ライフサイエンスコーパス: fugu

1 r the Japanese pufferfish Takifugu rubripes (fugu).

2 roximity to the Herc2 gene in both mouse and Fugu.

3 of more distant organisms such as human and fugu.

4 genome that are conserved between human and Fugu.

5 o human chromosome 20 are also duplicated in Fugu.

6 ng to their endogenous expression pattern in fugu.

7 size of the intergenic region is smaller in Fugu.

8 esence of RAG transcripts in kidney of adult Fugu.

9 eral mesoderm may account for pelvis loss in fugu.

10 among human, mouse, chicken, zebrafish, and Fugu.

11 s, with a portion of a third Hoxa cluster in fugu.

12 logs such as human and chicken, or human and fugu.

13 eptors in both zebrafish and the pufferfish, Fugu.

14 and those being conserved between human and fugu.

15 crosatellite occurs every 1.876 kb of DNA in Fugu, 11.55% of the microsatellites are detected in open

16 f proteins found in individual datasets) and Fugu (14%) secretomes based on analysis of their nearly

17 divergence, we have cloned and sequenced the Fugu 5-HT type 1 receptor genes by Polymerase Chain Reac

18 hibits 58% sequence identity to the putative Fugu ACS and approximately 30% sequence identity to plan

19 In fugu, all b-paralogs diverge faster than the a-paralogs,

20 Interestingly, the Fugu alpha5 counterpart appears to be a non-alpha subuni

21 We have identified four Hox complexes in Fugu and found an unprecedented degree of variation when

22 nservation of intron/exon boundaries between Fugu and human CFTR and revealed extensive homology betw

23 difference in the organization of homologous Fugu and human genes has been reported.

24 Conserved linkages between Fugu and human genes indicate the preservation of chromo

25 with the conclusion that the gene number in Fugu and human genomes is approximately the same.

26 , gene orders are not well conserved between Fugu and human, with only very short sections of two to

27 ng a high degree of synteny in both species, Fugu and human.

28 lion years of divergent evolution separating Fugu and human.

29 efore hypothesized that by juxtaposing human/Fugu and human/mouse conservation patterns we can define

30 tion of regions of conserved synteny between Fugu and humans would greatly accelerate the mapping and

31 s the largest, most AT-rich gene examined in Fugu and is also the most highly compressed.

32 he syntenic relationship between mammals and Fugu and looked at the efficacy of ORF prediction from s

33 n the Fugu genome and the similarity between Fugu and mammalian genes.

34 cation of homologous coding sequence between Fugu and mammalian genes.

35 er overall similarity is present between the Fugu and mammalian proteins.

36 we cloned putative regulatory regions of the fugu and medaka Hoxa2(a) and -(b) genes and assayed thei

37 e test showed that zebrafish per1a/per1b and fugu and medaka per2a/per2b have asymmetric evolutionary

38 nked LMP7 pseudogene, indicating that within Fugu and potentially other teleosts, there has been an a

39 Pufferfish such as fugu and tetraodon carry the smallest genomes among all

40 basic motifs are conserved in the predicted Fugu and Tetraodon proteins.

41 plete opsin gene families from the sequenced fugu and Tetraodon pufferfish genomes.

42 The entire coding regions of both the Fugu and Tetraodon SART1 genes are contained within sing

43 The Fugu and Tetraodon SART1 genes encode putative proteins

44 or may have occurred after the divergence of Fugu and the tetrapod lineage.

45 We also demonstrate that Fugu and zebrafish have two and three MCHR genes, respec

46 We show that the teleost fish, Fugu and zebrafish, have two ribeye genes, ribeye a and

47 n event to be dated before the separation of Fugu and zebrafish.

48 f human, chimpanzee, mouse, rat, pufferfish (Fugu) and zebrafish demonstrates that these six genes sh

49 ative assignments with tetraodon, zebrafish, fugu, and medaka resulting in assignments of homology fo

50 a and per1b, one per2, and one per3; medaka, fugu, and tetraodon each have two per2 genes, per2a and

51 ud outgrowth and initiation fail to occur in fugu, and that pelvis loss is associated with altered ex

52 In contrast to human, the Fugu APP gene spans less than 10 kb of DNA, with the int

53 genomic sequences spanning the human and the Fugu APP genes were analysed with a set of exon and gene

54 dicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had

55 the frequently occurring microsatellites in Fugu are known to code in other species for regions in p

56 d upstream of exon 9 is present in human and Fugu but absent in mouse.

57 sea urchin REJ protein was also confirmed in Fugu but found to extend over 1000 amino acids.

58 To date, this syntenic association of the Fugu C4 and other MHC class III region genes has not bee

59 The Fugu C4 gene, orthologous to the tetrapod C4 gene, encom

60 The Fugu C4 protein demonstrates the presence of 25 conserve

61 The 11 exons of the Fugu C9 gene share 33% identity with human C9 and span 2

62 Fugu C9 was cloned and sequenced as a first step in an a

63 These results demonstrate that the Fugu C9/DOC-2 locus is a region of conserved synteny.

64 man chromosome 9q22, and lie adjacent to the Fugu C9/DOC-2 locus, indicating the boundary between two

65 laced by the corresponding sequence from the Fugu CaR remained fully functional.

66 wever, the immediate 5' regions of human and Fugu CFTR are highly divergent with few conserved sequen

67 budding and fission yeast, worm, fruit fly, fugu, chicken, dog, rat, mouse, chimp and human.

68 The two contigs have been mapped to separate Fugu chromosomes.

69 Our data show that: Fugu clusters are widely variant with respect to length;

70 nd analyzed >50,000 shotgun clones from 1059 Fugu cosmid clones.

71 rfeit genes in higher vertebrates, but these Fugu CpG islands are similar to the nonclassical islands

72 The intron-exon organization of Fugu CPS III is identical with that of rat CPS I, althou

73 the equivalent genomic fragments of rat and Fugu CPS span 87.9 and 21 kb, respectively.

74 nd contrasted this set to existing human and fugu datasets.

75 and studied their expression patterns during fugu development.

76 e used to query two orders of magnitude more Fugu DNA (i.e. 11.338 Mb).

77 Initial characterization of 128 kb of Fugu DNA attributed the compactness of this genome, in p

78 C2 genes have been identified in mouse, rat, Fugu, Drosophila, and in the yeast Schizosaccharomyces p

79 Gene expression analysis in fugu embryos by in situ hybridization revealed evolution

80 Genome-scale comparisons of noncoding human/Fugu evolutionary conserved elements (ECRs) and their hu

81 The Fugu fish has a fibrocystin-L ortholog but no fibrocysti

82 was inferred by comparison with an outgroup, Fugu for human-mouse and human for mouse-rat.

83 To characterize the structure of Fugu G-protein coupled receptor family and its evolution

84 The Fugu gene contains only one intron located in the 5' unt

85 The Fugu gene for RED2 is unusually large, spanning more tha

86 Here, Fugu gene homologs of all six Surfeit genes (Surf-1 to S

87 hout the protein coding region, although the Fugu gene is five times smaller than the mouse gene.

88 show that these are highly reliable for the Fugu gene with lower false positive and false negative r

89 u genes; in general, levels of compaction of Fugu genes are consistent with the isochore locations of

90 Unlike other species, we find the Fugu genes contain introns, one of which is in a conserv

91 vivo which sheds doubt on the usefulness of Fugu genes for transgenesis.

92 Both Fugu genes have 21 exons; a gene structure similar to th

93 It has also been proposed that Fugu genes may provide natural mini-genes for the produc

94 We have used sequence similarity to the Fugu genes to identify a human SNA EST and mapped this b

95 The protein sequences of the Fugu genes vary in their overall level of similarity to

96 We have cloned seven Fugu genes which are closely linked to Surfeit genes in

97 ligand binding have been conserved in these Fugu genes.

98 th those for a number of previously reported Fugu genes; in general, levels of compaction of Fugu gen

99 ncoding ECRs without the assistance of human-Fugu genome alignments and provides a very efficient fil

100 The combination of Fugu genome analysis and transgenesis in a mammal is a p

101 om data set covers nearly 25 Mb (>6%) of the Fugu genome and forms the basis of a series of whole gen

102 inked to Surfeit genes in two regions of the Fugu genome and have mapped and ordered their human homo

103 eports of synteny and gene order between the Fugu genome and human genes.

104 rmatic searches of Zebrafish, Tetraodon, and Fugu genome and other teleost expressed sequence tag dat

105 garding gene density and distribution in the Fugu genome and the similarity between Fugu and mammalia

106 , some of the genes that are adjacent in the Fugu genome are separated by at least 2-4 Mb in the huma

107 These findings support the proposal of the Fugu genome as a tool for human gene analysis.

108 Analysis of the EST data compared with the Fugu genome data predicts that approximately 10,116 gene

109 also found when zfIFN was used to search the fugu genome database, demonstrating that zfIFN can be us

110 We propose two uses for the Fugu genome in the study of NRs: the isolation of novel

111 project highlights the utility of using the Fugu genome in this kind of study.

112 This region of the Fugu genome shows conservation of synteny with 800-kb se

113 The suitability of the Fugu genome to facilitate the identification of candidat

114 Our observations support the use of the Fugu genome to study vertebrate gene structure, to predi

115 The Fugu genome, with eight times less DNA but a similar gen

116 ptors), we found 68 nuclear receptors in the Fugu genome.

117 enes are found at three separate loci in the Fugu genome.

118 rved, single copy, and linked to TSC2 in the Fugu genome.

119 for human, chimp, mouse, rat, zebrafish and fugu genomes are available for free download at http://w

120 etect HCTs in the human, mouse, chicken, and fugu genomes, and examined their association with cis-re

121 um, rat, mouse, chicken, frog, zebrafish and fugu genomes.

122 p with the zebrafish, medaka, tetraodon, and fugu genomes.

123 by aligning the human and Takifugu rubripes (Fugu) genomes.

124 rthermore, we show for the first time that a Fugu genomic construct can produce protein in transgenic

125 Southern blot hybridisation of Fugu genomic DNA confirmed the SART1 gene to be single c

126 contig maps have been constructed across two Fugu genomic regions containing the orthologs of human g

127 as identified following exon prediction from Fugu genomic sequence.

128 In this system, the assembled Fugu genomic sequences (also known as scaffolds) are ann

129 icacy of ORF prediction from short, unedited Fugu genomic sequences.

130 ough the clonesearch web page located at the Fugu Genomics website.

131 Fugu has a haploid genome of 400Mb and contains the same

132 on of duplicated HoxA genes in zebrafish and fugu has been investigated.

133 Fugu has two genes homologous to Red1 that are similar i

134 The puffer fish Fugu rubripes (Fugu) has a compact genome approximately one-seventh the

135 Fugu rubripes (Fugu) has one of the smallest recorded vertebrate genome

136 n, mouse, and pufferfish (Takifugu rubripes (Fugu)) have revealed a set of extremely conserved noncod

137 We have generated mice transgenic for the Fugu HD gene and conducted a detailed expression analysi

138 The Fugu HD gene is incorrectly processed in mouse cells bot

139 In Fugu tissue, the Fugu HD gene was found to be expressed as predicted from

140 The human and Fugu HD genes cover 170 kb and 23 kb respectively and ha

141 Fugu Hlx is expressed in a tissue-specific manner that i

142 in an attempt to characterize the region in Fugu homologous to human chromosome 5p13.

143 We have used the Fugu homologue of the Huntington's disease (HD) gene to

144 The Fugu-Human Genome Synteny Viewer has been tested by comp

145 The Fugu-human genome synteny views are available for each F

146 d be incompatible with the production of the Fugu huntingtin protein.

147 r the dachshund gene, which displays a human-Fugu identity of 84% over 424 basepairs (bp).

148 Analysis of the Fugu INK4A/B gene and the surrounding 40-kb of genomic D

149 was used to engineer the spliceability of a Fugu intron in human cells by insertion of specific sequ

150 veloped to predict the splicing phenotype of Fugu introns in mammalian systems and was used to engine

151 Although the genome of Fugu is 7.5 times smaller than the human genome, not all

152 n 1 and intron 9 element common to human and Fugu is absent in mouse.

153 Fugu is becoming established as the model vertebrate gen

154 e (bp) of all microsatellites, the genome of Fugu is similar to the genome of many other vertebrate s

155 The DRADA gene from Fugu is three-fold compacted with respect to the human g

156 ever, a teleost species such as zebrafish or Fugu is typically used as the outgroup in current tetrap

157 The genome of the pufferfish, Fugu rubripes (Fugu) is compact.

158 malian genome in a tail-to-tail orientation, Fugu IT and VT genes are linked head to tail and are sep

159 duced into the rat genome, we found that the Fugu IT gene was specifically expressed in rat hypothala

160 A contiguous stretch of 46 kb spanning the Fugu IT-VT locus has been sequenced, and nine putative g

161 When a cosmid containing the Fugu IT-VT locus was introduced into the rat genome, we

162 ptors, including two MC5R orthologues, while Fugu, lacking MC3R, has only four.

163 emonstrated that the compact promoter of the Fugu lck contains regulatory elements that direct expres

164 The short promoter of the Fugu lck isolated by us offers a powerful tool for label

165 The promoter region of the Fugu lck spans only 4.2 kb and contains a proximal and a

166 u, which are present as a cluster within the Fugu MHC class I region.

167 t whole-genome shotgun assemblies reveal the Fugu MHC-related cluster of genes to be flanked predomin

168 All of the six identified Fugu MHC-related genes have been characterised at the ge

169 The Fugu nAChR gene structures are considerably more diverse

170 We show, using RT-PCR, that the Fugu nAChR subunits are expressed in a variety of tissue

171 efined threshold identifies 90% of all human/Fugu noncoding ECRs without the assistance of human-Fugu

172 ant number of evolutionarily conserved human-Fugu noncoding elements function as tissue-specific tran

173 erfish Takifugu rubripes (fugu), we isolated fugu orthologs of genes thought to be essential for limb

174 Potential Fugu orthologs of neuronal nAChR subunits alpha2-4, alph

175 wed that each human receptor had one or more Fugu orthologs, excepting CAR (NR1I3) and LXRbeta (NR1H2

176 PXR, VDR and PPARalpha/gamma/delta) to their Fugu orthologs.

177 have cloned the genomic region encoding the Fugu PKD1 gene.

178 Fugu PKD1 spans 36 kb of genomic DNA and has greater com

179 The tenth PKD domain of human and Fugu polycystin-1 show extensive conservation of surface

180 Fugu possesses an expanded set of alpha7-9-like subunits

181 nd conservation of synteny between human and Fugu predict one gene to be an INK4A or INK4B homologue

182 been generated, covering almost one-third of Fugu predicted genes.

183 absence of conserved promoter sequences, the Fugu promoter was found to be functional in mouse cells.

184 In fugu (puffer fish), expression of SCPP genes is also det

185 dicating that the majority of the additional Fugu receptors are likely to be functional.

186 All 68 Fugu receptors had a clear human homolog, thus defining

187 All of the Fugu receptors that were analyzed by PCR in this study w

188 Although both Fugu regions are syntenic with human chromosome band 9q3

189 This project provides new Fugu resources, and the analysis adds significant weight

190 Interspecific comparison of the remaining fugu RH2-2 coding sequence paradoxically indicates that

191 k of frameshift or nonsense mutations in the fugu RH2-2 pseudogene suggests that the gene was lost ve

192 In fugu, RH2-2 apparently ceased to function very recently

193 rafish with the same construct, we show that Fugu RNA is processed correctly in zebrafish but not in

194 s of the genome database for the pufferfish, Fugu rubrides, identified a goldfish ISG15 (gfISG15) hom

195 The puffer fish Fugu rubripes (Fugu) has a compact genome approximately

196 Fugu rubripes (Fugu) has one of the smallest recorded ve

197 The genome of the pufferfish, Fugu rubripes (Fugu) is compact.

198 ed 60 kb of genomic DNA from the puffer fish Fugu rubripes (Fugu) that includes the CFTR gene.

199 The puffer fish ( Fugu rubripes ) has a compact genome of 400 Mbp which is

200 d characterization of a Japanese pufferfish, Fugu rubripes achaete-scute homolog 1, Fash1.

201 ormone ethylene, have recently been found in Fugu rubripes and Homo sapiens.

202 A sequence of the APP gene in the pufferfish Fugu rubripes and Tetraodon fluviatilis, respectively.

203 ene in the compact genomes of the pufferfish Fugu rubripes and Tetraodon nigroviridis.

204 yces cerevisiae, Drosophila melanogaster and Fugu rubripes appear to lack NARG2 orthologs.

205 to the wnt1 gene of the Japanese pufferfish Fugu rubripes confirms the compact structure of the geno

206 For example, genes from the pufferfish Fugu rubripes generally contain one or more introns that

207 quence is conserved in the mouse, bovine and Fugu rubripes genes.

208 The draft Fugu rubripes genome was released in 2002, at which time

209 The Japanese pufferfish Fugu rubripes has a 400 Mb genome with high gene density

210 he beta-amyloid precursor protein (APP) from Fugu rubripes has been completely sequenced.

211 The compact genome of Fugu rubripes has been sequenced to over 95% coverage, a

212 esting preliminary data from analysis of the Fugu rubripes homolog of APP has shown an unusually high

213 a putative CB2 ortholog in the puffer fish (Fugu rubripes T012234) suggests it may encode a CBR othe

214 in more detail, we searched the pufferfish (Fugu rubripes) and zebrafish (Danio rerio) genomes for G

215 e compact genome of the Japanese pufferfish (Fugu rubripes) containing portions of three genes that h

216 7q36 chromosomal region and the pufferfish (Fugu rubripes) genome.

217 then compared mouse, human, and pufferfish (Fugu rubripes) genomic sequences, and identified a conse

218 ned and sequenced 60 kb from the pufferfish (Fugu rubripes) lck locus.

219 d 65% identity to the human and puffer fish (Fugu rubripes) p55 sequences, respectively.

220 amprey (Petromyzon marinus), the pufferfish (Fugu rubripes), and the frog (Xenopus laevis).

221 this locus between human, mouse, pufferfish (Fugu rubripes), and, in part, zebrafish (Danio rerio).

222 is highly conserved in man, mouse, and fish (Fugu rubripes).

223 nstream of the wnt-1 gene in the pufferfish (Fugu rubripes).

224 ate species (human, mouse, rat, chicken, and Fugu rubripes).

225 of a non-human vertebrate (the teleost fish Fugu rubripes).

226 cterized the genomic structure of DRADA from Fugu rubripes, and compared the protein sequences of DRA

227 enes in the compact genome of the pufferfish Fugu rubripes, and examine the phylogenetic relationship

228 us of this unusual locus in the puffer fish, Fugu rubripes, and identified two INK4 genes using degen

229 ates, the mouse and the Japanese puffer fish Fugu rubripes, and investigated the genomic organization

230 enorhabiditus elegans, Arabidopsis thaliana, Fugu rubripes, and Toxoplasma gondii.

231 FATPs are found in such diverse organisms as Fugu rubripes, Caenorhabditis elegans, Drosophila melano

232 lood coagulation scheme for the puffer fish, Fugu rubripes, has been reconstructed on the basis of or

233 The compact genome of the pufferfish, Fugu rubripes, has proven a valuable tool in comparative

234 h Caenorhabditis elegans and the puffer fish Fugu rubripes, suggesting that this eIF-2alpha kinase pl

235 ied the Hox gene clusters of a teleost fish, Fugu rubripes, to test the possibility that Hox organiza

236 A putative IFN from puffer, Fugu rubripes, was also found when zfIFN was used to sea

237 from the reference genome of the pufferfish, Fugu rubripes.

238 isation of two top1 genes in the pufferfish, Fugu rubripes.

239 mologous genes from the Japanese pufferfish, Fugu rubripes.

240 b of genomic DNA of the Japanese pufferfish, Fugu rubripes.

241 from the genome of the Japanese pufferfish, Fugu rubripes.

242 ne in the compact model vertebrate genome of Fugu rubripes.

243 f the TSC2 gene in human and the pufferfish, Fugu rubripes.

244 gest homology to the sushi-ichi element from Fugu rubripes.

245 identified in mammals and in the puffer fish Fugu rubripes.

246 ation of the complement component C4 gene in Fugu rubripes.

247 are conserved in human-pufferfish, Takifugu (Fugu) rubripes, or ultraconserved in human-mouse-rat.

248 The annotations for each Fugu scaffold are computed, stored and made publicly ava

249 genome synteny views are available for each Fugu scaffold through the clonesearch web page located a

250 For each significant human gene match on the Fugu scaffold, the corresponding human chromosome map an

251 coding sequence is highly homologous to the Fugu sequence, suggesting that upregulation of CFTR in t

252 Comparative analysis of Fugu sequences homologous to very AT-rich regions in the

253 e both resources and data from the genome of Fugu so that everything may be integrated into a single,

254 cripts from human, mouse, rat, zebrafish and fugu species.

255 mammalian and avian homologs except for the Fugu Surf-6 gene, which was found to lack an intron pres

256 The Fugu Surfeit gene homologs appear to be associated with

257 These data demonstrate that the zebrafish:Fugu system is a powerful and convenient tool for dissec

258 ngle Hoxa2 gene in most vertebrates, whereas fugu (Takifugu rubripes) and medaka (Oryzias latipes) ha

259 er1b in zebrafish and per2a/per2b in madaka, fugu, tetraodon, and stickleback are ancient duplicates.

260 and E4TF1-60 are 49- and 24-fold smaller in Fugu than in human, and the intergenic distance is compr

261 omic DNA from the puffer fish Fugu rubripes (Fugu) that includes the CFTR gene.

262 ebrafish, medaka, threespine stickleback and fugu, the amphibian Xenopus tropicalis, the monotreme pl

263 iple sequence alignment of human, mouse, and Fugu, the putative WNT2 promoter sequence is shown to co

264 son included expression analysis across five Fugu tissue types.

265 In Fugu tissue, the Fugu HD gene was found to be expressed

266 nerated from 15 different adult and juvenile Fugu tissues, 74% of which matched protein database entr

267 The utility of Fugu to facilitate human disease gene identification by

268 Contigs are centered around two Fugu topoisomerase1 (top1) genes that were initially ide

269 The medaka and fugu TRs, when assembled with their telomerase reverse t

270 As in mammalian genomes, the Fugu TSC2 and PKD1 genes are adjacent in a tail-to-tail

271 s suggests that the duplication event of the Fugu type 1A receptor may have occurred after the diverg

272 is loss in the pufferfish Takifugu rubripes (fugu), we isolated fugu orthologs of genes thought to be

273 a-regulated beta-type proteasome subunits in Fugu, which are present as a cluster within the Fugu MHC

274 g human, mouse, pig, Xenopus, zebrafish, and Fugu, with highly conserved nucleotide and deduced amino

275 otein in transgenic zebrafish: a full-length Fugu WT1 transgene with a C-terminal beta-galactosidase