when IS10 is antitermination of genes in the T-box leader family. T-boxes are anti-terminator form. This entry represents the conserved antiterminator structure. antizyme mRNA. The frameshifting efficiency is dependent on the level of a number of archaeal genomes. This family represents A number of closely related snoRNAs have been found in any significant complementarity with ribosomal RNA. apical localisation and the two stem-loop structures act to allow the appears to be a vertebrate specific microRNA and has now been appears to be Drosophila specific. Animal miRNAs are transcribed as ~70nt appears to be expressed from intergenic regions in HOX gene appears to be specific to humans. Animal miRNAs are transcribed as ~70nt a protein required for transcription from the major transfer Arabidopsis and rice have been named R63 and Z106 respectively. Arabidopsis homologue is annotated as snoR41 in the sequence archaea, bacteria and eukaryotes. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic archaea, the SRP19-helix 6 complex is thought to be involved in are close paralogues sharing the same host gene (FLJ10534) and are common to all cellular RNase P RNAs. Yet, there is are members of the C/D class of snoRNA which contain the C (UGAUGA) and D are necessary for genome replication. 2 RNA domains in the 5' UTR are not generally known and are estimated based on hairpin prediction. are predicted based on base pairing and cross-species are predicted based on conservation and base pairing and are not are predicted to guide 2'O-ribose methylation of the large 28S are predicted to guide the 2'O-ribose methylation of residue U22 are transcribed as ~70nt precursors (modelled here) and arm of the precursor, and both Arabidopsis and rice genomes arm of the precursor. The extents of the hairpin precursors (ARMV). as 40 genes, including the fhlA-encoded transcriptional activator as a 2'-O-ribose methylation guide for ribosomal RNA. a significantly shorter sequence length, appear to be related. a small complex (the U8 snoRNP) which is required for accumulation a small RNA called ctRNA (for counter-transcribed RNA) than is as mediating viral replication. a specific anti-codon) for a particular amino acid; and 'wobble' as possibly other, still unknown cellular RNAs. U23 can associated proteins. In S.aureus, RNAIII acts as the effector of the agr associates with RNA polymerase holoenzyme containing the sigma70 as the culture approaches the stationary phase of growth and is as U46.  U40 is encoded in intron 2 of the ribosomal protein S8 gene a subset of the six short sequence elements found in all U3 at 37 degrees C, almost silent at 30 degrees C and controlled by at each bend and when complexed with the two proteins it blocks At least 6 amino acid operons are known to be regulated by at least two small RNAs, DsrA and RprA, participate in the positive a transcriptional repressor related to the Myc/Mad family of transcription attenuation.  In each a leader sequence of 150-200 bp auto-regulated by transcript stability. rnc, the first gene in a wide variety of bacteria, CsrB RNAs are only known in (Bachellerie JP, Ganot, P unpublished data). U23 is encoded Bacillus subtilis, both copies appear to interact with RNA Bacillus subtilis, the riboswitch most likely controls gene bacteria (e.g. Bacillus subtilis) have a longer eukaryote-like bacteria. It is located in the 5' untranslated regions of mRNAs Bacterial tmRNA, also known as 10Sa RNA or SsrA, is named for its bacteria. The retron encodes a reverse transcriptase that is bacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a bamboo mosaic virus satellite RNA (satBaMV). The family is thought to be based on base pairing and cross-species conservation -- their based on conservation and base pairing and are not generally based on hairpin prediction. The products are thought to have regulatory based on the sequence of the mature RNA. based on which helix the 5' and 3' ends of the sequence base-pairing, i.e. permitting non-standard base-pairing at the base pairing is confined to a short 5' stem loop, but U6 snRNA base pairs with the 5' splice junction, thus defining the 5' bases in length and is composed of a hairpin like structure.  The bases in length. sroB is found in several Enterobacterial species but its bases in length. The function of this family is unknown. bases of the pRNA are essential for packing the viral DNA. The becomes stabilised in response to IL-1 or tumour necrosis factor alpha, and been been predicted and experimentally confirmed in a wide range been expressed in mouse (MI0000174 MI0000174]) and is predicted in human been found to be essential for efficient viral replication and it has been been found to enhance DI RNA accumulation by approximately 10-fold as well been identified for scaRNA ACA11. been shown to act as methylation guides for a number of RNA been shown to localise to the nucleoplasm and is proposed to been shown to retain its catalytic function, but is still essential for be homologous to Arabidopsis snoR13. being involved in wound-healing. It has been found that FGF-2 IRES believed that these RNAs, guided by a protein, Hfq, can mediate the believed to act as a negative regulator of repC transcription, be be longer at the 5' end than other pestivirus UTRs. This family belongs to the H/ACA box class of guide RNAs as it has the belongs to the H/ACA class of guide RNAs. U93 is predicted to guide belong to the H/ACA box class of guide RNAs as it has the be substituted by the trp transcription terminator without loss of between 135 and 170 bases in length. The t44 gene has been between organisms. bicistronic transcript. binding, and that both the 3' stem-loop and the Sm site are binding, and this results in modulation of gene expression. A class binding RNA which is found in the 3' UTR. AMV CP can stimulate the binding. This RNP complex is critical for mRNA bind to both aptamers to activate these genes and facilitate biocontrol model organism Pseudomonas fluorescens CHA0. GacA/GacS biosynthesis genes in other alpha-proteobacteria. Like the other blockage in RNA replication and it is thought that both the primary bodies. U88 is found associated with both fibrillarin and both Arabidopsis and rice genomes contain a number of related both HB11-99 and U106 snoRNAs share the same host gene. Most bound by iron response proteins (IRPs). The IRE is found in UTRs box C/D family function in directing site-specific 2'-O-methylation of box domains (termed U12-22 and U4-8). The 5' and 3' C/D domains box D or D' of the snoRNA, the methyltransferase activity is supposed to boxes A and A'), and a larger 3' domain (with boxes B, C, C', and box family function in directing site-specific 2'-O-methylation of breakpoint of chromosomal translocation t(3;6)(q27;q15). The U50HG (BTE) as found in barley yellow dwarf virus (BYDV), bean leafroll virus and (but not essential) for colony formation, though its exact function and but within introns of the ADP ribosylation factor gene in by Darzacq and called U91. Both the doublet (U12-22/U4-8) by promoting efficient translation of the stress sigma factor, RpoS. by recruiting a ribosomal 43S pre-initiation complex directly to by the amounts of two proteins, encoded by cotranscribed genes by the capsid connector protein (PFAM:PF05352). Only the first 120 by this complex pseudoknotted structure. Translation of the C8. This C/D domain was later found associated in tandem with (caf) enzyme appears to be involved in processing. In this case CAGGXXG that is found in up to 18 copies and has been Cajal bodies whereas the U4-8 single domain appears to accumulate called candidates 43,55 and 61. These RNAs have also been can individually mediate internal ribosome entry. However, the full length can lead to overexpression of Spi-1 which has been linked to cap-dependent mechanism it has been found to contain a IRES in its 5' UTR. cap-dependent translation pathway. capsid proteins so is found in a protein coding region. The family has cascade. case the mature sequence comes from both the 3' (miR-30) and 5' case the mature sequence comes from the 3' arm of the precursor. The catabolism and a positive regulatory effect on glycolysis. CD11 is a member of the C/D class of snoRNA which contain the C C/D box domain U91 (also known as U4-8) was identified by Darzacq C/D box snoRNA terminal stem structure. C/D box snoRNA U43 (RPL3). N.B. U83A/B/C have no sequence C/D family function in directing site-specific 2'-O-methylation CDK9/cyclin T complex (known as elongation factor P-TEFb). cells as well. RygB is adjacent to RygA a closely related RNA cell. The IRES achieves this by mediating the internal initiation of central region of 5S RNA. Thus, in addition to positively ceruloplasmin (Cp) gene called gamma interferon inhibitor of translation Changes in Spot 42 levels are implicated in affecting the adjacent charged tRNA of the regulatory amino acid the ribosome chemical modification and enzymatic cleavage experiments. chicken, and Xenopus laevis. chicory yellow mottle virus (CYMV) and arabis mosaic virus Chlamydomonas reinhardtii. The family is thought to be involved in the chloroplasts but are absent from archaeal and eukaryote nuclear chondrocyte specific 24 (ctgf/hcs24) mRNA has been shown to choroids plexus. No RNA target has been identified. chromosome 15. HBII-52 is exclusively expressed in the brain but is chromosome 15. Unlike most other snoRNAs, HBII-85 is expressed circle virus replication to unit-length satellite RNA. cis-regulation is unclear, but this element is postulated to C kinase (RACK1) gene in mammals (S. Griffiths-Jones, classical situation a sequence 32nt downstream of the stem is class of snoRNA which contain C (UGAUGA) and D (CUGA) box motifs. Most of class of snoRNA which contain H (ANANNA) and ACA box motifs. H/ACA box cleavage leads to the formation of 18S rRNA. Regions of the U17 cleavage of this RNA. cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule cleaved from a 45S precursor synthesised by RNA polymerase I). cleaves a divergent class of low-abundance pre-mRNA introns. cleaves the internal transcribed spacer 1 between 18S and 5.8S closely related, but are most likely to be SRP RNA derived pseudogenes. clustered within 0.5 kb at 13q14 in human, a region shown to be clusters. The hairpin precursors (represented here) are predicted cobalamin riboswitch (B12-element) which is widely distributed in 5' UTRs cobra and the Taiwan banded krait. These snoRNAs have extended code for KtrA and KtrB K+ transporters. code for proteins involved in methionine or cysteine biosynthesis colony formation, though its exact function and mechanism are combined into a single family here. Reference proposes that commonplace in nematodes. compilations of SRP components, with phylogenetic data and complementarity to mRNA. The involvement of Dicer in miRNA complementarity with ribosomal RNAs, but does have an 18-nt region complementary to part of the 5' UTR of the traJ mRNA. The complementary to part of the loop. In other Coronaviruses complementary with the upstream leader portion of RpoS messenger RNA, complete human U12-22/U4-8 scaRNA is composed of two tandem C/D complex assembly. component can be one of four small RNAs -- hY1, hY3, hY4 component of this motor. Structural analyses of the packaging comprising a region of the plasmid called RepI. RepI is negatively computationally and was later experimentally verified. mir-399 is thought computational screen in AT-rich hyperthermophiles. R9 was Computational screens have identified C/D box snoRNAs in concentration and synthesis. conditions. During heat shock however, the structure changes conditions such as heat shock and stress. conditions that inhibit cap-dependent translation. confirmed in a wide range of vertebrate species conformational change in the RNA molecule. The Hfq/RydC complex is then consensus sequence 5'-AGGA-3', and sequence analysis predicted consensus sequence, is found in plants, but is absent in conservation -- their extents are not known. In this case the conserved box D or D' of the snoRNA, the methyltransferase conserved bulge in the T-box antiterminator hairpin. conserved in citrus tristeza viruses. Replication signals are required for conserved sequence. These helices are called I, II and III. considerable sequence variation, particularly among the consists of a complex stem-loop region followed by a single stem consists of a stem domain topped by a flexibly paired loop; the 5' consists of domains II, III, IV and V which are known to be essential for contain a conserved secondary structure in the 3' UTR that contain a number of related miRNA precursors which give rise to contain C (UGAUGA) and D (CUGA) box motifs. Most of the members of the C/D contains 4 distinct domains -- the 5', central, 3' major and 3' contains a large symmetrical internal loop (LSL). H5 can repress contains a putative homologue in Drosophila (Griffiths-Jones SR, pers. contains mir-10, mir-51, mir-57, mir-99 and mir-100. mir-10, contains one IRE in its 5' UTR.  When iron concentration is low, contains several related snoRNAs from yeast and plants. contains snoR47, which has been shown to be homologous to U36, contains two stem-loops. HLE is essential for the mediation of contain the C (UGAUGA) and  D (CUGA) box motifs. Most of the members of the contamination. cooperatively bind glycine to regulate the expression of copies in rice (alternatively named snoZ181).  This family also copies of this snoRNA have been identified in Arabidopsis, and copper-containing glycoprotein produced by the liver and secreted into copy number through inhibition of replication initiator protein core of the complex structure involving helices 1-4. Coronaviruses are plus-strand RNA viruses with ~30kb genomes. Coronaviruses which can promote ribosomal frameshifting. This coronavirus stem-loop III and function as cis-acting elements for correct transport and localisation of bicoid mRNA during oocyte and embryo correlated with mRNA levels for the sdhCDAB operon, encoding corresponds to a portion of snoRNA ACA24. covalent linkage to the p53 tumour suppressor protein. Coxsackievirus B3 (CVB3) IRES-mediated translation, and it has been cross-species conservation -- their extents are not known. In CsrB, performs essentially the same function. Both sRNAs possess CsrC RNA binds multiple copies of CsrA Pfam:PF02599, a protein that (CUGA) box motifs. This family seems to be found exclusively in C (UGAUGA) and D (CUGA) box motifs. C/D box snoRNAs have C (UGAUGA) and D (CUGA) box motifs and guide the 2'-O-methylation of rRNA C (UGAUGA) and D (CUGA) box motifs. It is encoded in introns C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D cyanide (HCN) production, while increased metabolite production cytoplasm and activated in the posterior region. Repression is databases. U43 is hypothesised to guide methylation of D (CUGA) box motifs. Most of the members of the box C/D family function in deaminase acting on RNA (ADAR). The ADAR modification causes an decreased with cell growth. Specific cleavage products of this defective interfering (DI) deletion mutants, used to study RNA virus defective interfering (DI) RNA replication. degradation. It is thought that when glycine is in excess it will degradation of its own mRNA in response to changes in RNase E degradation of the message. In addition, other factors, such as the deleted or down-regulated in more than half of B cell chronic derived repeats. The threshold is artificially high to minimise Despite considerable investigation, very little is known about the destabilisation of the quorum-sensing master regulators LuxR/HapR mRNAs destabilising element (G-CSF SLDE). G-CSF is secreted by fibroblasts and developmental timing in C. elegans, and was later shown to be development and maintenance of the nervous system. The IRES development. This family represents a regulatory element found in the 5' DicF RNA is an antisense inhibitor of cell division gene ftsZ. differentiation. directing site-specific 2'-O-methylation of substrate RNAs. direct the pseudouridylation of U97 in human 18S rRNA discovered almost three decades ago. Spot 42 seems to discriminate poorly between real and Y RNA related disease adenomatous polyposis coli (APC).It is thought that disruption of the pseudoknot structure gives rise to a 50% drop in distance of bulged A from 3' splice site, some tertiary distant Bcl-2 homologue. The mature sequence is excised from the 5' arm of distinct roles in eukaryotes. In mitochondria it plays a direct divergent Drosophila and Arabidopsis sequences. DNA polymerase I levels. documented RNA target and they share the same host gene with the domain A, which closes helices 1 and 2, contains the cleavage domain mediates signal sequence recognition. In eukaryotes and domain of RNA polymerase II. This process is negatively domains are presented. This family represents the 5' domain, which domains domains and is predicted to guide 2'-O-methylation of domains (usually designated dI to dVI. This model and alignment domains with similar structures in tandem. The aptamers domain. The 3' domain has conserved protein-binding sites. Both domain (U12-22) as the 3' C/D box is represented by donor site of an intron. dorsoventral polarity in the oocyte. double during multiple inflammatory conditions. Plasma Cp has been double-helical elements and three loops (D, anti-codon, and T downstream genes. In Bacillus subtilis, this riboswitch is found downstream that can interact with this family to form kissing downstream (the histone downstream element, or HDE). The stem-loop D-RNA. This region is thought to be essential for viral replication and Drosophila. U21 snoRNA has a 13 nt region of complementarity Drosophila species. HLE is located in the 3'-UTR of the hairy gene and DsrA RNA regulates both transcription, by overcoming transcriptional D), the two domains being linked by a single-stranded dual tRNA and mRNA-like properties. Its role is to liberate the due to programmed frameshifting and is shorter than tau. The two products During replication of linear dsDNA viruses, the viral genome E2 belongs to the H/ACA class of snoRNAs.  E2 is involved in the E3 belongs to the H/ACA class of snoRNAs and is involved in the each splicing round, it is displaced from U6 (and the early embryogenesis, fushi tarazu mRNA is uniformly distributed early stage of this process such as template recruitment and/or replicase E. coli 6S RNA was the first noncoding RNA to be sequenced, but effect on glycogen biosynthesis, glyconeogenesis and glycogen effects of CsrA, presumably by sequestering this protein. efficient genome encapsidation. efficient initiation of reverse transcription. efficient modification of an adenosine to inosine by an adenosine efficient packaging. efficient translation at the AUG start codon, this family efficient viral replication. efficient viral replication and deletion of stem loop three is known to be efficient viral replication and is thought to be involved in genomic RNA efflux pumps and detoxification systems in response to harmful EIF4A1 (eukaryotic translation initiation factor 4A1) is shared either DsrA function. The sequence of the first stem-loop of DsrA is elegans (MI0000302 MI0000302]), mouse (MI0000150 MI0000150]) and human element allows cap-independent translation of TrkB which may be element and the conserved box D or D' of the snoRNA, the element (CRE). Members of this family are related to Bovine element (CRE). The family is thought to play a crucial role in replication element (CRE) which is found in the coding region of the RNA-dependent RNA element is a riboswitch that directly binds to TPP to element of structure-anchored repression (CAESAR), probably element of the Tombus viruses and is found in the 3' UTR. This family has elements impairs both viral replication and growth. elements in the fushi tarazu mRNA, one located within the 5' element. This family is known to interact with the R2-encoded reverse element which is thought to be essential for both plus and minus strand RNA element, which is widely distributed in eubacteria and also elongation factor-1 gamma in both pombe and cerevisiae. snoR38 guides embryogenic development and wound healing. The 5' UTR of VEGF encircle the embryo. The instability of fushi tarazu mRNA is encoded and are processed from the tissue-specific non-coding encoding homologs of the E. coli YgfA protein which is a putative encoding initiation factor 3 followed by ribosomal proteins L35 encoding ribosomal protein L19 (rplS). encoding ribosomal protein L21, a protein of unknown function, encoding ribosomal proteins L10 and L12 (rplJ-rplL). A encoding the L13-S9 (rplM-rpsI) ribosomal protein operon. end-independent translation of mRNA in the host cell. The IRES end of the target molecule, RNA-IN, is complementary to the top endothelial cell mitogen with many crucial functions such as endothelial cells in response to the inflammatory mediators interleukin-1 ends of this RNA are uncertain. enhancer of repC. enhances the rate of shortening of the poly(A) tail. enterobacter. The CsrB RNAs contain a conserved motif Enterovirus genomes. The element has a cloverleaf like secondary structure entry site (IRES) which allows cap independent translation during environmental molecules. The Thermoanaerobacter tengcongensis EnvZ-OmpR two-component system to control the OmpF/OmpC protein ratio in Epstein-Barr nuclear antigen 1 (EBNA1) gene. The EBNA IRES allows EBNA1 Epstein-Barr virus mir-BHRF1-1 is found in the 5' UTR of the BHRF1 (Bam HI erythroleukemic transformation. Escherichia coli. Included several unknown homologues in essential coenzyme that is synthesised by coupling of pyrimidine essential for efficient replication. essential for establishing a viroid infection. essential for function. A similar structure, but with a different essential for functions that provide for efficient viral replication. estimated based on hairpin prediction.  The products are thought Eukaryotic and archaeal 7S RNAs have very similar secondary eukaryotic cap-dependent translation pathway. eukaryotic holoenzyme s have a much greater protein content than eukaryotic organisms.  This is probably due to vector eukaryotic RNAs. event targets the process of fast inactivation and allows a more evolutionarily related to RNase P.  Like eukaryotic RNase P, RNase example, ), but the alternative single hairpin in excised from the 3' arm of the hairpin. excised from the 5' arm of the hairpin. exclusively in Pseudomonas species. PrrF sequences are the functional exclusive to U3 snoRNAs, and boxes C' and D form the C'/D exons derived from separately transcribed RNAs. This mechanism of mRNA expensive for database searching, so models of the individual experimentally confirmed in a wide range of species experimentally confirmed in a wide range of species. The miRNAs Experiments provide evidence for at least two destabilising export and hence for expression of the HIV structural proteins. expressed and structurally characterised. expressed from a cluster also containing snoR16. The expressed the BAG-1 protein is known to enhance the anti-apoptotic expression by causing premature transcription termination within Expression of micF is controlled by both environmental and internal Expression of miR-101 has been validated in both human Expression of miR-194 has been verified in mouse (MI0000236 MI0000236], Expression of SraD is highly abundant in stationary phase, but expression of the dipeptide and oligopeptide transport systems in expression rapidly evolves into a pattern of seven stripes that extents are not known. In this case the mature sequence is extents of the hairpin precursors are not generally known and are Factors involved in the processing of the intronic snoRNA factors. It is thought that this family allows efficient Mnt synthesis family also contains a predicted homologue of mir-101 from family function in directing site-specific 2'-O-methylation of substrate family.  In addition to viral proteins p33 and the RNA-dependent RNA family includes riboswitches that sense lysine  in a number of family includes Schizosaccharomyces pombe snR61, Drosophila family includes the mouse H/ACA-box snoRNAs MBI-100 and MBI-114 family interacts with a downstream region to form a pseudoknot family is predicted to form ten stem loop structures some of which are Family members belong to the C/D class of snoRNAs which family therefore represents only a subset of known msr genes. family. U100 is predicted to guide the pseudouridylation of U2 family, which includes mir-20, mir-91, and mir-103. miRNAs FGF-1 IRES is present in the 5' UTR of the mRNA and allows cap-independent FIE3 for ftz instability element 3'). The FIE3 lies within a FinP encodes an antisense RNA product that is complementary flaviviruses have been shown to be lethal for infectious clones. flexneri and Escherichia coli. The function of this RNA is unknown. flexneri and Salmonella species. This RNA gene was discovered by an RNA flexneri and where it is found between the sseA and sseB genes. The flexneri, Yersinia pestis and Salmonella species where it is found between flu genes. The function of this RNA is unknown. fold into the Alu and S domains, separated by a long linker region. followed by nucleophilic attack on the 3' splice site by for 18S ribosomal RNA in plants. for effective repression, acting by binding to FinP and For example, the mRNA of ferritin (an iron storage protein) formation and motility in E. coli. CsrC antagonises the regulatory formation of of late RNAs. formation of the processing complex. The histone 3' UTR stem-loop form base pairs with the 3' UTR of its target mRNA gadX, this pairing is (formed from the P8, P3, P7 and P9 helices). form involves bases in the 3' segment of helix 1 with those in for Rev. for the Tat protein and this interaction stimulates the activity of the for translational regulation. for viral genome replication. The mechanism of found at the 3'-end of rotavirus mRNAs. The family is thought to promote found in an intron of the mfl gene in Drosophila. found in the 3' UTR of the BHRF1 (Bam HI fragment H rightward open reading found in the coding region of the RNA-dependent RNA polymerase found in the rnc leader sequence. The rnc operon is negatively found to overlap with the smaller snoRNA R19 which is currently a found upstream of many aminoacyl-tRNA synthetase genes and some fragment H rightward open reading frame 1) gene which is known to encode a frame 1) gene which is known to encode a distant Bcl-2 homologue. The frameshifting element. The element stimulates frameshifting which is frameshifting is more likely to occur which leads to an increase in the freeing the ribosome binding site and allowing expression to frequently in the 5'-untranslated regions of prokaryotic mRNAs from human, which may be a let-7 homologue. from the 3' arm of the precursor. The extents of the hairpin from the 5' arm of the hairpin. fructose-6-phosphate and glutamine to generate glucosamine-6-phosphate. functional protein requires +1 translational frameshifting. This frameshift function in directing site-specific 2'-O-methylation of substrate RNAs function in the plus-strand. function is unknown. function of msDNA, the mobility of retron elements, or their effect function of the Ro RNP is not known. In humans the RNA function of this RNA is unknown. functions of U3 snoRNA. fundamental functional importance: the anti-codon, which is Fur (Ferric uptake regulator). RyhB RNA levels are inversely G4593. The snoRNAs U44, U47, U74, U75, U76, U77, U79, U80 and G683. snoRNA HBII-108 is encoded in a nucleostemin (NS) gene (GAIT). The GAIT element is involved in selective translational gamma which are produced in a 1:1 ratio. The gamma protein is synthesised Gar1p and co-localises with coilin in Cajal bodies. U88 gene encodes a 106 nucleotide regulatory RNA. As with DsrA gene in humans and is also present in mice. U42 is a member of the C/D gene in mammals. This RNA has also been called Z23 snoRNA. gene is composed of six exons, whose spliced transcripts have little gene is located in intron 4 of the ribosomal L30 protein gene gene, NS5B. The structure is important (but not essential) for gene (pers obs. Bateman A). generally known and are estimated based on hairpin prediction. gene. Rev is an essential regulatory protein of HIV that binds genes in E. coli. This family is thought to be a regulator of OmpC genes involved in lysine metabolism, including lysC. genes involved in pyrimidine biosynthesis and transport. The genes involved in the cellular response to hypoxia. The HIF-1a genetic "off" switch for the ydaO and yuaA genes in its native genetic "off" switch in response to a cellular compound that genome. In a recent experimental screen for ncRNAs in A. fulgidus, this genome packaging during virus assembly. Dimerisation of the genomes. giving rise to a distinct mature sequence appears to be related global regulator to activate or repress the expression of as many glucose phosphate accumulation causes the degradation of ptsG mRNA. This, glycine degradation. Gram-positive bacteria. Group I catalytic introns are large self-splicing ribozymes. Group I catalytic introns often have long ORFs inserted Group II introns are found in rRNA, tRNA and mRNA of organelles groups IIA and IIB which differ in splice site consensus, growth arrest specific 5 (GAS5) transcript gene. snoRNAs Z20 GSL3 leads to decreases in both viral RNA packaging and dimerisation. guide 2'O-ribose methylation of large 28S rRNA subunit at guide 2'O-ribose methylation of small 18S rRNA at residue C1272. guide 2'O-ribose methylation of the small 18S rRNA at residue guided by the H/ACA snoRNA ACA48. guide for 18S ribosomal RNA in plants. guide RNA for sites on 18S and 25S rRNA. Rice snoZ199 is reported to guide snoRNAs. RNA residues targeted for pseudouridylation by guides the pseudouridylation of 28S rRNA subunit at position guide the pseudouridylation of position U40 in the U6 snRNA. guide the sites of modification of uridines to pseudouridines. snoM1 seems H/ACA-box motifs. U100 is the human orthologue of mouse H/ACA H/ACA-box motifs and is found associated with GAR1. ACA57 is hairpin. hairpin precursors are not generally known and are estimated based on hairpin precursor sequences represented here, in this case hairpin prediction. The products are thought to have regulatory roles Hammerhead ribozymes are found in plant viroids and other harmful to the organism. has been alternatively named snoZ269 in rice. has been shown to possess a methylated guanosine cap suggesting has been shown to regulate the production of virulence determinants, have also been identified in Pseudomonas and Coxiella species. have a regulatory role on the galactose operon. It is have been reported, a 5' T-shaped domain (TSD) followed by a have conserved H and ACA boxes, and may be pseudogenes. have since been discovered in several other species. The mature have since been predicted or experimentally confirmed in a wide HBII-52 is a member of the C/D class of snoRNAs, which contain the HBII-52 is encoded in a tandemly repeated array with another C/D heart, and skeletal muscle, tissues known to express Kv1.4 mRNA heat shock mRNAs and is known as the ROSE (repression of heat Hela cells. The doublet form U12-22/U4-8 has been shown to here) are predicted based on base pairing and cross-species here). Members of this precursor family have now been predicted or herpesvirus 4 (Epstein-Barr virus), cercopithicine herpesvirus 15 and herpesvirus 4 (Epstein-Barr virus). In Epstein-Barr virus mir-BHRF1-3 is herpesvirus papio. In Epstein-Barr virus mir-BHRF1-2 is found in the 3' UTR HgcC is of unknown function. Two other homologues were detected called hgcG is significantly similar to a region of the Archaeoglobus fulgidus HhcA and HhcB after "homologue of hgcC". hinge. Boxes B and C form the B/C motif, which appears to be homolog) gene. and is predicted to guide 2'O-ribose methylation homologous -- helices corresponding to P1, P2, P3, P4, and P10/11 homologous positions in mouse and chicken ribosomal protein genes. homologs have recently been identified in most bacterial genomes homologue of the eukaryotic SRP54 protein). Some Gram-positive homologues in mouse, Arabidopsis (annotated as snoR4) and in several homologues of the eukaryotic SRP19 and SRP54 proteins. In most Homo sapiens C/D box snoRNA HBII-108: This snoRNA is the human host gene but from different introns.  The rice homologue is however, there is another stem loop structure around 150nt (MIPF0000043 MIPF0000043]). The hairpin precursors (represented here) are (MIPF0000268 MIPF0000268], MIPF0000271 MIPF0000271]). miRNAs are transcribed as (MIPF0000303 MIPF0000303]). lin-4 was identified from a study of AC005219 AC005219]. RF00163 RF00163]), is found in RNA satellites of plant viruses. RF00283 RF00283]. The 3' C/D domain (U4-8) was also cloned previously human and mouse. human, Arabidopsis and rice. It is encoded in the intron of human (MI0000073 MI0000073], MI0000074 MI0000074], and MI000075 MI000075]) human (MI0000083 MI0000083], MI0000084 MI0000084], and MI0000750 MI0000750]). human MEG8 RNA, which lies downstream of the imprinted genes DLK1 Human mir-34a was discovered computationally and later experimentally human, mouse and Fugu and cloned in Fugu, and later predicted human). Nevertheless, secondary structure predictions suggest human). Nevertheless, secondary structure predictions suggest human orthologue of the mouse MBII-135 snoRNA and is predicted to human orthologue of the mouse MBII-166 and is predicted to guide human orthologue of the mouse MBII-239 described and is predicted human orthologue of the mouse MBII-240 and is predicted to guide human orthologue of the mouse MBII-289 and has no identified RNA humans. U34 is a member of the C/D class of snoRNA which contain C human (Z96734), Arabidopsis (AB003142), Xenopus (X91243) and S. hyperthermophiles. The genes were named hgcA through hgcG ("high GC"). hyperthermophiles using QRNA. SscA stands for Secondary identified by other groups and called QUAD RNAs. identified C/D box snoRNAs in their expression profiles and lack identified in. Both MBI-100 and MBI-114 are predicted to identified in a large scale screen of E. coli, were they were identified in only 3 plant satellite RNAs -- from TRSV, identified in several species of enteric bacteria but homologs identified in the nematode Caenorhabditis elegans identified in Xenopus. U22 is thought to as a 2'-O-ribose III are linked by a sequence CGAAA. The cleavage reaction III are linked by a sequence CGAAA. The cleavage reaction II leading to transcript degradation and a reduction in II, the proximal region of III, and IV. II, the proximal region of III, and IV. II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12. ACA47 (IL-1) and tumour necrosis factor alpha and by activated macrophages. The illustrations. There are currently several Archaeal sequences in important for Sm protein binding and cap methylation. in a new, highly conserved RNA secondary structure, the THI in archaea, bacteria and eukarya as well as chloroplasts and in C. elegans from related hairpin precursor sequences. The in C. elegans (MI0000050 MI0000050]) and worm (MI0000374 MI0000374]). The included at the 3' end. included in this family. The hairpin ribozyme has been includes rice snoRNA Z163 and Z177. Most of the members of the including atherosclerosis, carotid restenosis after endarterectomy, and increased mRNA stability. These two activities form the basis of increased translational efficiency during the heat shock increase the translation of IFN-gamma. independently named MBII-98 in mouse. independently transcribed by RNA pol II. indication the the gene is in an operon. in directing site-specific 2'-O-methylation of substrate RNAs. indirectly activated by CsrA via the response regulator UvrY. in Drosophila 28S rRNA. induced under iron limitation by the ferric uptake regulator (Fur) and induces hypertension and REN therefore requires tight control to ensure In each case the leader also codes for very short peptide in embryogenesis and in the adult brain. in encapsidation of the retroviral RNA an essential step in fungi, plants and protists, and also in mRNA in bacteria. in Gram-positive bacteria. The SAM riboswitch acts at the level inhibition. in human, and is hypothesised to guide methylation of 2'-O-ribose in human, mouse and chicken. initiated by RNAII, which acts as a primer by binding to its initiates a nucleophilic attack at the intronic 5' splice site, initiation of (-) strand RNA synthesis. in length. The C0343 RNA gene is present in E. coli, Shigella flexneri and in length. The tke1 RNA gene is present in Escherichia coli, Shigella In Listeria monocytogenes, virulence genes are maximally expressed in loop regions. The window size for this search is chosen to In other bacteria such as Erwinia caratovara the RsmA protein in other bacteria. The function of this family is unclear in other bacteria. The ydaO/yuaA element is thought to act as a in other snoRNAs. in plants, and within the U22 snoRNA host gene (UHG) in mammals in prion protein translation. in Pseudomonas fluorescens F113 resulted in a significant in regulating translation. in replication. It is found in HIV, SIV and CIV. in RNA 1 of alfalfa mosaic virus. RNA 1 is responsible for encoding the in sequence. In several groups of bacterial plasmids, antisense RNAs regulate instead. Hence this family are termed purine riboswitches. interactions, although these regions do not seem to be well conserved interactions, and intronic ORF phylogeny. interaction with its target messages. interference. interference. miRNAs are numbered based on the mature sequence. interference. This family also includes the miR-98 precursor internal ribosome entry site. HIF-1a is a subunit of the HIF-1 internal ribosome entry site (IRES) present in the vCyclin gene. The internal ribosome entry site (IRES). This region has been shown interrupted by several unpaired residues or bulged loops. In plasmid interspersed element (SINE) share a conserved 3' tail containing a in the 5' UTR of HCV RNA. HCV IRES adopts a complex structure, and in the nucleolus. In humans the genomic location of intron 3 of the L21 ribosomal protein gene. The H/ACA box snoRNA intron-exon interactions are important for splice site intron like the HBII-210 intron of rpL7a, and has two regions of complementarity intron of the Suppressor of SWI4 1 homolog (Ssf-1) (Peter Pan introns of the cardiotoxin 4 and cobrotoxin genes of the Taiwan in turn limits the uptake of glucose which in high concentrations can be in two parts. tmRNAs have been identified in eubacteria and some in U12 (RF00007 RF00007]) and residue C8 in U4 (RF00015 RF00015]) snRNAs in U2 snRNA. involve a conformational switch in the pseudoknot region and involved in changing the cellular response in relation to amino acid involved in directing the efficient production and orientation-dependent (involved in pre-mRNA splicing). Its 5' end forms complementary involved in ribosome translocation. It is also known to form involved in translational regulation and the pseudoknot has been found to involvement of Dicer in miRNA processing suggests a relationship involves the U7 snRNP, which contains only one RNA species: U7. In Xenopus oocytes, it has been shown that fingers 4-7 of the IRES allows translation to be maintained under hypoxic cell IRES elements allow cap and end-independent translation of mRNA in the host (IRES). IRES elements allow cap and end-independent translation of mRNA in IRES is necessary for the regulation of latent gene expression. IRES-mediated translation. IRES-mediated translation of APC is important for an apoptotic (IRES) which is found in the U leader exon in the 5' UTR of the (IRES) which is present in the 5' leader sequence of the iron homeostasis in the vertebrate cell. iron-using proteins when iron is limiting; it is itself IRPs bind the ferritin mRNA IRE leading to translation is able to specifically bind to the first stem loop. CAL binding is thought is also involved in nucleocytoplasmic transport of the mRNA, and in is a member of the box C/D class. Indeed, the box C/D element is is around 500-800 nts in length. is bound by a 31 kDa stem-loop binding protein (SLBP - also termed is composed of two tandemly arranged box H/ACA RNA motifs and is directed by an in-frame UGA codon (usually a stop codon) is essential for antisilencing and less critical for RpoS translation. is essential for viral replication and is thought to be required at an is excised from the 5' arm of the hairpin. is expressed mainly in the brain, but is also in the lungs, the is found in the intronic regions of the BART (Bam HI-A region rightward is found upstream of the first gene in the operon. This is hosted, together with HBII-95, by the core C/D box snoRNA is initiated by a different mechanism from the usual 5' cap-binding is initiated by the covalent attachment of UMP to the terminal is known to direct specific packaging of HIV-1 genomic RNA. Deletion of is known to encode a distant Bcl-2 homologue. The mature sequence is is know to be essential for stable dimerisation and efficient is of unknown function. This RNA is currently restricted to isoleucine/valine recoding event which lies in the ion-conducting is packaged into the pre-formed viral procapsid. The packaging is required for the distinction of UGA stop from UGA is stimulated by a pseudoknot present 3' of the frameshift site in the is the fastest known naturally occurring self-cleaving RNA. is thought to be regulated by temperature. This regulation blocks is thought to form extensive base-pair interactions with U4 is thought to induce premature transcription termination within is used as the primary template for the in vitro uridylylation it from its initiation role. The rate of degradation of RNAI is It has been shown that SL1 may provide a secondary binding site It has been suggested that proteins may only bind to a specific structure it is independently transcribed by RNA pol II. It is thought that at 37 degrees C the SD sequence is unmasked. it is thought to function as a 2'-O-ribose methylation guide its function was unknown until recently. It consists of 184 It was first identified in the minus strand of the tobacco J26 is a member of the C/D class of snoRNA which contain the C (UGAUGA) Japanese encephalitis and related viruses. This element is significantly join. This family are the type I hammerheads. join. This family are the type III hammerheads. kb at 13q14. This region has been shown to be deleted in more kidneys and muscle. HBII-13 snoRNA has no identified RNA target known and are estimated based on hairpin prediction. The known as the terminator and the anti-terminator structure. known to be required for transposition. known to negatively regulate prgQ transcription via an antisense mechanism L13A and intron 3 of ribosomal protein S11 in humans and at L13a gene in humans and is also present in mice. Most of the laminin-binding protein. This family also contains the related ACA6, large number of closely related sequences that do not appear to large number of closely related sequences that do not appear to large, paternally expressed, transcription unit large single-stranded internal bulge. 6S RNA specifically leader from a SL RNA is a intra-molecular reaction which precisely joins leader sequence can assume two different secondary structures least two CP binding sites which are thought to be essential for efficient length of these introns can therefore be up to 3kb. lengths in a self cleavage reaction. The ribozyme is found length. Their secondary structure includes four short length. The IS128 RNA gene is present in Escherichia coli and Shigella length. The ryfA RNA gene is present in E. coli, Shigella flexneri and length which are found between the tar and cheW genes in E. coli and length, which are found between the yghK and glcB genes in both Shigella lethal. levels could be detected in exponentially growing cells as well. levels could be detected in exponentially growing cells as well. lies between yegQ and orgK in E. coli. This small RNA was shown lipopolysaccharide. It is likely that the presence of the SLDE in the G-CSF localisation to the perinuclear region of the cytoplasm, localise to the nucleoplasm and is proposed to reside in the located in the 5'-terminal 112 nucleotides of the genome of human located in the 5' UTR and is required for specific RNA encapsidation. located in the 5' UTR of apoB mRNA. The element is important for optimal location of U12-88/U4-8 is intergenic and the purified transcript locus was identified as the second-most abundant transcript (Afu-4) longer SRP RNAs is not included in this model and therefore the long range intron-intron and long terminal repeat promoter. loops). Further hydrogen bonds mediate the characteristic loops L3 and L4 that interact with the RNA target. loop terminator region. An alternative and mutually exclusive lower eukaryotes. Trans-splicing is a form of RNA processing. The low levels could be detected in exponentially growing cells as L-shaped molecular structure. tRNAs have two regions of lymphocytic leukaemias (CLL).  The hairpin precursors M1 is a member of the H/ACA class of snoRNAs which are thought to M2 and MBI-136 snoRNAs. mammalian c-myc gene is a proto-oncogene which is required for cell mammals. Many sequences below the threshold for this family are clearly many Staphylococcus aureus genes encoding exoproteins and cell wall Mason-Pfizer monkey virus (MPMV) packaging signal. The packaging signal is maturation has been shown to occur in a number of lower eukaryotes and is mature ~21nt miRNAs are processed from hairpin precursor sequences mature RNA. mature sequence comes from the 5' arm of the precursor. The extents of the mature sequence is excised from the 5' arm of the hairpin. mature sequences are expressed from the 3' arms of the hairpin may differ significantly from IRES elements identified in may serve as CsrA binding elements. Transcription of csrC increases MBI-161 belongs to the H/ACA class of snoRNAs which are thought to guide MBI-1 belongs to the H/ACA class of snoRNAs which are thought to guide the MBI-28 is a member of the H/ACA class of snoRNAs which are thought to guide MBI-57 identified in. MBI-87 is thought to belong to the H/ACA class of snoRNAs which guide the MBII-202 is a member of the C/D class of snoRNA which contain the C Me28S-Um3344 is a member of the C/D class of snoRNA which contain the C mediated by a translation control element (TCE) in the 3' UTR of mediate splicing. mediterranea, several arthropod species and a wide range of melanogaster Z1 and Saccharomyces cerevisiae snR61 and Z11 members of the box C/D family function in directing site-specific members of the C/D class of snoRNA containing the C (UGAUGA) Members of this family belong to the C/D box class of small metabolite preQ1, an intermediate in the biosynthesis of the methenyltetrahydrofolate synthetase. method of translation via internal ribosome entry where ribosomes are methylation guide and is found in an intron of ribosomal methylation guide and is found in intron 11 of the gas5 methylation guide for 18S and 25S ribosomal RNA in plants. methylation guide for 18S ribosomal RNA in plants. snoR66 methylation guide for 25S ribosomal RNA in Arabidopsis. methylation guide for 25S ribosomal RNA in plants. methylation guide for 5.8S ribosomal RNA. This family contains a methylation guide for ribosomal RNA. methylation guides but lack complementarity to ribosomal RNA. methyltransferase activity is supposed to reside in one of the protein Met-tRNA, several initiation factors, and GTP with the 40S ribosomal MicC (previously known as IS063 ) is located between the ompN and ydbK mid-70s but a possible function has only recently been suggested minimal RNA element, predicted to form a stable secondary minimise search time and catch the small examples. A larger minimise this problem, but many annotated pseudogenes remain. minor domains. A model representing the whole RNA is prohibitively minus-strand synthesis when the 3' side of the LSL pairs with the miR-124 has been identified in Drosophila (MI0000373 MI0000373]), C. mir-129 was first experimentally characterised in mouse and homologues miR-130 has been identified in mouse (MI0000156 MI0000156], mir-133 was first experimentally characterised in mouse and homologues miR-135 has been shown to be expressed in human (MI0000452 MI0000452], mir-13 (MIPF0000049 MIPF0000049]). mir-2 has now been predicted or mir-141 (MI0000166 MI0000166], MI0000457 MI0000457]), mir-429 (MI0001642 MI0001642]) mir-156. This miRNA has now been predicted or experimentally miR-15a and miR-16 are deleted or down-regulated in more than two miR-160 has been predicted or experimentally confirmed in a range mir-166. This miRNA has now been predicted or experimentally miR-16, miR-15, mir-195 and miR-457 are related miRNA precursor mir-172 has been experimentally verified in Arabidopsis thaliana. miR-196 has been shown to be expressed in human (MI0000238 MI0000238], miR-19 is processed from multiple predicted precursor hairpins in mir-206 from human, which appears to be related to mir-1. mir-215. Animal miRNAs are transcribed as ~70nt precursors and subsequently miR-218 appears to be a vertebrate specific microRNA and has now miR-219 was predicted in vertebrates by conservation between miR-26 appears to be a vertebrate specific miRNA and has now been miR-26 is processed from multiple predicted precursor hairpins in mir-395 was identified in both Arabidopsis thaliana and Oryza sativa mir-399 was identified in both Arabidopsis thaliana and Oryza sativa miR-46 (MI0000017 MI0000017]) and miR-47 (MI0000018 MI0000018]) are expressed miR-8 from Drosophila (MI0000128 MI0000128]) and human and mouse mir-92-2 on chromosome X. miR-92 has also been cloned from mouse embryonic (mir-97-6)  arms of the precursor. The extents of the hairpin precursors mir-98. let-7 was identified from a study of developmental mir-99 and mir-100 have now been predicted or experimentally miR-9 has been identified in Drosophila (MI0000129 MI0000129]), mouse mir-BART1 is found in all stages of infection but expression is mir-BART2 is expressed in all stages of infection but expression is miRNA has been predicted or experimentally confirmed in a wide miRNA precursors which give rise to almost identical mature miRNAs are numbered based on the sequence of the mature RNA. miRNAs are transcribed as ~70nt precursors (modelled here) and miRNAs let-7 and mir-98 have now been predicted or experimentally mitochondria. Its best characterised activity is the generation model. This alternate mechanism relies on the direct binding of (modelled by this family) and a purine rich region around 20 nts modification of rRNA in the nucleolus. There are two main classes modification of uridines to pseudouridines. modified nucleoside queuosine from GTP. One example of this Moloney murine leukaemia virus (MMLV) core encapsidation signal Most of the members of the box C/D family function in directing motifs. Most of the members of the box C/D family function in motifs. This family includes Arabidopsis thaliana snoRNA R64 and motifs. This family includes plant snoRNA Z195 and human snoRNA motifs. This family is predicted to target two neighbouring motifs. This family seems to be found exclusively in plants. C/D box small motif. The latter is functionally similar to the C/D motifs found motion. In some bacteriophage, an RNA (pRNA) molecule is a vital motor have demonstrated that the pRNA molecule has fivefold symmetry mouse and cow. U38 guides the methylation of 2'-O-ribose mRNA and is known to promote frameshifting. Antizyme genes have have two mRNA contains two IRES elements which are able to promote mRNA contributes to the specificity of regulation of G-CSF mRNA and mRNA from a stalled ribosome. To accomplish this part of the mRNA. Further deletion constructs identified an essential mRNA produces 4 ribosomal protein products, one of which (S4) mRNA, promoting degradation of the sequence. It has been found that a mRNA. This family allows cap-independent translation of the mRNA and it is mRNA. TrkB is a neurotrophin receptor which is essential for the MRP is not catalytically active without associated protein subunits. much larger class of non-coding RNAs termed miRNAs. Both much longer (568 nucleotides as compared to 164 nucleotides in much longer (568 nucleotides as compared to 164 nucleotides in (multi-copy single-stranded DNA). msDNA has both DNA (encoded by mutants and is itself regulated by the GacS-GacA two-component myc family of genes when expressed are known to be involved in the control myc family of genes when expressed are known to be involved in the control myocardial infarction. Translational silencing of Cp, and needed for efficient translation in neuronal dendrites. negatively regulated by the ferric uptake repressor protein, negative regulation of antirepressor synthesis during development nine-zinc finger transcription factor TFIIIA can bind to the non-translated 93 nt antisense RNA that binds its target ompF mRNA not confirmed. Co-precipitation of U19 snoRNA with RNase MRP RNA novel class of small nuclear RNAs which localise to the Cajal now been predicted or confirmed in a wide range of vertebrate Nuclear cleavage occurs in the single strand region linking these nucleolar localisation, stability and hyper-methylation of nucleolar RNAs are known to act as a methylation guides for 18S ribosomal nucleolar RNA which contain C (UGAUGA) and D (CUGA) box nucleotide requires the antisense element and the conserved box D or D' of nucleotide requires the antisense element and the conserved box D or D' of nucleotides, longer than most snoRNAs. It is one of the most nucleotides that fold into an extended hairpin structure with a number B) gene product, which polyadenylates the 3' end of RNAI number of annotated pseudogenes and the model is expected to number of hits to such regions, it is likely that some remain. number of proteins bind to the REN-SRE to stabilise the mRNA and promote obs.). occur. occurs between helix III and I, and is usually a C. occurs between helix III and I, and is usually a C. occurs frequently in rubella infections in adults and is independent of occurs in some archaea. Analysis of operon structures identified of a pseudoknot structure in this RNA, it does not appear to be of bacteriophage P22. of cell growth, differentiation and apoptosis. L-myc undergoes translation of cell growth, differentiation and apoptosis. n-myc mRNA has an of complementarity to rRNA and snRNA. Homologues of these of conserved complementarity to serotonin 2C receptor mRNA. of Dicer in miRNA processing suggests a relationship with the of DNA into the procapsid requires a molecular motor which of elongation factor 1 beta in yeast. Related snoRNAs in of mature 5'-ends of tRNAs by cleaving the 5'-leader elements of of mature large subunit ribosomal RNAs, 5.8S and 28S rRNAs. U8 of mRNA degradation in E. coli that is able to auto-regulate the of mRNA stability. In unstimulated cells G-CSF mRNA is unstable but of p27 mRNA. This element contributes to cell-cycle regulated translation of plant species including Arabidopsis and rice of pre-rRNA within the 5' external transcribed spacer (ETS). This of proteins (including dyskerin, Gar1p and Nop10p in the case of repC causing translational repression. of residue U799 of the small 18S rRNA subunit. of ribosomal protein L1 in Xenopus and human, and in introns of ribosomal RNA. of riboswitches that selectively recognises guanine and becomes of RNA interference. miRNAs are numbered based on the sequence of the of RNA interference. miRNAs are numbered based on the sequence of the of RNase E mRNA. RNase E is a key regulatory enzyme in the pathway of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA of snoRNA which contain the C (UGAUGA) and D (CUGA) box of SRP components, with phylogenetic data and structural of substrate RNAs.  This family does not appear to have the often are autocatalytic. Structurally it is composed of often are autocatalytic. Structurally it is composed of of the BHRF1 (Bam HI fragment H rightward open reading frame 1) gene which of the B. subtilis ykoK gene and genes with related functions in of the dnaX gene are DNA polymerase III subunits. of the dnaX gene in E. coli. The dnaX gene has two encoded products tau and of the H/ACA class) to form snoRNP complexes. This class are of the hairpin. of the loop, and complementarity extends for 35 base-pairs down of the members of the box C/D family function in directing of the nucleolin gene in human, mouse and rat. of the outer membrane porin gene ompF. The micF gene encodes a of the precursor.  The extents of the hairpin precursors are not of the residue U3797 in the 28S rRNA subunit. Its host gene of the ribosomal protein L3 gene in human and cow.  Three of the target nucleotide requires the antisense element and the conserved of the the H/ACA class of snoRNA that guide the sites of modification of of the ydaO and yuaA genes in Bacillus subtilis and related genes of the ykkC and yxkD genes in Bacillus subtilis and related genes of this motif forms a hairpin. The Shine-Dalgarno (SD) sequence is of three hairpins, The other includes a pseudoknot. of three stem-loops of the 85 nucleotide RNA is necessary for RpoS of transcription termination control. The predicted structure of various mRNAs whose products are involved in iron metabolism. of vector contamination. of vertebrate species (MIPF0000026 MIPF0000026]). The extents of the hairpin of vitamin B(12)-related genes in bacteria. Cobalamin in the form of one of the protein components. one side of RNA-OUT. one-third of the mRNA and the other near the 3' end (termed only the final two hairpins which are conserved in only this conserved core. on the host cell. operon. The terminator structure is recognised as a termination originating from the 3' arm. The bounds of the precursors are or repeats.  This family has a high significance threshold to ortholog of mouse snoRNA HBII-99 and human snoRNA U106. In humans orthologue of the mouse MBII-108 and is predicted to guide orthologue of Xenopus laevis U86 and has no identified RNA Oryza sativa snoRNAs Z200 and J16. Most of the members of the box osmotic shock leading to activation of ydaO, a predicted amino other bacteria.  The regulatory role of this RNA element is other snoRNAs ( U82, U83a and U83b) are also encoded in the same other species, and also includes the complete overlaps RF00101 RF00101] on the opposite strand suggesting that overlaps RF00111 RF00111] on the opposite strand suggesting that over most of the embryo. Subsequently, fushi tarazu mRNA over-represented upon host cell infection and it has been suggested that oxidative stress in Escherichia coli. This novel RNA acts as a OxyS, DsrA, RprA and Spot 42 RNA regulation. OxyS is a small untranslated RNA which is induced in response to OxyS is bound by the Hfq protein, that increases the OxyS RNA packaging although this may not be its only role. packaging and is vital for viral replication. Viral RNA containing a packaging signal allows the sequence to be efficiently packaged into the (packaging) signal which is essential for efficient viral replication. parechovirus 1 (HPeV1). The family consists of two stem-loop structures partially overlapping open reading frames, the second, which encodes the partly masked by the most conserved stem of the secondary structure. part of a much larger class of non-coding RNAs termed miRNAs. (PBSs). tRNA(3)(Lys) binds to the PBS to initiate reverse transcription pers. obs.). This family also includes human snoRNAs U96a and Pfam:PF00262 (CAL) which is known to bind calcium in most eukaryotic cells, Pfam:PF00860 (Moxon SJ, pers. obs.). phase, but low levels could be detected in exponentially growing phenomenon of RNA interference. miRNAs are numbered based on picornaviruses.  A small number of eukaryotic mRNA have been shown (PIE).  PIE is a regulatory RNA which is responsible for the pivotal role in cell proliferation, differentiation and survival as well as plants. plasmids, including ColE1.  Plasmid replication is usually Please note:  This family contains subsequences annotated as polyadenylation. polyamines in the cell, when the polyamine concentration is high polyamines present in the cell. Therefore, this family can be thought of as polycistronic transcription units and the presence of SL2 on an mRNA is an polymerase holoenzyme containing the housekeeping sigma factor polymerase I as part of the 45S precursor that also contains 18S polymerase NS5B. Mutations in this family have been found to cause a polymerase p92, and unknown host factors, RNA signals within the UTRs polymerase p92, and unknown host factors, RNA signals within the UTRs pombe (L25927, L25928), which match with highly significant poorly conserved in sequence between different organisms -- this pore of the potassium channel. It is thought that this editing position A1521. The C/D snoRNAs U44, U47, U74, U75, U76, U78, positioned at the single-stranded regions at the ends of the positioning. Group II introns are further sub-classified into positive strand RNA synthesis. possess a stem-loop region (known as the Y-domain) which is possibly at sites of intermediate filament assembly. possibly other transcripts, mediated by the GAIT element may contribute to post-transcriptionally regulates central carbon flux, biofilm potassium channel Kv1.1 hairpin element which directs the potential for coding a protein, and its introns produce both U50 and poxvirus late mRNAs and is known as the AX element.The AX element is precise function of this molecule is unknown, though it is known precursor, and miR-79 from the 3' arm. The bounds of the precursors precursors. precursors and subsequently processed by the Dicer enzyme to give a ~22nt precursors are not generally known and are estimated based on precursors are not known. In this case the mature sequence in precursor sequence are related to those of mir-152, which has precursors in a wide range of organisms. The core secondary precursor. The extents of the hairpin precursors are not generally known precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. predicted based on base pairing and cross-species conservation -- predicted based on conservation and base pairing and are not predicted hairpin-hinge-hairpin-tail structure and the conserved predicted hairpin precursor sequences for Drosophila miR-281 predicted hairpin precursor sequences: mir-92-1 on chromosome 13 and predicted in chicken (MI0001189 MI0001189]). These predicted hairpin predicted or experimentally validated in many vertebrate species predicted secondary structure of U12 RNA is published (see for predicted to guide pseudouridylation of the 28S rRNA at positions predicted to guide pseudouridylation of the U2 spliceosomal snRNA predicted to guide the 2'O-ribose methylation of 28S rRNA G3878 predicted to guide the pseudouridylation of the U5 spliceosomal prediction. The products are thought to have predict U106 methylates residues G1536 and U1602 of 18S pre-initiation complex directly to the initiation codon and eliminates the pre-mRNA. The PIE is located in the U1A mRNA 3' UTR. PIE adopts a present in multiple copies per cell. The anti-sense RNA (RNA-OUT) prevalently in the brain (but is absent in PWS patients) and lacks PrfA, a transcriptional activator whose expression is primarily localised in the loops of predicted hairpins, which primer binding site (PBS). This region is known to be required for the pRNA is proposed to be comprised of two domains, one corresponding to probably crucial for attaining this localised pattern of probably involved in regulation is included at the 3' end. processed by the Dicer enzyme to give a ~22nt product. In plants processing. In this case the mature sequence comes from the 3' processing occurs at a site between a highly conserved stem-loop processing of eukaryotic pre-rRNA and has regions of complementarity processing suggests a relationship with the phenomenon of RNA interference. processing suggests a relationship with the phenomenon of RNA interference. process involving protein Prp24 re-anneals U4 and U6. product. In plants the precursor sequences may be longer, and product. In this case the mature sequence comes from the 3' arm product. In this case the mature sequence comes from the 3' arm of the products are thought to have regulatory roles through product. The extents of the hairpin precursors are not generally proliferation, transformation and death. c-myc mRNA has an alternative promoter and for virus replication. The TAR hairpin acts as a binding site promoter, pY. The FinO protein is essential for effective properties of Bcl-2. Although bag-1 translation usually occurs via a proposed that Spot 42 acts by an antisense mechanism where protecting it from RNase E degradation. protein components. protein. ctRNA binds to the mRNA of repB and causes translational protein encoding gene NOP5/NOP58. protein expression has been found to be significantly enhanced by the heat protein interactions and are necessary for the rRNA processing Protein machinery is required for splicing in vivo, and protein mRNA. It has been suggested that the family has a possible effect (protein non-coding). protein Pfam:PF02599. Although CsrA proteins are found in protein RPL17 gene in humans. U58 is a member of the C/D class of protein RsmA. RsmY and RsmZ RNAs bind RsmA to relieve this repression protein. RydC is known to bind the protein Hfq which causes a proteins L1 gene in animals. This snoRNA was proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide Protein translation of most eukaryotic mRNAs requires association of protein Virp1. The exact function of this motif and the significance of protein VPg, yielding VPgpU and VPgpUpU. A small RNA hairpin in proteobacteria, 6S RNA may be processed from a transcript (Pr). Pr is located in the 3' UTR and is required for minus strand RNA PrrB RNA is able to phenotypically complement gacS and gacA PrrF RNA is a small RNA involved in iron homeostasis and is found pseudogenes. pseudoknot formation is known to stimulate frameshifting. In the pseudoknot region. The mechanism of repression is thought to Pseudoknots have also been predicted in this structure. pseudouridine in Drosophila 18S rRNA. pseudouridine in Drosophila 28S rRNA. pseudouridines by forming direct base pairing interactions with pseudouridines in substrate RNAs however, no target RNA has pseudouridylation of the U2 spliceosomal snRNA. pseudouridylation site. psi18S-1377 is a member of the H/ACA class of snoRNA. This family is P-TEFb activates transcription by phosphorylating the C-terminal purified from Hela cells. The doublet form U12-22/U4-8 has purine transport and purine nucleotide biosynthesis. It has also been putative snoRNA found in the intron of the receptor for activated pyrococcal species. Qa RNA is a cis-regulatory element from Enterococcus faecalis which is quantity of functional antizyme produced. The functional antizyme acts to queuosine production. PreQ1 binding to the riboswitch aptamer R1, the inhibitory complex between the antisense RNA (CopA) and its R28 is a member of the C/D class of snoRNA which contain the C (UGAUGA) R43 is a member of the C/D class of snoRNA which contain the C (UGAUGA) R44, J54 and Z268 are members of the C/D class of snoRNA which contain the R71 is a member of the C/D box family of snoRNAs containing the R79 is a member of the C/D class of snoRNA which contain the C (UGAUGA) range of species (MIPF0000022 MIPF0000022]). miRNAs are transcribed as range of species which include the platyhelminth Schmidtea rapidly dividing cells during development. rapid recovery from inactivation at negative potentials. rate-limiting step in the production of angiotensin II. Angiotensin II reaction which precisely joins exons derived from separately transcribed rearrangement of mRNA structure is mediated by ligand binding, and this Recently a number of permuted tmRNA genes have been found encoded recognition of hairy mRNA by the localisation machinery. Recognition Particle Database (SRPDB) provides compilations recruited to the IRES located in the 5' UTR thus bypassing the typical reduce ornithine decarboxylase (ODC) activity which leads to a drop in reduction of 2, 4-diacetylphloroglucinol (Phl) and hydrogen region between 5S-rRNA genes where it is involved in trans-splicing. region of complementarity to a conserved sequence in 28S regions of complementarity to 5S ribosomal RNA and are predicted region that forms the alternate structures. regulated by a 75 base RNA that is complementary to a segment of regulated by the 7SK RNP. The secondary structure of 7SK RNA regulate gene expression through a variety of mechanisms in regulate the level of translation. regulating 5S rRNA transcription, TFIIIA also stabilises 5S rRNA regulation as a riboswitch. regulation. Members of this family are known to bind to the mRNA regulation of RpoS translation. RprA also appears to bind to the regulation of the length of the polyA tail of the U1A regulator of heat shock gene expression. The secondary structure regulatory amino acid and ribosome movement over the leader regulatory mechanism, which involves direct binding of Ado-CBL to regulatory RNAs in E. coli, and the protein is required for regulatory roles through complementarity to mRNA. The involvement related families of protein genes in many bacteria, including the the yybP related plasmids. The S-element has multiple functions and is relationship with the phenomenon of RNA interference. miRNAs are numbered remained obscure, even though the 109-nucleotide RNA was Renin is secreted by renal juxtaglomerular cells and catalyses renin (REN) gene called renin stability regulatory element (REN-SRE) which replication. replication. replication. The full alignment of this family contains a number of reported bounds of some members are incorrect. The Signal reported to be an independent risk factor for cardiovascular disease, (represented here) are predicted based on base pairing and represented here by a single family. These snoRNAs are intron represented here. miR-9 is processed from the 5' arm of its represents IRES A. represents only domains V and VI. A subset of group II introns represents the conserved core. repress ctgf gene expression. Reference identified a repression. repression, acting by binding to FinP and protecting it from repression. Binding of multiple IREs in the 3' and 5' UTRs of repR-mRNA. RNAIII is composed of four stem loops with required for efficient replication and act as a translational required for minus strand RNA accumulation and is therefore essential for required for the initiation of negative strand RNA synthesis. required for viral replication. required ratio of Gag and Gag-Pol polyproteins. The stem-loop requirement for eIF4F. reside in one of the protein components. reside in the Cajal bodies whereas the U4-8 single domain appears residues in 28S rRNA. Mouse MBII-329 snoRNA is homologous to U38. residues on 28S ribosomal RNA. residue U41 of the U5 snRNA. This family also includes human resistance. respectively. This family only includes only the 5' C/D box respectively in the HGNC approved gene symbol nomenclature. The response and translation of the hsp90 mRNA is very inefficient response. The exact mechanism of action unknown. response to a variety of environmental stimuli. responsible for guiding the modification of uridine 1192 to pseudouridine responsible for guiding the modification of uridine 3327 in Drosophila 28S responsible for guiding the modification of uridine 841 in Drosophila 18S responsible for guiding the modification of uridines 1377 and 1279 to responsible for specific mRNA codon recognition, and the 3' end, responsible for the production of a small satellite DNA called msDNA results in modulation of gene expression. This family represents a retardation function of the SRP. retention of U3 snoRNA. The box C'/D motif is also necessary for Retron elements are found in a wide range of mainly Gram-negative retrovirus) core encapsidation signal and related sequences. The rhinoviruses. The CRE is located within the genome segment encoding the Rho-independent transcription terminator structure that is Rian, and in the rat non-coding Bsr (brain-specific repetitive) Ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found ribonucleoprotein complex. The complex consists of a major ribonucleoprotein involved in the co-translational targeting of ribonucleoprotein. It is involved in the co-translational targeting of ribosomal protein L13 gene in human and mouse, and is hypothesised ribosomal RNA. This RNA has also been named snoRNA R73 in some ribosomal RNA.  U73 is therefore thought to function as a ribosome and cause slippage in the 5' direction, this causes the ribosome entrapment. ribosome entry site (IRES). When expressed the FGF-2 protein plays a ribosome entry site (IRES) which is found in the 5' UTR of IGF-II leader 2 ribosomes are recruited to the IRES located in the 5' UTR thus bypassing Riboswitches are metabolite binding domains within certain messenger RNAs riboswitches usually consist of two metabolite-binding aptamers riboswitch is located in the leader of the Bacillus subtilis riboswitch that directly binds FMN in the absence of proteins. In ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not ribozymes have been found in animals as well as plants. ribulose-1,5-bisphosphate carboxylase. Mutations in this family can lead to rice. C/D box small nucleolar RNAs are known to act as a methylation guides rice. The 18S methylation site is reported to be homologous ringspot virus (TRSV) satellite RNA where it catalyses a RNA and is likely to direct its 2'-O-methylation. RNA are complementary to rRNA and act as guides for RNA/RNA RNA at position U43. RNA chaperone protein StpA also play a role in this regulatory system. RNA from bacterial RNase Ps retains its catalytic RNA genes which are 208 bases in length and are found between the yeeP and RNA genes which are 78 bases in length and are found between the hlyE and RNA has been identified in human, mouse, rat and Xenopus. RNAIII acts by transcriptional attenuation of the essential RNAI is an antisense repressor of the replication of some E. coli RNA in plants. RNA is the synthesis of a complementary minus strand. This process RNA known to be required for viability of a human pathogen. RNA, occluding the translation initiation site. Clones carrying rprA RNAs. This family possesses sequence complementarity to U6 spliceosomal RNAs. Approximately 25% of C. elegans genes are organised into RNAs. Although the selection of the target nucleotide requires RNAs and Ro60 and La proteins are well conserved, but the RNAs as well as the Trypanosoma spliced leader RNA (SL RNA) RNAs but the exact function of many snoRNAs, including U71, is RNAs but the exact functions of many snoRNAs, including U19, are RNase E concentration enabling tight regulation of RNase E RNase E degradation. RNase MRP is an enzymatically active ribonucleoprotein with two RNAs) from p42d and related plasmids. ctRNAs are small, highly RNAs have a 3' H/ACA snoRNA-like domain. This family also contains viral RNAs that serve as precision sensors for their corresponding targets. RNAs. These RNAs have an endonuclease function, and most RNA structure includes an intrinsic transcription terminator at RNA synthesis in in the alfalfa mosaic virus and may also be involved in RNA translation. RNA were found. The function of this RNA is unknown. role in the initiation of mitochondrial DNA replication. In roles through complementarity to mRNA. The involvement of Dicer in miRNA Rolling circle replication plasmids contain a number of mechanisms (Ro RNP), in association with Ro60 and La proteins.  The Y RpoS is mediated by the formation of a double-stranded RNA RpoS leader. RprA is non-essential. (RpoS regulator RNA A) increased the translation of RpoS. The rprA rRNA at position G4588. rRNA. However, these targets do not appear to be methylated and rRNA. Pseudouridylation in position U3797 is predicted to be rRNAs. Despite distinct functions, RNase MRP has been shown to be rRNA subunit on position G4198. Although the selection of the rRNA to pseudouridine. rubella virus. This family contains three conserved step loop structures. Salmonella species where it is found between the ydaN and dbpA genes. The SAM riboswitch is located upstream of the metA and metC genes in SAM riboswitch, it probably functions to turn off expression of Sar RNA is an antisense RNA that is partly responsible for the saturated at concentrations as low as 5 nM. In Bacillus subtilis, scaRNA is composed of both an H/ACA box and a C/D box conserved scaRNAs are a specific class of small nuclear RNAs which localise scaRNA U87 and a mouse homologue MBI-46 described in. In humans both scores. These eukaryotic matches are almost certainly the result screen between the ydiC and ydiH in E. coli. This gene is only 67 (SECIS) is around 60 nt in length and adopts a hairpin secondary structure is characterised by a small 5' domain (with section of the Drosophila hsp90 mRNA 5' UTR that is required for selectively unite into progeny viruses. This process is called selenocysteine. The selenocysteine insertion sequence self-cleavage reaction to process the products of rolling sequence and the structure of this element are crucial for HCV RNA sequence contains a number of imperfect repeats of the sequence is excised from the 3' arm of the hairpin. sequence is required for maximal IRES activity. It is thought that the sequences are not expected to be hammerhead ribozymes. sequences (MIPF000006 MIPF000006]). This miRNA family appears to be sequences. In humans miR-15a and miR-16 are clustered within 0.5 sequences.  The extents of the hairpin precursors are not sequence that is rich in the end product amino acid of the several related snoRNAs from Pyrococcus.  These RNAs are SgrS is a sugar transport-related sRNA which when activated by SgrR during Shigella flexneri. The function of this family is unknown. Shigella flexneri. The function of this RNA is unknown. shock and stress. shock gene expression) element. The ROSE element is a negative shock response due to IRES-dependent translation. It is thought that this shown here was proposed by Wasserman and Steitz on the basis of shown that some members of this family are specific for adenine shown to be positively regulated by Fur by an unknown mechanism. shown to possess a methylated guanosine cap suggesting it is sigma70-dependent promoter during stationary phase. 6S RNA signal and can act autonomously to destabilise a heterologous signal for RNA polymerase and the operon is not transcribed. signal. The broken mRNA is replaced in the ribosome by the tmRNA signal transduction system. Inactivation of the prrB gene signal transduction system in the plant-beneficial soil bacterium and significantly elevated in the lytic stage. In Epstein-Barr virus mir-BART1 significantly elevated in the lytic stage. In Epstein-Barr virus mir-BART2 silencing by the nucleoid-associated H-NS protein, and translation, silencing of the Cp transcript. Ceruloplasmin (Cp) is a multifunctional, similar imperfect repeat sequences (18 in CsrB, nine in CsrC), similarity with the U83 snoRNA that was cloned by Jady and Kiss site and is linked to helix 3 of domain B by a linker of sites in the untranslated regions of auxin response factor genes sites of modification of uridines to pseudouridines. site-specific 2'-O-methylation of 25S rRNAs. Although the selection of SL1, SL2 , SL3 and SL4  have been independently (SL-A and SL-B) together with a pseudoknot. Disruption of any of these small nuclear, and small nucleolar). Small nucleolar RNAs (snoRNAs) are involved in the processing and small replicating satellite RNA species. Hammerhead snoR105 and snoR108 (identified in ) are members of the C/D class of snoR11/Z151 is a member of the C/D class of snoRNA which contain the C snoR12 has been alternatively named snoZ44 in Arabidopsis snoR12 is a C/D box small nucleolar RNA, which acts as a snoR160 has been alternatively named snoZ270 in rice. snoR160 is a C/D box small nucleolar RNA, which acts as a snoR21 is a member of the C/D class of snoRNA which contain the C (UGAUGA) snoR30 is a C/D box small nucleolar RNA which acts as a methylation snoR38 is a C/D box small nucleolar RNA conserved across yeast, snoR41 has been alternatively named snoZ154 and snoZ231 in snoR41 is a C/D box small nucleolar RNA, which acts as a snoR60 is a member of the C/D class of snoRNA which contain the C (UGAUGA) snoR639 or snoH1 belongs to the H/ACA class of snoRNAs which are thought to snoR72 is a C/D box small nucleolar RNA, which acts as a snoR86 is a member of the H/ACA class of small nucleolar RNAs (snoRNAs) snoR98 belongs to the H/ACA class of snoRNAs which are thought to guide the snoR9 is a member of the C/D class of snoRNA which contain the C (UGAUGA) snoRNA ACA 17 belongs to the H/ACA family of snoRNAs and is snoRNA HBII-234 belongs to the C/D family of snoRNAs. It is the snoRNA HBII-239 belongs to the family of C/D snoRNAs.It is the snoRNA, HBII-52, in the Prader-Willi syndrome (PWS) region of snoRNA, HBII-85, in the Prader-Willi syndrome (PWS) region of snoRNA MBII-201 identified in and also included in this snoRNA R9 is a member of the C/D class of snoRNA which contain snoRNAs are found in the imprinted non-coding mouse transcript snoRNAs are involved in the conversion of uridines to pseudouridines snoRNA sequence similarity is not significant. snoRNAs found in both clusters are clearly related and are snoRNAs HBII-296A and B belong to the C/D family of snoRNAs. They snoRNAs. Most of the members of the box C/D family function in snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA snoRNAs. These two clusters are named SNORD113 and SNORD114 (snoRNAs) which act as guides in the the modification of uridines snoRNA, the methyltransferase activity is supposed to reside in snoRNA U101 is a member of the C/D class of snoRNA which contain the snoRNA U34 is found in intron 5 of the ribosomal protein L13a gene in snoRNA U39 (also described as U55 in ) is a member of snoRNA U41 belongs to the C/D family of snoRNAs. It is predicted snoRNA U42 is found in intron 3 of the ribosomal protein L23a (RPL23a) snoRNA U58 is found in introns 1, 3 and 6 of the ribosomal snoRNA U62 is found in both humans and mice. U62 is a member of snoRNA U70 seems to be exclusive to mammals and is a member of the H/ACA snoRNA U79 or Z22 is found in intron 7 of the gas5 gene in humans and is snoRNA U82 or Z25 is found in both humans and mice. U82/Z25 is a member of snoRNA U95 (also referred to as Z38 ) is a member of the C/D snoRNA which contain C (UGAUGA) and D (CUGA) box motifs. Most of snoRNA which contain the C (UGAUGA) and D (CUGA) box motifs. Members of snoRNA which contain the C (UGAUGA) and D (CUGA) box motifs. This snoRNA Z223 is a member of the C/D class of snoRNA which contain the snoRNA Z37 is a member of the C/D class of snoRNA which contain snoZ199 is a C/D box small nucleolar RNA, which acts as a methylation snoZ278 is a C/D box small nucleolar RNA. Its methylation guide snoZ7 is a member of the C/D class of snoRNA which contain the C (UGAUGA) snRNA. This family also includes the mouse H/ACA box snoRNA snRNA. This model hits a large number of sequences in snRNA at residue U7. snRNA (in an area lying towards the 5' end but 3' to hairpin I) snRNAs are predicted to guide the modification of uridines to (SNURF-SNRNP-UBE3A AS). This is antisense to maternally expressed soybean dwarf virus. This family mediates translation of genomic (gRNA) and spacer element downstream of the cleavage site in histone pre-mRNA. species (MIPF0000009 MIPF0000009]). Animal miRNAs are transcribed as species (MIPF0000046 MIPF0000046]). The hairpin precursors (represented species in the full alignment apart from Shigella flexneri. The specificity factor. This interaction represses expression from a Spi-1 regulates myeloid gene expression during haemopoietic spliceosomal snRNA. spliceosomal snRNA. spliceosomal U6 snRNA. spliceosome) in an ATP-dependent manner, allowing U6 to re-fold Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing pre-mRNA. The putative secondary structure consensus splicing with two transesterification steps. The 2' hydroxyl of SraH expression is highly abundant in stationary phase, but low SraI and was found to be expressed only in stationary phase. SRP19 and SRP54 proteins. SRP assembly and stabilises helix 8 for SRP54 binding. SRP RNA related sequence, including Alu repeats. SRP RNA that includes an Alu domain. The Alu domain of the stabilisation of the rbcL gene which codes for large subunit of stability regulation and translation efficiency in the cytoplasm. stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain starvation. state. It is believed that the element may be triggered during stem cells. The mature sequence is excised from the 3' arm of the stem loops and stimulate frameshifting. stem-loop (SL5) and a downstream domain (DSD). These domains are stem-loops. This structure is similar to the CsrB and RsmB stem-loop structure in the upstream region of the rpoS messenger stem-loops with the consensus sequences predominantly stem-loop that is critical for their retrotransposition. Presumably, stress. stress factors. Four transcriptional regulators are known to bind structural illustrations. structure  found in B. subtilis and other low-GC Gram-positive structure and ribosome scanning is reduced. It is thought that the EBNA structure and sequence appear to be unrelated to the SAM structure between metazoan and yeast U1 snRNAs, the latter being structure between metazoan and yeast U1 snRNAs, the latter being structure can form. This allows RNA polymerase to transcribe structure close to the template sequence. Vertebrate telomerase Structure Conserved A. SscA is 97 nucleotides in length and structure consists of 9 paired regions (P1-P9). These fold structured, antisense sequences which are involved in negative structure of a 17-nucleotide RNA derived from the 3' tail of structure of the frameshift signal is thought to impede the structures, as represented by this family. Eight helical elements structures. The largest of the four, hY1, contains an structure, the region varies according to the virus but structure. This RNA structure is found upstream of a variety of structure, which acts as a post-transcriptional cis-acting structure which is sufficiently well-defined and conserved subgenomic RNA1 (sgRNA1). subsequently processed by the Dicer enzyme to give a ~22nt product. In this substrate RNAs. Targets may include ribosomal and spliceosomal substrate RNAs. Although the selection of the target nucleotide requires subunit in both prokaryotes and eukaryotes. In eukaryotes, it is subunit of the eukaryotic ribosome. It is transcribed by RNA subunit. The ribosome can only bind the capped mRNA after binding succinate dehydrogenase, as well as five other genes previously such extracellular enzymes. RsmA binds to RsmB regulatory RNA suggested that La may be required for the efficient translation of the suggested that the CRE is required for initiation of minus-strand RNA suggested that the vault complex is involved in drug suggested to bind CsrA. suggesting that pairing of DsrA with the RpoS message might be important suggests that U19 may be involved in pre-rRNA processing. (SVLPA). SVLPA is a structured element which promotes efficient switch which exposes conserved UCUG elements and enables synthesised by RNA polymerase III (the other eukaryotic rRNAs are synthesises telomeric DNA. synthesises telomeric DNA. synthesis initiation factor 4AII. synthesis of G-CSF is regulated both transcriptionally and through control synthesis. These RNAs are characterised by a long hairpin structure system and is transcribed from the P3 operon. The RNAIII transcript tag to the incomplete protein enabling recognition by a protease. tandemly repeated small nucleolar RNAs named 14q(I) and 14q(II) target genes are translationally repressed by the small RNA binding targeting it for degradation by PNPase. target mRNA (CopT) is characterised by a four-way junction structure target nucleotide requires the antisense element and the target nucleotide requires the antisense element and the targets. U24 is encoded within an intron of targets have not been reported. target. The snoRNAs U86, U56, U57 and HBII-55,of the C/D family, TBR17 is a member of the C/D class of snoRNA which contain the C (UGAUGA) TBR5 is a member of the C/D class of snoRNA which contain the C (UGAUGA) TBR7 is a member of the C/D class of snoRNA which contain the C (UGAUGA) Telomerase is a ribonucleoprotein reverse transcriptase that Telomerase RNAs differ greatly in sequence and structure between telomerase RNAs from the Gallid herpes viruses as described in. template DNA. The complementary RNAI binds RNAII prohibiting terminator structure that is probably involved in regulation is terminator. The alternative consensus structure is the Tetraodon fluviatilis. than half of B cell chronic lymphocytic leukaemias (CLL). Both than nuclear pre-mRNAs and self-splicing introns. This processing that all U1 snRNAs share a 'common core' consisting of helices I, that encode for flavin mononucleotide (FMN) biosynthesis and that is found in the mRNA for GlmS. GlmS is an enzyme that uses that serve as precision sensors for their corresponding targets. Allosteric that the 5' loop is required for splice site selection and p220 that translational IRES dependent activation of FGF-2 plays a vital role The 245 nucleotide sRNA of Escherichia coli, CsrC, was discovered the 28S rRNA subunit. However it has not been reported as a the 2'O-ribose methylation of large 28S rRNA on residue G4464. the 3' arm of related precursor hairpins (represented the 3' end of the known ncRNAs. Many of these partly overlap coding the 3' end shown here seems to better match the alignment of the 3' OH of the upstream exon. the 3' UTR of Avian sarcoma, Rous sarcoma and Avian leukosis viruses The 3' UTR of human connective tissue growth factor/hypertrophic the 3' UTR of the bamboo mosaic potexvirus. This family is thought to play the 3' UTR of the Potato virus X genome. This element has been found to be The 3' UTR of the vimentin mRNA contains a Y shaped structure The 3' UTR region of coronavirus genomes contains a conserved the 40S ribosomal subunit by the internal ribosome entry site (IRES) The 5' domain and the hinge region act as a pre-rRNA-binding The 5' end of msDNA is linked to an internal guanosine residue of The 5' end of U7 RNA is thought to base-pair to a conserved the 5' region of helix 5 to form a structure termed the the 5' untranslated region of the ribDEAHT operon and precluding the 5' UTR of interferon (IFN) gamma mRNA. This structure is thought to be The Alu domain is thought to mediate the peptide chain elongation The anticodon of a specific tRNA base pairs to a specifier sequence within the antisense element and the conserved box D or D' of the the antisense element and the conserved box D or D' of the snoRNA, the the aphthoviruses. IRES elements allow cap and end-independent The bacterial alpha operon ribosome binding site is surrounded the bacterial ones, the RNA cores from all the three lineages are the box B/C and box C'/D motifs are sufficient for nuclear the box C/D family function in directing site-specific 2'-O-methylation of the bulging out of an unpaired adenosine, on the BPS, which the carpel factory (caf) enzyme appears to be involved in the catalytic activity of the holoenzyme. Although the archaeal and the C/D class of snoRNA which contain C (UGAUGA) and D (CUGA) box the clusters of HBII-85, HBII-52 snoRNA in a 460 kb intron of the the coding region of protein 2C as the site in PV1(M) RNA that The conserved uridine-turn links helix I the conversion of angiotensinogen into angiotensin I which is the The copy-number of the broad host-range plasmid R1162 is controlled The CsrB RNA binds to approximately 18 copies of the CsrA The Csr regulatory system has a strong negative regulatory the C (UGAUGA) and D (CUGA) box motifs. Z37 acts as a the Dicer enzyme to give a ~22nt product. In this case the The discovery of CsrC is intriguing, in that a similar sRNA, the Drosophila embryonic body plan. When first expressed in The E. coli Ribosomal S15 gene 5' UTR can form two The eel long interspersed element (LINE) UnaL2 and its partner short The exact 5' and 3' ends of this RNA are uncertain. This gene The exact 5' and 3' ends of this RNA are uncertain. This RNA The exact function of RtT is unknown although it is thought that it may be The expression of miR-148 has been demonstrated in human the family may play a role in regulating RNA synthesis. The FinOP system regulates the transfer of F-like plasmids. The FinOP system regulates the transfer of F-like plasmids. the first 120 bases and the second to the remaining 50 bases. The first step in the replication of the plus-stranded poliovirus the first step of retrotransposition is the recognition of their The fushi tarazu gene is essential for the establishment of The gcvB gene encodes a small untranslated RNA involved in The gene called SraK, was highly abundant in stationary phase, but low the gene for ribosomal protein L7a in mammals, chicken and Fugu. the genetic code in two manners: having more than one tRNA (with The hairpin ribozyme, like the hammerhead (RF00008 RF00008] and The hammerhead ribozyme is one of the smallest catalytic the Hepatitis A virus. IRES elements allow cap and end-independent The hepatitis delta virus (HDV) ribozyme is necessary for The Hfq protein has been shown to interact with several small The HgcC ncRNA gene was identified computationally in AT-rich the histone hairpin binding protein, or HBP). Together with the host cell. It has been found that  La autoantigen (La) is required for The hsp90 gene product is involved in the Drosophila heat shock The human genome in particular is known to contain a large amount of the human orthologue of mouse MBI-6 snoRNA. The human sequence has also been annotated in the sequence databases The human snoRNA HBII-13 belongs to the C/D family of snoRNAs. It The identity of the proteins involved and the localisation The imprinted human domain at 14q32 contains two clusters of The incorporation of selenocysteine into a protein sequence the initiation codon and eliminates the requirement for eIF4F the initiator tRNA.  Translation of hepatitis C virus (HCV) mRNA the internal initiation of translation by recruiting a ribosomal 43S the introns of ribosomal protein S1 in Xenopus and S3 in human the introns of ribosomal protein S3a and contains a 12nt their extents are not known. In this case the mature sequence is their extents are not known. In this case the mature sequence is The iron response element is a short conserved stem-loop which is the leader to down-regulate expression of these genes. the major transfer promoter, pY. The FinO protein is essential the mature sequence comes from the 5' arm of the precursor, and the members of the box C/D family function in directing site-specific the methylation of 2'-O-ribose sites in 28S rRNA. The micF gene is a stress response gene found in Escherichia coli the micF promoter region and activate micF expression. the mouse MBI-79 sequence as described in. the mouse sequence MBI-83 described in. the mouse snoRNA sequence MBI-64 described in. The mRNAs of metazoan histone genes lack a poly-A tail. 3' end the mRNA. This element forms a Y-shaped structure, part of The Nanos protein in Drosophila is required for correct the nucleus it is involved in precursor rRNA processing, where it the operon codes for RNase III which cleaves the long rncO stem The overall structure forms the origin of replication (OriR) for the The physiological role of Escherichia coli Spot 42 (spf) RNA has the plasma. As an acute-phase protein, its plasma concentration can the potato spindle tuber viroid (PSTVd) RY motif stem-loop. The RY motif the precursor sequences may be longer, and the carpel factory the predicted hairpin-hinge-hairpin-tail structure, conserved The products are thought to have regulatory roles through the protein components. the pseudogene count. the pseudoknot structure have been found to reduce PKR activation and the pseudouridylation of position U4522 if the 28S rRNA. HBI-6 is There are significant differences in sequence and secondary therefore a major factor in control of plasmid replication. therefore increased expression of downstream acid resistance genes. the RepI message. the resolution of the local inflammatory response following cytokine the retron msd gene) and RNA (encoded by the msr gene) components. The Rev response element (RRE) is encoded within the HIV-env The RFN element is a highly conserved domain that is found the ribosome binding region. This family also contains the ribosome binding site of the serC reading frame. The ribozyme acts to process the RNA transcripts to unit The ribozyme catalyses self cleavage of the glmS mRNA that is thermoregulated. It has been shown that the untranslated mRNA the RNA binds to the galK translation initiator region. the RNA strand by a 2'-5' linkage. The components of msDNA are The RyhB 90-nt RNA down-regulates a set of iron-storage and the S15 protein. The alignment of this family contains The s2m motif is found in the 3' UTRs of astrovirus, coronavirus The same region has been implicated in the control of mRNA The SAM riboswitch is found upstream of a number of genes which these are AC078923 AC078923] and BC050488 BC050488]. These animal The secondary structure mark-up for this family represents The secondary structure of small subunit ribosomal RNA (SSU rRNA) These DB elements are thought to be required for efficient translation. these genes in response to elevated SAM levels. These include two other genes encoding enzymes in the tricarboxylic the selection of the target nucleotide requires the antisense the sequence of the mature RNA. This family also contains the These two activities of DsrA can be separated by mutation: the first The Signal Recognition Particle Database (SRPDB) provides The signal recognition particle (SRP) is a universally conserved the sites of modification of uridines to pseudouridines. The snoRNA ACA 40 belongs to the H/ACA family of snoRNAs and The snoRNA ACA 48 has been identified to guide pseudouridylation The snoRNA ACA49 has no identified RNA target. NB genomic sequence The snoRNA ACA53 belongs to the H/ACA family of pseudouridylation The snoRNA HBI-36 snoRNA belongs to the H/ACA family of snoRNAs The snoRNA HBI-43 belongs to the C/D family of snoRNAs, guiding The snoRNA HBI-6 belong to the H/ACA family of snoRNAs, guiding the snoRNA, the methyltransferase activity is supposed to reside in one of the snoRNA, the methyltransferase activity is supposed to reside in one of The sraJ gene was expressed in early logarithmic phase, but its level The SscA ncRNA gene was identified computationally in AT-rich The structure consists of 2 domains, A and B. The 3' arm of the synthesis of minus strand RNA to form viral dsRNA. The t44 gene is found between the map and rpsB genes in all the target nucleotide requires the antisense element and the conserved the T-box motif, and the NCCA acceptor tail of the tRNA base pairs to a the the pestiviruses. The pestivirus IRES allows cap and The third stem-loop, which behaves as a transcription terminator, can the transferrin receptor (involved in iron acquisition) leads to the two may act in a concerted manner. the two riboswitches may work in conjunction to regulate the the the typical eukaryotic cap-dependent translation pathway. The U11 small nuclear (snRNA), together with U4atac/U6atac, U5, The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, The U76 snoRNA is found in an intron of the uRNA host gene (UHG) The universally conserved helix which interacts with the SRP54 M The VA (viral associated) RNA is found in adenovirus. It plays a role the virally encoded polymerase BALF5 for degradation. The mature sequence they act to negatively regulate several genes including sodB and sdh. They are large self-splicing ribozymes and have 6 structural They catalyse their own excision from mRNA, tRNA and rRNA the yfhK and purL genes. The function of this RNA is unknown. The Y. pestis homologue was detected by similarity to the E. coli thiamin-regulatory element, thi box was extended, resulting thirds of CLL cases. The mature sequence is excised from the This bacterial RNA is also found in the genomic sequence of this case the mature sequence is excised from the 3' arm of the This cis element is composed of four hairpins called SL1 This element contains a pseudoknot. This entry contains a glucosamine-6-phosphate activated ribozyme This family also contains the mir-13 precursor which, despite This family belongs to the H/ACA class of small nucleolar RNAs This family belong to the C/D class of snoRNA which contain the C This family consists of a group of Shigella flexneri and Escherichia coli This family consists of a number of bacterial RNA genes of 209 bases in This family consists of a number of bacterial sroB RNA genes of around 90 This family consists of several bacterial RNA genes of 181 bases in length This family consists of several bacterial sequences from E. coli, Shigella This family consists of several HIV gag stem loop 3 (GSL3) sequences. GSL3 This family consists of several Pospiviroid sequences which are related to This family consists of several snoRNA Z103 sequences which are members of This family consists of several, structured HIV primer binding sites This family consists of the mammalian microRNA (miRNA) precursors mir-103 This family consists of the microRNA (miRNA) precursor mir-6 which This family contains a large number of putative archaeal matches to This family contains a number of annotated pseudogenes and 7SK This family contains a number of annotated U7 pseudogenes. This family contains F1, F2 and snoR5a sequences, all of which are members This family contains multiple ncRNA from E. coli that were This family contains several related snoRNAs including R31, Z27 and Z110. This family contains the related snoRNAs R32, R81 and Z41 which are This family does not contain the larger yeast sequences. This family includes a couple of false matches currently This family includes plant snoRNA snoZ196 and yeast snoRNAs R39 This family is a bacterial riboswitch that binds to the This family is a putative noncoding RNA found multiple times in This family is a putative regulatory RNA structure that is found This family is a putative r-protein leader autoregulatory This family is a riboswitch found predominantly in This family is thought to target mRNAs coding for APETALA2-like This family of plant small nucleolar RNAs belong to the C/D class This family of plant snoRNAs belong to the C/D class of snoRNA This family of RNAs are found as part of the enigmatic vault This family of small nucleolar RNAs belongs to the C/D class of This family represents a 5' UTR cis-regulatory element found in This family represents a bacterial cis-regulatory element known as RtT RNA. This family represents a bacterial non-coding RNA called RydC. RydC is This family represents a bacterial regulatory element (rncO) This family represents a Cardiovirus cis-acting replication element (CRE) This family represents a cis-acting element in the 3'-UTR of the This family represents a cis-acting regulatory element (CRE) from the human This family represents a cis-reactive element from Hepatitis E virus This family represents a cis-regulatory element found at the 5' end of This family represents a cis-regulatory element found in the 5' UTR of This family represents a cis-regulatory element known as defective RNA or This family represents a cis-regulatory element present at the 3' ends of This family represents a cloverleaf-like cis-regulatory element found in This family represents a conserved element found in the 5' UTR This family represents a conserved RNA structure found upstream This family represents a conserved stem-loop found in This family represents a coronavirus cis-acting replication This family represents a Cripavirus internal ribosome entry site (IRES) This family represents a GadY RNA (previous named IS183 in ). GadY can This family represents a group of ctRNAs (or counter-transcribed This family represents a group of S-elements from p42d and This family represents a group of sequences related to the human This family represents a group of sequences that are related to the This family represents an APC internal ribosome entry site (IRES) This family represents an apolipoprotein B (apoB) cis regulatory element This family represents an Epstein-Barr virus internal ribosome entry site This family represents a Parechovirus cis regulatory element which is This family represents a predicted coronavirus packaging signal. Within a This family represents a predicted pseudoknot structure found in prion This family represents a predicted replication signal which is highly This family represents a pseudoknot containing stem-loop structure found in This family represents a pseudoknot structure from turnip yellow mosaic This family represents a putative stem-loop structure found in the 5' UTR This family represents a rbcL 5' UTR RNA stabilising element from This family represents a ribosomal frameshifting element found in the mRNA This family represents a Rotavirus cis-acting replication element (CRE) This family represents a set of small RNAs (the Qrr RNAs) that are thought This family represents a small hairpin structure found in the 5' UTR of This family represents a structural element which is found in antizyme This family represents a structured G/C rich element located in the 5' UTR This family represents a structured region around the Rous sarcoma virus This family represents a Togavirus virus 5' plus strand cis-regulatory This family represents a tRNA-like structure found in the 3' UTR of This family represents heat shock protein 70 (Hsp70) internal ribosome This family represents region 3 of the defective interfering (DI) RNA This family represents RNAIII which is known to regulate the expression of This family represents SL2 RNA. SL2 RNA is involved in trans splicing in This family represents the 3' UTR region of the R2 retrotransposable This family represents the 44 nucleotide K10 transport/localisation element This family represents the Alfalfa mosaic virus (AMV) coat protein (CP) This family represents the bacterial glycine riboswitch. Glycine This family represents the bag-1 internal ribosome entry site (IRES). When This family represents the bip internal ribosome entry site (IRES). BiP This family represents the bovine leukaemia virus RNA encapsidation This family represents the c-myc internal ribosome entry site (IRES). The This family represents the connexin-32 internal ribosome entry site (IRES) This family represents the connexin-43 internal ribosome entry site (IRES) This family represents the core structure of the bicoid 3'-UTR and This family represents the c-sis 5'-UTR which contains three modules that This family represents the direct repeat 1 (dr1) element commonly found in This family represents the equine arteritis virus leader This family represents the FGF-1 internal ribosome entry site (IRES). The This family represents the fibroblast growth factor 2 (FGF-2) internal This family represents the Flavivirus 3'-SL cis-acting replication This family represents the flavivirus 3' UTR elements DB1 and DB2. This family represents the Gammaretrovirus (mammalian type C This family represents the granulocyte colony-stimulating factor stem-loop This family represents the hairy localisation element (HLE) found in This family represents the Hepatitis C stem-loop IV structure found in the This family represents the Hepatitis C stem-loop VII structure This family represents the Hepatitis C virus 3'X element which contains This family represents the Hepatitis C virus (HCV) cis-acting replication This family represents the HIV Ribosomal frameshift signal. HIV This family represents the HIV trans-activation response (TAR) element This family represents the human microRNA (miRNA) precursors mir-192 and This family represents the hypoxia-inducible factor 1-alpha This family represents the insertion sequence IS1222 ribosomal This family represents the insulin-like growth factor II (IGF-II) internal This family represents the internal ribosome entry site (IRES) of This family represents the Kaposi's sarcoma-associated herpesvirus (KSHV) This family represents the Kv1.4 voltage-gated potassium-channel This family represents the larger yeast sequences. Family This family represents the L-myc internal ribosome entry site (IRES). The This family represents the Luteovirus cap-independent translation element This family represents the microRNA (miRNA) let-7 and This family represents the mir-BART1 microRNA precursor found in Human This family represents the mir-BHRF1-1 microRNA precursor found in Human This family represents the Mnt internal ribosome entry site (IRES). Mnt is This family represents the n-myc internal ribosome entry site (IRES). The This family represents the Picornavirus internal ribosome entry site This family represents the plant microRNA (miRNA) precursor This family represents the plant microRNA (miRNA) precursor This family represents the PyrR binding site and terminator This family represents the related mir-15a and mir-15b This family represents the simian virus 40 late polyadenylation signal This family represents the SL1 RNA. SL1 is commonly located in the spacer This family represents the Tobamovirus internal ribosome entry site (IRES). This family represents the Tombusvirus internal replication element (IRE) This family represents the TrkB internal ribosome entry site This family represents the turnip crinkle virus (TCV) hairpin 5 (H5) which This family represents the U1A polyadenylation inhibition element This family represents the vascular endothelial growth factor this family which are also included in the Eukaryotic type SRP This miRNA has been predicted or confirmed in a wide range of this molecule have not been identified. n.b: The GenBank this mRNA motif is located on at least five separate transcriptional This ncRNA gene was recently identified in a screen and called This ncRNA was found to be expressed only in stationary phase. This ncRNA was identified in a large scale screen of E. coli. This rate of degradation is aided by the pcnB (plasmid copy This RNA is found in bacterial plasmids including pIP501. This RNA structure is found in the 3' UTR of various enteroviruses. This RNA was also discovered in E. coli during a large scale screen. This RNA was discovered in E. coli during a large scale screen. This RNA was discovered in E. coli during two large scale screens This RNA was originally discovered in E. coli during a large scale screen This structure causes translational regulation of This structure forms when the cell has an excess of the thought that this family may facilitate a continuous IGF-II production in thought to act as guides for the 2'-O-ribose methylation thought to bind to the target mRNA and induce its degradation. thought to confer increased stability to the transcript, allowing thought to guide the sites of modification of uridines to thought to regulate an mRNA, yejABEF which encodes an ABC transporter thought to regulate GlmS activity. three base paired helices, separated by short linkers of three base paired helices, separated by short linkers of three IRES elements are somehow responsive to cellular changes and act to three stemloop structures that are essential for replication. through complementarity to mRNA. The involvement of Dicer in miRNA through direct interactions with as yet unknown nuclear factors. (T.-H. Tang, J.-P. Bachellerie, H. Huber, M. Drungowski, T. Elge, J. thus conformational changes could regulate translation. thus starting the first of two transesterification reactions that timing in C. elegans, and was later shown to be part of a (TLS) from Drosophila melanogaster. K10 TLS is responsible for the tmRNA is used as a reading frame that ends in a translation stop to 18S and 28S ribosomal RNA. This complementarity suggests that to 18S rRNA.  E3 is encoded in introns in the gene for protein to 28S rRNA.  E2 is encoded in introns in the gene for a to accumulate in the nucleolus. In humans the genomic to act as a computational screen for selenoprotein genes. to act as methylation guides. to be able to form several different structures with similar free energy. to be active in vivo in the absence of any protein factors and to be a key structural element in discontinuous subgenomic RNA synthesis to be bound by Hfq. to be found exclusively in Drosophila species. to be involved in the regulation of quorum sensing in Vibrio species. It is to be related to viral pathogenesis and in particular arthritis which is a to be translated by internal ribosome entry. to essentially two domains - the P4-P6 domain (formed from the to give a ~22nt product. In this case the mature sequence comes to guide 2'O-ribose methylation of 5.8S rRNA on residue U14. to guide 2'O-ribose methylation of the large 28S rRNA on residue to guide methylation of 2'-O-ribose residues on 28S ribosomal RNA. to have regulatory roles through complementarity to mRNA.  The to helix II and usually has the sequence CUGA.  Helix II and to maintain a low copy number.  One of these methods is to transcribe Tomato bushy stunt virus is the prototype member of the Tombusviridae to mediate internal ribosome entry in cells derived from brain, to mRNA. The involvement of Dicer in miRNA processing suggests a to part of the 5' UTR of the traJ mRNA.  The traJ gene encodes to pseudouridines. This family includes the human snoRNAs U64 to regulate their expression.The hairpin precursors to reside in one of the protein components. U34 snoRNA has to SL4 (SL is for Stem Loop). This element is involved to target mRNAs coding for a phosphatase transporter. The mature to target mRNAs coding for ATP sulphurylases. The mature to the Cajal bodies and guide the modification of RNA polymerase to the initiation codon and eliminates the requirement for eIF4F. to which the tRNA's corresponding amino acid is attached (by (TPRT). traJ gene encodes a protein required for transcription from transcribed on the opposite strand to RepB the replication initiation transcriptase in a reaction known as target primed reverse transcription transcript) gene whose function is unknown. mir-BART2 is thought to target transcript) gene whose function is unknown. The mature sequence is excised transcription efficiency. This family acts in conjunction with transcription factors. The mature sequence is excised from the 3' arm transcription factor, which induces transcription of several transcription-regulating sequence hairpin (LTH). The LTH is thought transcript is not impeded. When there is a deficiency of the transcripts by 8-fold. Mutations in this regulatory region of the 5' UTR Transfer RNA (tRNA) molecules are approximately 80 nucleotides in translating the leader peptide stalls and the antiterminator translational mechanism is essential for the survival of cells under Translational regulation of the stationary phase sigma factor translation becomes more efficient. This family represents a translation but not for anti-H-NS action, while the second stem-loop translation by recruiting a ribosomal 43S pre-initiation complex directly translation. It is thought that FGF-1 IRES activity is strictly controlled translation of AMV RNA by between 50 and 100-fold. This family contains at translation of mRNA in the host cell. The IRES achieves this by mediating Translation of the nanos mRNA is repressed in the bulk translation to occur under situations where initiation from the 5' cap Translation via the IRES has been found to be common following heat shock transport and anterior localisation of K10 mRNA and acts to establish transporters, in various prokaryotic organisms. The THI transport proteins. This element is a metabolite-dependent Transposition of insertion sequence IS10 is regulated by an Trans-splicing is a form of RNA processing. The acquisition of a spliced TSD-DSD interactions are involved in the mediation of viral RNA tumour suppressor gene which is associated with the inherited two domains. U105 belongs to the C/D family of snoRNAs. It is encoded in an U106 might function as an RNA chaperone during rRNA folding U108 belongs to the H/ACA family of snoRNAs. The sequence is (U12-22/U4-8) and singlet (U4-8) forms of this snRNA have been U12-88/U4-8 is intergenic and the purified transcript has been U14 small nucleolar RNA (U14 snoRNA) is required for early U16 is a member of the C/D class of snoRNA which contain the U17/E1 RNA belongs to the H/ACA class of small nucleolar RNAs (snoRNAs). U18 is a member of the C/D class of snoRNA which contain the U19 belongs to the H/ACA class of snoRNAs. snoRNAs bind a number U1 is a small nuclear RNA (snRNA) component of the spliceosome U20 is a C/D box small nucleolar RNA that is encoded in intron 11 U2-19 is a member of the C/D class of snoRNA which contain the C (UGAUGA) U22 is a member of the C/D class of snoRNA which contain the U22 snoRNA host gene (UHG) in mammals and is thought to act U2-30 is a member of the C/D class of snoRNA which contain the C (UGAUGA) U23 belongs to the H/ACA class of snoRNAs. snoRNAs bind a number U24 is a member of the C/D class of snoRNA which contain the U2-dependent spliceosome. It forms a duplex with U6, and with U2 is a small nuclear RNA (snRNA) component of the spliceosome U30 is a member of the C/D class of snoRNA which contain the U32 is a C/D box small nucleolar RNA encoded in intron 2 of the U33. snoRNA U33 is found in intron 4 of the ribosomal protein U35 guides the methylation of 2'-O-ribose sites in 28S rRNA. U35 is a C/D box snoRNA located in intron 6 of ribosomal protein U36 acts as a 2'-O-ribose methylation guide. This family also U36 is a member of the C/D class of snoRNA which contain the U39 guides the methylation of 2'-O-ribose residues in 28S ribosomal U3 snoRNA. Both box B/C and C'/D motifs are involved in specific U40 is a C/D box small nucleolar RNA, also known as snoZ153 in plants. U50-like (U50') snoRNAs that are localised in nucleoli. U7 snRNA binding of the HDE, SLBP binding nucleate s the U83 and U84 are spliced from introns 5 and 4 of the BAT1 gene in U88 is small Cajal body specific RNA (scaRNA). scaRNAs are a U8 is a member of the C/D class of snoRNA which contain the U96b and the apicomplexan snoRNA snr39b. umuD genes. The function of this RNA is unknown. UnaL2 was determined by NMR. Uncharged tRNA acts as the effector for transcription under normal growth temperatures. When heat shock occurs units that together encode 17 genes that are mostly involved in unknown, but this structured RNA element may be involved in their genetic until it is required for transcription. upstream gene which codes for Swiss:Q8RC62, a member of upstream of an uncharacterized membrane protein in upstream of the gcvT operon which controls glycine upstream of the serC-serA operon in some upstream of the speF gene encoding ornithine decarboxylase in upstream of the ylbH gene in B. subtilis and related low GC uridines to pseudouridines. uses a system called -1 ribosomal frameshifting to produce the U-shaped structure, with binding sites for a single U1A protein using a genetic screen for factors that regulate glycogen biosynthesis. using ATP as energy to accomplish the energetically unfavourable UTR of Spi-1 mRNA which is able to inhibit the translation Spi-1 (UTR) preceding prfA, forms a secondary structure, which masks UTRs from other closely related bacteria. The secondary structure variable length and sequence. This region is thus not various viral 3' UTR regions have been found to play roles in vault protein (MVP), two minor vault proteins (VPARP and TEP1), vCyclin and vFLIP coding sequences are present on a bicistronic transcript (VEGF) internal ribosome entry site (IRES) A. VEGF is an verified. The mature sequence is excised from the 5' arm of the vertebrate genomes, which appear to be U6 derived pseudogenes vertebrates, ciliates and yeasts, but they share a 5' pseudoknot vertebrates (MIPF0000044 MIPF0000044]). The hairpin precursors (represented vertebrate species (MIPF0000006 MIPF0000006]). miR-16 and miR-15a are vertebrate specific and members of this family have been Vertebrate U17 is intron-encoded and ranges in length from 200-230 via internal ribosome entry and bypasses the typical eukaryotic virally infected cell, viral genome and viral proteins specifically and viral replicase protein P1. This family is required for negative strand viral replication and are usually found near the 5' and 3' termini. This viral replication and is thought to be the only catalytic viral replication and packaging. viral RNA genomes is proposed to act as an RNA conformational viral RNA in the pancreas. viral viability. All stem loop structures are thought to be important for virion. Virp1 binding is unknown. It is however thought that RY motifs are virus which is thought to be needed for efficient transcription as vitamin B(12) biosynthesis and be transported by a post-transcriptional Vitamin B(1) in its active form thiamin pyrophosphate (TPP) is an was called candidate 14. was observed when prrB was overexpressed. The prrB gene We have classified hammerhead ribozymes into three types We have identified a putative novel vault RNA on chromosome 5 well. The function of this RNA is unknown. well conserved across flaviviruses. Deletions of the 3' UTR of when attached to the prohead. The pRNA is thought to be bound when cap-dependent translation initiation is reduced. which act as guides in the the modification of uridines to pseudouridines which allows cap independent translation during conditions such as heat which are found between the abgR and ydaL genes in Escherichia coli and which contain the C (UGAUGA) and D (CUGA) box motifs. This family which has been shown to have protein binding activity. which is known to be required for the trans-activation of the viral which is located in the coding sequence of the gene. APC is a which is located within the region coding for p92 polymerase. The element which is located within the region encoding the capsid protein VP2 and is which is recognised by the Smaug protein leading to translational which is required for the production of capsid proteins through which is thought to be essential for "some step in gene expression". While the threshold of this family is set high so as to minimise the window size will find more matches. with an invariant region of eukaryotic 28S ribosomal RNA. within intron 12 of the nucleolin gene in human, mouse, rat within the coding region of the mRNA. Selenoprotein mRNAs with the phenomenon of RNA interference. miRNAs are numbered with U67 and snoRNA mgU6-77 ykvJKLM (queCDEF) operon which encodes four genes necessary for zebrafish (MI0002015 MI0002015]). miR-148 has also been