ライフサイエンスコーパス: pseudogene

1 (PCR) assays targeting the opa gene and porA pseudogene.

2 , a gene currently classified as a suspected pseudogene.

3 ted by a frameshift mutation, resulting in a pseudogene.

4 d wheat, predicted to create a nonfunctional pseudogene.

5 ke in insects, an AGO duplicate has become a pseudogene.

6 ysis we propose that GGPPS5 (At3g14510) is a pseudogene.

7 Ptr1 in tomato and in Solanum pennellii is a pseudogene.

8 ng, and chromatin marks associated with each pseudogene.

9 . thaliana ARC1 ortholog is a highly decayed pseudogene.

10 ics of a functional gene while ifs becomes a pseudogene.

11 hlights an example of a non-functional toxin pseudogene.

12 y chorion genes and transcriptionally active pseudogenes.

13 f making functional and stable proteins from pseudogenes.

14 plant genomes are in the process of becoming pseudogenes.

15 tudied 16 full-length protein equivalents of pseudogenes.

16 cation were either absent or present only as pseudogenes.

17 660 cancer samples for somatically acquired pseudogenes.

18 well-known virulence factors, as well as 11 pseudogenes.

19 opose a model for the evolution of B-located pseudogenes.

20 n chromosome 1 (1q12-21), were thought to be pseudogenes.

21 me found 34 full-length TPS genes and 18 TPS pseudogenes.

22 peline correspond to annotated nonfunctional pseudogenes.

23 ht be explained by the activity of B-located pseudogenes.

24 estimates for the globin and immunoglobulin pseudogenes.

25 amination were expressed non-coding RNAs and pseudogenes.

26 in size and harbors three true genes and two pseudogenes.

27 ternative isoforms or potentially translated pseudogenes.

28 ial identification of potentially functional pseudogenes.

29 olved in de novo synthesis of folate are all pseudogenes.

30 cificity and functions of selected expressed pseudogenes.

31 otated open reading frames (ORFs), excluding pseudogenes.

32 ng for miRNAs might be a general activity of pseudogenes.

33 we analyze the interrelationship of SDs and pseudogenes.

34 ed repetitive elements (SINEs) and processed pseudogenes.

35 ns, a non-functional gene network of allelic pseudogenes.

36 ations, suggesting possible evolution toward pseudogenes.

37 uch as transposons, repetitive elements, and pseudogenes.

38 nal resistance genes and multiple resistance pseudogenes.

39 ene conversion of chromosomally encoded msp2 pseudogenes.

40 nt genes tend to give rise to many processed pseudogenes.

41 ere considered to be functional and 12 to be pseudogenes.

42 ssociation of transposable elements with SLF pseudogenes.

43 r small ORFs in annotated noncoding RNAs and pseudogenes.

44 d from genes that were previously considered pseudogenes.

45 ative splicing, non-coding transcription and pseudogenes.

46 sm respond to the artificial reactivation of pseudogenes?

47 Ten SNPs in (CRP pseudogene-1) CRPP1 and CRP genes were associated with s

48 ived RNAs, most prominently 5S ribosomal RNA pseudogene 141 (RNA5SP141), bound to RIG-I during infect

49 f a ProTalpha gene, thus far classified as a pseudogene 7.

50 (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes

51 seen in the largely uniform distribution of pseudogenes across the genome, their preservation in are

52 The 5Bq homoeoalleles became a pseudogene after allotetraploidization.

53 Notable differences arise in the pseudogene age distribution, with multiple retro-transpo

54 A reservoir of pseudogene alleles encoding the primary adhesin VlhA occ

55 stop codons in ORFs.PUK1orthologs and other pseudogenes also displayed stage-specific expression and

56 ch as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes o

57 Two exceptions were an unprocessed pseudogene and a bona fide lncRNA gene, both with open r

58 intergenic, antisense, and intronic but also pseudogene and enhancer loci.

59 le classes, including miRNA, piRNA, lincRNA, pseudogene and repeat elements.

60 n real data, GeneScissors reports 53.6% less pseudogenes and 0.97% more expressed and annotated trans

61 Two SLF pseudogenes and 28 potential protein-coding genes were i

62 a study to reproduce experiments that linked pseudogenes and cancer proves that understanding RNA net

63 on-coding RNAs such as long non-coding RNAs, pseudogenes and circular RNAs.

64 odels demonstrate the oncogenic potential of pseudogenes and indicate that ceRNA-mediated microRNA se

65 The classification identifies 140 novel pseudogenes and makes possible improved annotation for t

66 anded largely owing to an increase in naming pseudogenes and non-coding RNA genes, and we now have >3

67 ula (52) and Lotus japonicus (53), including pseudogenes and non-functional sequences that were ident

68 ight of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidops

69 RNAs, we considered the associations between pseudogenes and parental genes (targets).

70 ntronic, and intergenic transcripts but also pseudogenes and retrotransposons.

71 r, we have defined the relationships between pseudogenes and segmental duplications.

72 , we identified 127 CNDs that were processed pseudogenes and some of which were expressed.

73 bidopsis CDA family members except AtCDA are pseudogenes and that most plants only require a single C

74 which the A. thaliana assembly was updated, pseudogenes and transposon genes were re-annotated, and

75 ompetitive endogenous RNAs (such as the PTEN pseudogene), and methylation, whereas the tumor suppress

76 me, TLR11 is represented in humans only by a pseudogene, and the major question of how innate and ada

77 13,529 annotated soybean genes are putative pseudogenes, and 1736 currently unannotated sequences ar

78 ses carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements.

79 repeats, often result in duplicated genes or pseudogenes, and affect highly studied genes such as GBA

80 thesis about how messenger RNAs, transcribed pseudogenes, and long noncoding RNAs "talk" to each othe

81 t intergenic regions containing transposons, pseudogenes, and other repetitive sequences.

82 t only protein-coding but also RNA genes and pseudogenes, and outline the changes in approach and eth

83 ome methods by providing consistent gene and pseudogene annotations extended by similarity-based gene

84 We integrate the pseudogene annotations with the extensive ENCODE functio

85 ecific biological pathways; up-regulation of pseudogenes, antisense RNAs, and unannotated coding isof

86 nswer research questions and to annotate our pseudogenes appropriately.

87 The activity data of each pseudogene are stored in an associated resource, psiDR,

88 gether, we provide evidence that transcribed pseudogenes are a significant contributor to the transcr

89 everal tissues, raising the possibility that pseudogenes are also a potential source during the RNase

90 correspond to those encoded within the human pseudogenes are called retrocyclins.

91 Pseudogenes are considered nonfunctional genomic artifac

92 Even when identified, pseudogenes are considered to be rare and tend to be ign

93 Pseudogenes are defined as fragments of once-functional

94 Pseudogenes are degraded fossil copies of genes.

95 Pseudogenes are found in many genomes and are not always

96 As both resulting pseudogenes are homozygous in all human populations, we

97 Pseudogenes are ideal markers of genome remodelling.

98 In rodents, only motilin receptor pseudogenes are identified.

99 We find that pseudogenes are lineage specific, much more so than prot

100 Further, residual homeobox pseudogenes are observed in the three lineages.

101 re 93% nucleotide sequence identity, whereas pseudogenes are only 82% identical.

102 The majority of human pseudogenes are processed, resulting from a retrotranspo

103 On the contrary, pseudogenes are surprisingly prevalent and can persist f

104 Pseudogenes are thought to be inactive gene sequences, b

105 Finally, we find that ~15% of the mouse pseudogenes are transcribed, and that highly transcribed

106 hermore, in each strain about a fifth of all pseudogenes are unique, reflecting strain-specific evolu

107 expectation-maximization (EM) algorithm, and pseudogenes are utilized to construct appropriate statis

108 (<20x read depth) or high sequence homology (pseudogenes) are complemented by amplicon-based sequenci

109 tely distinguish between phenotype genes and pseudogenes (area under curve-receiver operating charact

110 remains complex due to the presence of many pseudogenes arising from whole-genome duplication-genera

111 ng the phosphatase and tensin homolog (PTEN) pseudogene as a model system, that antisense lncRNAs int

112 evidence, however, indicates novel roles for pseudogenes as regulators of gene expression.

113 mediated by piRNAs with retrotransposons and pseudogenes as regulatory sequences.

114 tribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression

115 man genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on

116 elective sweeps, so we see a large number of pseudogenes associated with highly duplicated families s

117 present a decision-tree approach to classify pseudogenes based on their (and their parents') characte

118 re enriched in the Breakpoint Cluster Region pseudogene (BCRP) block, suggesting the existence of a p

119 The KAT1 gene is annotated as a pseudogene because it contains two overlapping ORFs.

120 Nonfunctional unitary pseudogenes belonging to these pathways are found in sev

121 rexpress either the full-length murine B-Raf pseudogene Braf-rs1 or its pseudo "CDS" or "3' UTR" deve

122 show that HISN6B of Col-0 is not a defective pseudogene, but a stably silenced epiallele.

123 mline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not

124 over, we can precisely identify these parent pseudogenes by overlap with ancestral SD loci.

125 srupt chromatin organization while processed pseudogenes can create accessible chromatin.

126 Despite this many peptide identifications in pseudogenes cannot be annotated due to the absence of or

127 We identified 4010 pseudogene clusters and 146 clusters of fs-genes apparen

128 deletion rate resulted in a depletion of the pseudogene complement.

129 genome containing over a thousand predicted pseudogenes, comprising a third of its genome.

130 ce and limited genomic sequences indicates a pseudogene containing frame shifts and premature stop co

131 and tetarimycin) and to the silent, cryptic pseudogene-containing, environmental DNA-derived Lzr gen

132 ifferences between LLG and S26/3 to occur in pseudogene content, in transmembrane head/inc family pro

133 In vitro experiments demonstrated that pseudogenes contribute to cell transformation through se

134 Thirty-seven ITS pseudogenes could be easily detected according to nucleo

135 ns between CYP2D6 and evolutionarily related pseudogenes CYP2D7 and CYP2D8, high copy number variatio

136 hesion defects, independent of the expressed pseudogene DDX12p.

137 bacterial and one host marker, the putative pseudogene DeltaybgF and the mitochondrial gene COI, res

138 Interestingly, many of the pseudogene-derived proteins were predicted to be enzymes

139 molecular and cellular functional roles for pseudogene-derived proteins.

140 finding as well as functional annotation and pseudogene detection up to the generation of output read

141 sequences, while the sequence of the second pseudogene differed.

142 sed analysis reveals a significant number of pseudogenes differentially expressed among established t

143 ses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particul

144 nce/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovi

145 Here we report pseudogene efeU repair that restores the iron uptake sys

146 queried to discover information about human pseudogene evolution.

147 ressed among established tumour subtypes and pseudogene expression alone can accurately classify the

148 Our study highlights the potential of pseudogene expression analysis as a new paradigm for inv

149 dical significance and clinical relevance of pseudogene expression have not been assessed in a system

150 Here we generate pseudogene expression profiles in 2,808 patient samples

151 ancer types, the tumour subtypes revealed by pseudogene expression show extensive and strong concorda

152 Strikingly, in kidney cancer, the pseudogene expression subtypes not only significantly co

153 Characterization of pseudogene expression, however, has remained confined to

154 rce that enables high-throughput analyses of pseudogene expression.

155 We have built a knowledge base of human pseudogenes, extending the existing SO framework to inco

156 ion of a parent gene gives rise to a 'parent pseudogene', followed by further duplication creating du

157 letions appear to have the largest effect on pseudogene formation and loss of regulatory regions.

158 rotransposition of U6/L1 RNAs leads to U6/L1 pseudogene formation; and a unique cohort of U6/L1 chime

159 erse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 no

160 Additionally, all msp2 functional pseudogenes from two strains of A. marginale were detect

161 riptional consequences include expression of pseudogenes from UTRs or introns of target genes.

162 Although individual pseudogenes have been implicated in tumour biology, the

163 Pseudogenes have long been considered as nonfunctional g

164 ion; (iii) mutants with nonfunctional genes (pseudogenes) have been circulating and recombining for l

165 of short interspersed elements and processed pseudogenes, have made an indelible impact on the struct

166 ic orangutan Popy-A and the 5' part of human pseudogene HLA-Y, carried by approximately 10% of HLA ha

167 RNA annotation capabilities, and support for pseudogene identification.

168 h, pearleye (Benthalbella dentata), became a pseudogene in a similar fashion about 130 million years

169 pK, YapJ, and YapX) was present as a gene or pseudogene in a strain-specific manner and only in Y. pe

170 tously expressed second gene, which became a pseudogene in C(4) Flaveria species.

171 pose at 1-54 times the frequency of a marked pseudogene in HeLa HA cells.

172 lyses detected the transcription of a RNASE1 pseudogene in several tissues, raising the possibility t

173 AlthoughclpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence sug

174 r gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolution

175 ure of CPS10B, thereby identifying wcrG as a pseudogene in this serotype.

176 nes, but the 11 ndh genes are represented as pseudogenes in a small clade of 13 species.

177 ed approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle c

178 wever, in vivo evidence for a causal role of pseudogenes in cancer development is lacking.

179 g evidence for the functional involvement of pseudogenes in carcinogenesis and suggest MYLKP1 as a po

180 We also annotate 165 unitary pseudogenes in mouse, and 303, in human.

181 ast decade has suggested important roles for pseudogenes in physiology and disease.

182 In particular, it reveals that many pseudogenes in SDs likely did not arise directly from pa

183 ents, and this suggests that most duplicated pseudogenes in SDs were likely disabled around the time

184 Duplicated pseudogenes in the human genome are disabled copies of f

185 /mammalian split and relics of some exist as pseudogenes in the human genome.

186 The presence of numerous mitochondrial pseudogenes in the mitochondrial genomes of several spec

187 , we present a genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred

188 Analysis of the full complement of msp2 pseudogenes in the St.

189 There are 146 P450 genes, plus 11 pseudogenes, in M. domestica, representing a significant

190 result, for example, in recycling processed pseudogenes into mRNAs or lncRNAs with regulatory roles.

191 this, we asked: can we artificially express pseudogenes into novel and functional proteins?

192 ng RNA species, including natural antisense, pseudogenes, intronic long noncoding RNAs (lncRNAs), and

193 he transcriptional regulation of the B-CAP-G pseudogene is uncoupled from the standard regulation of

194 e first established that duplication of msp2 pseudogenes is common among A. marginale strains: all se

195 reductase (DHFR) previously thought to be a pseudogene known as dihydrofolate reductase-like protein

196 nt inbred lines were found to harbor Zmtps21 pseudogenes lacking conserved motifs required for farnes

197 Unlike the pseudogene-laden RAGEs of O. tsutsugamushi, REIS encodes

198 About 15% of the pseudogene-like fragments on Bs are transcribed in a tis

199 pseudogenes linked to HPs, homology modelling and non-co

200 Lethe, a pseudogene lncRNA, is selectively induced by proinflamma

201 regulates hundreds of lncRNAs, including 54 pseudogene lncRNAs, several of which show exquisitely se

202 These findings suggest that expression of pseudogenes lncRNAs are actively regulated and constitut

203 es possible improved annotation for the 3172 pseudogenes located in SDs.

204 PKD genetic diagnosis is complicated by PKD1 pseudogenes located proximal to the original gene with a

205 t a minimal segmental change in a duplicated pseudogene locus is sufficient for immune escape from th

206 how that piRNAs derived from transposons and pseudogenes mediate the degradation of a large number of

207 events and copy number-polymorphic processed pseudogenes missed by other methods.

208 usly annotated protein-coding genes, and 169 pseudogenes, most of them disabled after primates diverg

209 The human SIGLEC17P pseudogene mRNA is still expressed at high levels in hum

210 r "A coding-independent function of gene and pseudogene mRNAs regulates tumour biology" (Poliseno et

211 m 'A coding-independent function of gene and pseudogene mRNAs regulates tumour biology' by Poliseno e

212 One of the insertion mutations mapped to pseudogene Msed_1517 and extended its reading frame an a

213 e functionality of myosin light chain kinase pseudogene (MYLKP1) in human cells and tissues by RT-PCR

214 in-coding regions, which includes translated pseudogenes, non-coding RNAs and upstream open reading f

215 describe the extent of variation in gene and pseudogene numbers between individuals arising from inac

216 lular variability of mtDNA content and mtDNA pseudogenes (Numts) in nDNA.

217 osophila species that are predicted to carry pseudogenes of Gr64e had reduced glycerol sensitivity.

218 ubstitution (~1.4 x 10(-9)/site/year) of the pseudogenes of these aquatic species as well as some pro

219 The duplication of PKD1 exons 1-32 as six pseudogenes on chromosome 16, the high level of allelic

220 nd the duplication of PKD1 exons 1-33 as six pseudogenes on chromosome 16.

221 tion statistically reduced the corresponding pseudogene or gene (Figure 2G; Poliseno et al., 2010).

222 sis and M. leprae have since accumulated new pseudogenes or acquired specific deletions.

223 The seven remaining genes are pseudogenes or encode proteins that do not function cata

224 likely to be attributed to the expression of pseudogenes or other OCT4 variants.

225 An additional 220 genes (4.7%) are pseudogenes or phantom genes.

226 nbred mouse strains (available via the mouse.pseudogene.org resource).

227 to pervasive architectural flaws (including pseudogenes, parasitic mobile elements, and needlessly b

228 ed by blocks containing classical Patr-A and pseudogene Patr-H.

229 in ORFs in mouse transcripts, as are 74% of pseudogene peptides, 24% of uORF peptides and 32% of dOR

230 At one extreme, some pseudogenes possess conventional characteristics of func

231 In particular, we emphasized pseudogenes potentially relevant to this cancer.

232 the 1000 Genomes project, producing lists of pseudogenes potentially under selection.

233 etrotransposon insertions and 8000 processed pseudogenes (PPs) in the human genome.

234 ntracellular and symbiotic bacteria in which pseudogenes predominate, this review discusses the impor

235 Also, we see a uniform decay of pseudogene promoter activity relative to their coding co

236 Most importantly, pseudogenes provide an insight into prokaryotic evolutio

237 d by the PTEN tumour suppressor gene and its pseudogene PTENP1 and the critical consequences of this

238 tably impact expression of the corresponding pseudogene PTENP1.

239 aralogs of ITS sequences, including putative pseudogenes, recombinants, and multiple functional ITS c

240 spurious ORFs and to distinguish coding from pseudogene regions.

241 Moreover, we show that pseudogenes regulate mRNA stability via the piRNA pathwa

242 mplexity and functions, but the formation of pseudogenes remains a problem for this mechanism.

243 es, the identification and categorisation of pseudogenes remains problematic.

244 Consequently, we hypothesized that the msp2 pseudogene repertoire arose via gene duplication, allowi

245 The overall pseudogene repertoire in mouse is similar to that in hum

246 Pseudogenes represent open reading frames that have been

247 Thus, formation of processed pseudogenes represents a new class of mutation occurring

248 uplicated-duplicated or duplicated-processed pseudogenes, respectively.

249 s include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio

250 The covS sensor in M23ND was identified as a pseudogene, resulting in the attenuation of speB functio

251 filing data, we show that 40% of lncRNAs and pseudogene RNAs expressed in human cells are translated.

252 ypes together with its antisense transcribed pseudogene RPSAP52.

253 excludes potential artefacts emanating from pseudogenes, segmental duplications, and template switch

254 a natural host, as is a completely divergent pseudogene sequence in an otherwise conserved locus.

255 of disrupting allelic and non-allelic (e.g. pseudogene) sequences have received scant scrutiny and,

256 We describe a pseudogene sharing homology to exons 2 through 5 of huma

257 nsembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QT

258 ructure of the sm-amp-x gene and two related pseudogenes sm-amp-x-psi1 and sm-amp-x-psi2 allows traci

259 Here, we report a comparison of pseudogenes spanning three phyla, leveraging the complet

260 s to other cancer-related genes that possess pseudogenes, such as oncogenic KRAS.

261 In contrast, worm and fly pseudogenes tell a story of numerous duplication events.

262 more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurren

263 In addition, a somatic pseudogene that integrated into the promoter and first e

264 redominant V(D)J joining to a proximal Trdv3 pseudogene that lies just upstream of the normal boundar

265 verall, we reveal the roles of a transcribed pseudogene that may display properties of an oncofetal m

266 assemblies contain conserved alpha-defensin pseudogenes that are closely related to functional myelo

267 isingly prevalent, genome-wide expression of pseudogenes that could be categorized as ubiquitously ex

268 list also includes 41 candidate misannotated pseudogenes that encode primate-specific short proteins.

269 Oct4 splice-variant isoforms and transcribed pseudogenes that warrant further study.

270 Maries strain had two identical pseudogenes, the Florida strain had one whose sequence w

271 ell and includes both functional alleles and pseudogenes, the latter identified by mutations resultin

272 onstruct a PRG for 46 (mostly HLA) genes and pseudogenes, their genomic context and their characteriz

273 duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and tr

274 view discusses the importance of identifying pseudogenes to fully understand the abilities of bacteri

275 enes, and found a large ratio of partial and pseudogenes to intact OR genes (2:1), suggestive of a dy

276 sequences, but recent evidence of extensive pseudogene transcription raised the question of potentia

277 Here, we describe a systematic analysis of pseudogene "transcription" from an RNA-Seq resource of 2

278 Pseudogene transcripts can provide a novel tier of gene

279 This pseudogene was flanked by C. porcellus homologs of two g

280 tly, a non-coding RNA expressed from a human pseudogene was reported to regulate the corresponding pr

281 four open reading frames as intact genes or pseudogenes was found to differ between Francisella spec

282 types (i.e., protein coding, noncoding, and pseudogenes) was associated with islet expression levels

283 The pseudogene we describe is likely the product of a genomi

284 By analyzing a set of untranscribed pseudogenes we show that the Z-susceptibility just downs

285 elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor

286 ternatively spliced variants and transcribed pseudogenes were expressed in abundance.

287 neage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome.

288 However, 43 ORs, including several known pseudogenes, were different, such that mRNA expression d

289 It can help identify pseudogenes (which accumulate mutations), analyze raw DN

290 ignal was for AL118508, a non-protein coding pseudogene, which completely lies within CD93's genomic

291 Murine TLR10 is a disrupted pseudogene, which precludes investigation using classic

292 on of nucleotide substitutions per site in a pseudogene with its surrounding SD region allows us to e

293 Finally, we compare our pseudogenes with conservation and variation data from pr

294 nserved non-coding human elements are recent pseudogenes with conserved ancestral genes; and (ii) whe

295 coding counterparts and identify a number of pseudogenes with conserved upstream sequences and activi

296 id changes, including editing of 69PUK1-like pseudogenes with stop codons in ORFs.PUK1orthologs and o

297 n-less genes and inactive germline processed pseudogenes, with likely overlapping biosynthetic proces

298 d 107 novel transcripts and expression of 38 pseudogenes, with many demonstrating differential expres

299 a broad spectrum of biochemical activity for pseudogenes, with the majority in each organism exhibiti

300 post-genomic' applications: (i) when finding pseudogenes within the human genome, frameshift alignmen