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| ncRNA classification |
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There
are 109 traditional ncRNA classes in NONCODE. Here is a introduction of all these ncRNA classes :
4.5S RNA: a short half-life and appears to be associated with poly-A mRNAs in vivo and is specific to some species in Rodent.
5.3S RNA: localized predominantly on ribosomes and also in the fraction of native 40S ribosomal subunits known to contain translation preinitiation complexes.It was supposed that 5.3S RNA is transcribed by RNA polymerase III and involved in protein synthesis regulation in plant cells under heat shock conditions at the level of translation initiation.[1]
6Sa RNA (ssaA): is functional when cells divide actively.[2]
6S RNA (ssrS): involved in stationary phase regulation of transcription by the sigma70-holoenzyme.[3]
7H4 RNA: selectively expressed in the endplate zone of skeletal muscle and is upregulated during early postnatal development and after denervation.[4,5]
7SK RNA: discovered as an abundant small nuclear RNA and found that 7SK RNA binds the CDK9/cyclin T complex (known as elongation factor P-TEFb). P-TEFb activates transcription by phosphorylating the C-terminal domain of RNA polymerase II. The 7SK RNP negatively regulates this process.[6,7]
adapt15 RNA: expressed in response to treatment with low concentration of hydrogen peroxide.The adapt15 transcripts are primarily located in the cytoplasm, and they are associated with polysomes.[4,8]
adapt33 RNA: inducible by hydrogen peroxide.A large fraction of adapt33 transcripts is associated with polysomes.[4,9]
aHIF RNA: natural antisense transcript derived from HIF1alpha gene sequences encoding the 3' untranslated region of HIF1alpha mRNA and is specifically overexpressed in all nonpapillary clear-cell renal carcinomas examined, but not in the papillary renal carcinomas examined.[10]
Air RNA: transcripted from imprinted and required for silencing autosomal imprinted genes.[11]
anti-CLST11240 RNA: antisense RNA CLST11240.
BC1 RNA: arose from a monomeric ID repeat and has been recruited or exapted into a function of the nervous system. This class is specific to rodents.[4,12]
BC200 RNA: arose from a monomeric Alu element and has been recruited or exapted into a function of the nervous system. This class is specific to primates.[13]
bft RNA: bereft RNA[14]
bic RNA: a novel gene activated by proviral insertions in avian leukosis virus-induced lymphomas, may play a role in growth control.[4,15]
BM1 RNA: transcripted from short interspersed element. The level of the Bm1 transcripts increases in response to either heat shock, inhibiting protein synthesis by cycloheximide or viral infection.[16]
BORG RNA: Bone Morphogenetic protein-Responsive RNA.[4,17]
Bsr RNA: preferentially expressed in the rat central nervous system. It is encoded by asingle locus consistsing of 100-150 copies of tandemly repeated 0.9 kb sequence.Bsr is specific for Rattus and was not found in other rodents.[18]
bxd RNA: transcripted from bithoraxoid (bxd) region of the Ultrabithorax domain in the bithorax complex of Drosophila melanogaster.[19]
CCLS96.1 RNA: may encode a non-coding RNA preferentially transcribed in reproductive organs of Silene latifolia.[20]
CMPD-associated ncRNA: suggested to play a role in differentiation or sex determination. Disruption of this gene may therefor be responsible for sex reversal in CMPD patients.[4,21]
CR20 RNA: identified as a cytokinin-repressed gene in excised cotyledons of cucumber. [4,22]
csrB RNA: binding to CsrA appears to interfere with binding of CsrA to glg mRNA, and CsrA acts to decrease glg mRNA stability by interfering with translation of the glg mRNA.[6,23]
DD3 RNA: prostate-specific genes which are highly overexpressed in prostate cancer cells.[4,24]
DGCR5 RNA: a product of a gene disrupted by a balanced translocation that is associated with DiGeorge syndrome - the ADU breakpoint. Transcription from this gene produces a series of alternatively spliced, noncoding RNAs during mouse and human embryogenesis.[4,25,126]
DicF RNA: causes inhibition of the formation of the constriction and the separation of the replicated chromosomes into the daughter nucleoids and interferes with FtsZ mRNA translation.[26,27]
DISC2 RNA: a non-coding RNA molecule that is antisense to DISC1(Disrupted-In-Schizophrenia 1). An arrangement that has been observed at other loci where it is thought that the antisense RNA is involved in regulating expression of the sense gene.[28]
DsrA RNA: stimulates RpoS production during log phase growth at low temperature and acts to inhibit H-NS translation and affects biosynthesis of capsular polysaccharide via increased production of the activator RcsA, due to inhibition of H-NS mediated transcriptional silencing.[29,30]
dsrB RNA: antisense RNA.Transcription is regulated by RpoS and DsrA RNA.[31]
ENOD40 RNA: presumed to play a central regulatory role in the Rhizobium-legume interaction, being expressed well before the initiation of cortical cell divisions resulting in nodule formation.[32]
ERalpha antisense RNA: antisense RNA.[33]
Finp RNA: in conjunction with the protein FinO, constitutes a repressor for conjugative DNA transfer.[6,34]
flmB RNA: binds to the flmA RNA and suppresses the expression of the lethal product, presumably by blocking coupled translation of ORF70 and flmA.[35]
FMR1P binding RNA: binding to 78-kDa protein, FMRP.[36]
G8 RNA: a small cytoplasmic RNA that is induced in response to heat shock. It is responsible for establishment of thermotolerance.[4,37,128]
G90 RNA: expressed at very high levels in the small intestine and at lower levels in large intestine, testis and kidney.G90 transcripts are present only in post-mitotic cells.[4,38]
gadd7 RNA: activated in response to DNA damage and also to some extent in cases of other stress conditions (e.g. starvation), whose effect is growth arrest.[4,39]
GcvB RNA: involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.[6,40]
GNAS1-as RNA: a complex imprinted gene located on a human chromosome 20q13. It encodes an ¦¡ subunit of the stimulatory guanine nucleotide-binding protein Gs, coupling the activated forms of transmembrane hormone receptors to the intracellular generation of cAMP.[41]
gRNA: function in RNA editing that has been found only in the mitochondria of kinetoplastids in which mRNAs are edited by inserting or deleting stretches of uridylates.[42,43]
GUT15 RNA: be used by plants as a modulator to interrelate stress and ABA signaling networks for controlling growth and development in response to the shifting environment.[4,44]
H19 RNA: is transcripted from imprinted region.[45,46]
His-1 RNA: transcribed as a single spliced and polyadenylated cytoplasmic RNA that shares several features in common with the emerging class of untranslated RNAs and involved in an oncogenic pathway that controls cell cycle progression.[49]
Hoxa 11-AS RNA: is a homeobox gene that is expressed in developing limbs and caudal body. A presence of abundant, natural antisense Hoxa 11 transcripts was observed. These transcripts are polyadenylated and alternatively spliced. The RNA is an active product involved in the regulation of Hoxa 11.[50]
hsr-omega RNA: found in complexes with heterogenous nuclear RNA binding proteins (hnRNPs) in the interchromatin space. The nuclear transcripts (hsr-omega-n) may regulate the trafficking and availability of hnRNPs in the nucleus.[4,51,52]
IGF2AS RNA: a paternally expressed from imprinted region.[53]
IPW RNA: a paternally expressed gene cloned from the Prader-Willi syndrome (PWS) region and is not expressed in individuals with PWS, and is thus a candidate for involvement in this disorder.[4,54]
KLHL1 antisense RNA: an endogenous antisense RNA that overlaps the transcription and translation start sites as well as the first splice donor sequence of the sense gene. The sense transcript encodes a 748 amino acid protein with a predicted domain structure typical of a family of actin-organizing proteins related to the Drosophila Kelch gene, and so has been given the name Kelch-like 1 (KLHL1).[55]
Ks-1 RNA: identified in certain types of cells in honeybee central nervous sysytem and possibly involved in the regulation of neural functions.[4,56]
KvlQT1-AS RNA: transcripted from imprinted region.[57]
lbiRNA: (lipopolysaccharide biosynthesis interfering RNA)shown to affect the biosynthesis of the O-specific polysaccharide of lipopolysaccharide (LPS) in various enterobacterial strains.[4,58]
meiRNA: isolated as one of the factors involved in molecular control of meiosis in yeast. [4,59]
MESTIT1 RNA: paternally expressed non-coding RNA that may be involved in the regulation of MEST expression during development.[60]
meuRNA: meiotic expression upregulated,antisense RNA.[61]
MHM RNA: (male hypermetylated RNA) transcripted from imprinted region.[4,25]
MicF RNA: a non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.[62,63]
miRNA (microRNA): the reverse complement of another gene's mRNA transcript and inhibit the expression of the target gene.[64,65,66]
msr RNA: a reverse transcriptase that is responsible for the production of a small satellite DNA called msDNA (multi-copy single-stranded DNA).[67,68]
Msx1-AS RNA: expressed only in differentiated dental and bone cells with an inverse correlation with Msx1 protein.The ratio between Msx1 sense and antisense RNAs is a very important factor in the control of skeletal terminal differentiation.[4,69]
NaPi-2b1 RNA: antisense RNA.[70]
nc1 RNA: induced after planthopper infestation.
NCRMS RNA: (non-coding RNA in Rhabdomyosarcoma)[71]
Ntab RNA: specifically expressed in rat central nervous system. It was proposed to participate in targeting and/or regulation of localised translation of other mRNA species. [4,72]
NTT RNA: found only in activated, but not resting, T cells. NTT RNA may have a role in the regulation of neighboring genes. [4,73]
OxyS RNA: plays a regulatory role in the oxidative stress response and is involved in regulation of fhlA , rpoS, and multiple additional genes.[74,75]
PAN RNA: the most abundant transcript encoded by human Herpesvirus 8;polyadenylated and transcribed by RNA transcribed by polymerase II. It was proposed that it may be responsible for inhibition of splicing of the host genes by hybridization with a short region of U12 snRNA.[4,76]
PCGEM1 RNA: a prostate-specific gene, is overexpressed in prostate cancer with potential functions in prostate cell biology and the tumorigenesis of the prostate gland.[77,78]
pgc RNA: identified and found to be localized in polar granules.pgc RNA is an essential role in an essential role.[79]
Plasmid_R1162 RNA: negatively regulates RepI by complementary to a segment of the RepI message.[6,80]
pRNA: uses a complex of six identical short RNA sequences as mechanical components (utilizing ATP for energy) of its DNA packaging machinery.[81]
PrrB_RsmZ RNA: able to phenotypically complement gacS and gacA mutants and is itself regulated by the GacS-GacA two-component signal transduction system.[6,82]
repairRNA: encoded upstream of rsr, that accumulate following UV irradiation.[83]
ReplicationControl RNA: antisense RNAs regulate copy number through inhibition of replication initiator protein synthesis.[84]
Rian RNA: exclusively expressed from maternal allele, and is exclusively localized in the nucleus.[4,85]
RNase MRP RNA: an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing.[6,86]
RNase P RNA (rnpB): a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5'-ends of tRNAs by cleaving the 5'-leader elements of precursor-tRNAs.[6,87]
roX RNA: required for X chromosome inactivation.[88,4]
RprA RNA: (RpoS regulator RNA A)participate in the positive regulation of RpoS translation.RprA also appears to bind to the RpoS lead.[127]
rtT RNA: is probably released from the primary transcript of tyrT during tRNA processing and suggest a modulatory effect on stringent response.[89]
RyhB RNA: down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur (Ferric uptake regulator).[4,90]
sar RNA: an antisense RNA that is partly responsible for the negative regulation of antirepressor synthesis during development of bacteriophage P22.[6,33]
satellite RNA: [91]
scAlu RNA: found in cytoplasm and transcripted from alu repeat. This class is specific to primates.[92]
scaRNA: a class of small RNA molecules that found within the cajal bodies are involved in chemical modifications of snRNAs.[93]
ScYc RNA: is present throughout embryonic development and is localized in the yellow crescent. It is associated with the cytoskeleton and segregated to the muscle cells during ascidian embryogenesis. The ScYc RNA may be a new member of a growing family of noncoding RNAs that play important roles in growth and development.[4,94]
self-splicing ribozyme RNA ( include Hairpin ribozyme RNA and Hammerhead ribozyme RNA): Hairpin ribozyme RNA is found in RNA satellites of plant viruses and catalyses a self-cleavage reaction to process the products of rolling circle virus replication to unit-length satellite RNA. Hammerhead ribozyme RNA have an endonuclease function, and most often are autocatalytic.[6,47,48]
snoRNA: a class of small RNA molecules that found within the nucleolus are involved in chemical modifications of ribosomal RNAs (rRNAs) and other RNA genes, for example by methylation and pseudouridylation.[64,95,6]
snRNA: a class of small RNA molecules that are found within the nucleus of eukaryotic cells. They are involved in a variety of important processes such as RNA splicing (removal of introns from hnRNA). They are always associated with specific proteins, and the complexes are referred to as small nuclear ribonucleoproteins (snRNP) or sometimes as snurps.[96,97,64]
sok RNA: inhibits hok mRNA translation by preventing ribosome entry at the hok mRNA 5'-end.[98,99]
spot 42 RNA (spf): involved in wild-type DNA polymerase I activity and is responsible for selective inhibition of translation of a particular gene (galK) within the mRNA transcribed from the galactose operon. spot 42 RNA occludes interaction of the ribosome with the galK Shine-Dalgarno sequence.[100,101]
spx RNA: chimeric RNA,originated as an insertion of a retroposed sequence of the ATP synthase chain F gene at the cytological region 60DB since the divergence of Drosophila melanogaster from its sibling species 2-3 million years ago. This retrosequence, which is located at 102F on the fourth chromosome, recruited a nearby exon and intron, thereby evolving a chimeric gene structure.[129]
SRA RNA: has been found to function as a specific co-activator of several steroid receptors, including receptors for androgens, estrogens, glucocorticoids and progestins. SRA RNA is associated in a ribonucleoprotein complex with the steroid receptor coactivator 1 (SRC-1). Expression of different isoforms is cell-type-specific.[4,102]
srnC RNA: antisense RNA of srnB mRNAs.[103,104]
SRP RNA: an RNA-protein complex present in the cytoplasm of cells that binds to the mRNA of proteins that are destined for secretion from the cell.[105,106,107]
telomerase RNA: a RNA component of ribonucleoprotein reverse transcriptase that synthesises telomeric DNA.[108,109]
tmRNA (10Sa RNA, ssrA): liberates the mRNA from a stalled ribosome and have been identified in eubacteria and some chloroplasts but are absent from archaeal and eukaryote nuclear genomes.[6,110,111]
t-ncb RNA: expressed only in CTLs.[4,112]
TPSI1 RNA: tomato (Lycopersicon esculentum L.) phosphate starvation-induced gene (TPSI1).The TPSI1 transcripts are rapidly induced in roots and leaves during Pi starvation which suggest that TPSI1 gene expression may be a part of the early Pi starvation response mechanism in plants.[4,113]
Tsix RNA: an antisense gene to Xist whose major promoter is located 15 kb downstream of the Xist gene. The primary transcript of Tsix covers at least 40 kb and overlaps full length of Xist. Tsix transcript undergoes complex processing (alternative splicing, polyadenylation). [4,114]
TTY2 RNA: identified as Y chromosome linked testis specific transcripts. They are expressed in adult and fetal testis and the adult kidney.[4,115]
UBE3A antisense RNA: is transcripted from imprinted region and maternally expressed. Antisense to Ubiquitin-protein ligase E3A mRNA.[116]
UptR RNA: restores viability by a new way of suppressing toxicity in E. coli.[117]
VA RNA: is found in adenovirus. It plays a role in regulating translation.[6,118]
vault RNA (vRNA): found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.[6,119]
XIST RNA: required for X chromosome inactivation.[120,121]
Xlsirt RNA: found in the vegetal cortex of Xenopus oocytes and suggested that they constitute structural components responsible for the localization of other RNAs.Xlsirt was shown for to be responsible for the localization of the Vg1 mRNA, which becomes dispersed after destruction of the Xlsirt RNAs with antisense oligodeoxynucleotides.[4,122]
Y RNA: components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins.[123,124]
ZNF127 AS RNA: antisense transcript in the Prader-Willi syndrome critical region ,imprinted region.[125]
snlRNA: small nuclear-like RNA, snlRNAs have a distinct motif(IM3) mostly located in the 3'-terminal half of the transcipts.[130]
sbRNA: stem-bulge RNA, sbRNAs have two distinct motifs(IM1 and IM2) located at the 5'- and 4'-termini.[130]
piRNA: Piwi-interacting RNA, frequently 29 to 30 nucleotides in length, often clustered in the genome.[131,132]
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