ライフサイエンスコーパス: pseudogene

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

2 ng, and chromatin marks associated with each pseudogene.

3 . thaliana ARC1 ortholog is a highly decayed pseudogene.

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

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

6 s work that suggested that the MHV-1 HE is a pseudogene.

7 vergence from its paralog without becoming a pseudogene.

8 ied 14 protein-coding genes and one putative pseudogene.

9 s signs of degenerating into a non-expressed pseudogene.

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

11 , a gene currently classified as a suspected pseudogene.

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

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

14 660 cancer samples for somatically acquired pseudogenes.

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

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

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

18 peline correspond to annotated nonfunctional pseudogenes.

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

20 estimates for the globin and immunoglobulin pseudogenes.

21 amination were expressed non-coding RNAs and pseudogenes.

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

23 ternative isoforms or potentially translated pseudogenes.

24 ial identification of potentially functional pseudogenes.

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

26 cificity and functions of selected expressed pseudogenes.

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

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

29 we analyze the interrelationship of SDs and pseudogenes.

30 ed repetitive elements (SINEs) and processed pseudogenes.

31 r small ORFs in annotated noncoding RNAs and pseudogenes.

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

33 n, 15 kb of DNA in single-copy Y-chromosomal pseudogenes.

34 d from genes that were previously considered pseudogenes.

35 sites than for synonymous sites, introns, or pseudogenes.

36 sion of the PseudoPipe pipeline) to identify pseudogenes.

37 we attempt to recover "fossilized" ancestral pseudogenes.

38 e cytochrome b6f complex were inferred to be pseudogenes.

39 ative splicing, non-coding transcription and pseudogenes.

40 s tend to be enriched with a large number of pseudogenes.

41 photosynthetic liverwort was detected in six pseudogenes.

42 y chorion genes and transcriptionally active pseudogenes.

43 f making functional and stable proteins from pseudogenes.

44 plant genomes are in the process of becoming pseudogenes.

45 tudied 16 full-length protein equivalents of 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 ew coding sequences had been predicted to be pseudogenes, 151 (approximately 35%) reveal apparent err

50 dy we analyzed the sequences of 20 genes and pseudogenes (22,814 nucleotides).

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

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

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

54 The 5Bq homoeoalleles became a pseudogene after allotetraploidization.

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

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

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

58 The M. lepromatosis pseudogenes analyzed that were also pseudogenes in M. le

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

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

61 In humans, CHIA-L1 (hCHIA-L1) is an apparent pseudogene and has the highest homology to CHIA.

62 Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) dist

63 her nonsynonymous mutations mapped to a pmpG pseudogene and to predicted coding sequences encoding a

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

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

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

67 olate has the largest genome with the fewest pseudogenes and IS elements suggests that this isolate's

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

69 obacterium leprae are mostly associated with pseudogenes and may be contributing to gene loss followi

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

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

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

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

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

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

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

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

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

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

80 The Y. pestis nghA ortholog is a pseudogene, and overexpression of functional nghA reduce

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

82 13,529 annotated soybean genes are putative pseudogenes, and 1736 currently unannotated sequences ar

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

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

85 WAGO-1 silences certain genes, transposons, pseudogenes, and cryptic loci.

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

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

88 and dolphin possess no functional V1Rs, only pseudogenes, and suffered inactivating mutations in the

89 s in the region, CG33221 and GP-CG32779, are pseudogenes, and the chimeric gene Crg1 is subject to ba

90 We integrate the pseudogene annotations with the extensive ENCODE functio

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

92 nswer research questions and to annotate our pseudogenes appropriately.

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

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

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

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

97 Pseudogenes are considered nonfunctional genomic artifac

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

99 Pseudogenes are defined as fragments of once-functional

100 Pseudogenes are degraded fossil copies of genes.

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

102 In rodents, only motilin receptor pseudogenes are identified.

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

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

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

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

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

108 Pseudogenes are thought to be inactive gene sequences, b

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

110 (<20x read depth) or high sequence homology (pseudogenes) are complemented by amplicon-based sequenci

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 eprae pseudogenes, suggesting that they were pseudogenes before divergence.

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

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

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

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

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

126 An inverted repeat pseudogene can also generate abundant small RNAs directl

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

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

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

130 Among the 115 pseudogenes confirmed in C. dubliniensis are orthologs o

131 In the 168 lineage, rpmGC is a pseudogene containing a frameshift mutation.

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

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

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

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

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

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

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

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

143 The conversion of rcsA to a pseudogene during Y. pestis evolution, therefore, was a

144 queried to discover information about human pseudogene evolution.

145 on genes in the F. tularensis subspecies are pseudogenes, explaining the unusually strong restriction

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

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

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

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

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

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

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

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

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

155 In addition, pseudogene families are associated with key statistics,

156 Pseudofam is a database of pseudogene families based on the protein families from t

157 Twis distinguish sRNAs derived from loci of pseudogene families, three types of DNA repeats, structu

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

159 oduction of CHC22 in mice, which have only a pseudogene for this protein, caused aberrant localizatio

160 All species examined had pseudogenes for trnI and trnA, however, deletions in the

161 Pseudogenes for trnV, trnI (GAU), and trnA (UGC) were se

162 as evidence of genome degradation, including pseudogene formation and chromosomal deletions, when com

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

164 e extensive degradation through deletion and pseudogene formation.

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

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

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

168 Here we show that a subset of pseudogenes generates endogenous small interfering RNAs

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

170 Pseudogenes have long been considered as nonfunctional g

171 Thus, it is possible that these "pseudogenes" have alternative, noncatalytic functions th

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

173 has higher percentage identity to the human pseudogene hCHIA-L1 (91.7%) than to hCHIA (84%).

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

175 RNA annotation capabilities, and support for pseudogene identification.

176 gene was present as a transposon-interrupted pseudogene in 12 of 47 isolates of nonclinical origin.

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

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

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

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

181 throughout the deuterostome lineage but is a pseudogene in humans and other primates.

182 dicating that this gene has been an inactive pseudogene in primates for at least 40 million years.

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

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

185 open reading frame, suggesting that rbf is a pseudogene in UAMS-1.

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

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

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

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

190 omatosis pseudogenes analyzed that were also pseudogenes in M. leprae showed nearly neutral evolution

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

192 Comparison of the pseudogenes in S. Gallinarum with those identified previ

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

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

195 rited retroposition: the source of processed pseudogenes in the genome.

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

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

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

199 Pseudogenes in virulence determinants suggest that the p

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

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

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

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

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

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

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

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

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

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

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

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

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

213 onless GLTP as a primate-specific, processed pseudogene marker.

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

215 Thus, processed pseudogenes might serve as fossilized footprints of the

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

217 cern mutations in PMS2 from mutations in its pseudogenes, more mutation carriers have been identified

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

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

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

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

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

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

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

225 ous IS elements, genomic rearrangements, and pseudogenes of C. burnetii isolates are consistent with

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

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

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

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

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

231 r which the orthologs in S. Typhi are either pseudogenes or are absent.

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

233 lling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected co

234 available for download from http://ontology.pseudogene.org.

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

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

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

238 Pseudogenes populate the mammalian genome as remnants of

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

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

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

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

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

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

245 Most importantly, pseudogenes provide an insight into prokaryotic evolutio

246 Pseudogenes (Psi) are nonfunctional genomic sequences re

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

263 tive ages were similar to those of M. leprae pseudogenes, suggesting that they were pseudogenes befor

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

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

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

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

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

269 el gene content and disparate collections of pseudogenes that may contribute to isolate virulence and

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

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

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

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

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

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

276 Pseudogene transcripts can provide a novel tier of gene

277 f functional chemosensory receptor genes and pseudogenes vary enormously among the genomes of differe

278 f duplication and rearrangement of genes and pseudogenes via a birth and death process primarily medi

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 ectively, but the level of matching for five pseudogenes was only 79.1%.

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

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

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

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

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

288 -tubulin monomers, though minor isoforms and pseudogenes were identified.

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

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

291 bout 4.6% of protein-coding genes seem to be pseudogenes, which is a relatively large fraction.

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

293 Replacement of the pseudogene with the functional Y. pseudotuberculosis rcs

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

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

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

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

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