• Genomics & Informatics
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• v.3 no.3
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• pp.80-85
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• 2005

HExDB is a database for analyzing exon and splicing pattern information in Homo sapiens. HExDB is useful for specific purposes: 1) to design primers for exon amplification from cDNA and 2) to understand the change of ORFs by alternative splicing. HExDB was constructed by integrating data from AltExtron which is the computationally predicted exon database, Ensemble cDNA annotation, and Affymetrix genome tile published recently. Although it may contain false positive data, HExDB is good starting point due to its sensitivity. At present, there areas many as 2,046,519 exons stored in the HExDB. We found that $16.8\%$ of the exons in the database was constitutive exons and $83.1\%$ were novel gene exons.

• Molecules and Cells
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• v.42 no.1
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• pp.8-16
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• 2019

Mutations in the ${\beta}-catenin$ gene (CTNNB1) have been implicated in the pathogenesis of some cancers. The recent development of cancer genome databases has facilitated comprehensive and focused analyses on the mutation status of cancer-related genes. We have used these databases to analyze the CTNNB1 mutations assembled from different tumor types. High incidences of CTNNB1 mutations were detected in endometrial, liver, and colorectal cancers. This finding agrees with the oncogenic role of aberrantly activated ${\beta}-catenin$ in epithelial cells. Elevated frequencies of missense mutations were found in the exon 3 of CTNNB1, which is responsible for encoding the regulatory amino acids at the N-terminal region of the protein. In the case of metastatic colorectal cancers, in-frame deletions were revealed in the region spanning exon 3. Thus, exon 3 of CTNNB1 can be considered to be a mutation hotspot in these cancers. Since the N-terminal region of the ${\beta}-catenin$ protein forms a flexible structure, many questions arise regarding the structural and functional impacts of hotspot mutations. Clinical identification of hotspot mutations could provide the mechanistic basis for an oncogenic role of mutant ${\beta}-catenin$ proteins in cancer cells. Furthermore, a systematic understanding of tumor-driving hotspot mutations could open new avenues for precision oncology.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.3
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• pp.309-312
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• 2004

We performed exon trapping in order to locate functional genes on chicken chromosomes (GGA) and to identify functional gene sequences from chicken cosmids. Sequence analysis of 100 clones revealed 17 putative exons, five of which were identified with known sequences in a gene database search: thymopoietin beta (TMPO), U5 snRNP-specific 40 kDa protein (HPRP8BP), dihydropyridine receptor alpha 1 subunit (CACNL1A3), cystein string protein (CPS) and C15orf4. We attempted to map the genes to chicken chromosomes by using FISH and linkage analysis. The chromosomal localizations were GGA1 (TMPO), GGA10 (C15orf4), GGA23 (HPRP8BP) and GGA28 (CPS) by FISH and linkage analysis, while that of CACNL1A3 was predicted to be on a microchromosome by FISH but not by linkage analysis. Comparative mapping analyses between chickens and humans for the genes revealed both known and new synteny. The syntenic conservation between GGA1 and human chromosome (HSA) 12q23 (TMPO) and between GGA10 and HSA15q25 (C15orf4), were consistent with a recent publication, while two new syntenies were observed between GGA28 and HSA20q13.3 in CPS and between GGA23 and HSA1p34-35 in HPRP8BP. The information of presently mapped genes can contribute as anchor markers based on functional genes and the construction of a comparative map.

• International Journal of Industrial Entomology and Biomaterials
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• v.15 no.2
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• pp.123-130
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• 2007

The Hsp 20.8 and Hsp 90 cDNA sequence retrieved from NCBI database and consists of 764 bp and 2582 bp lengths respectively. The corresponding cDNA homologus sequences were BLAST searched in Bombyx mori genomic DNA database and two genomic contigs viz., BAAB01120347 and AADK01011786 showed maximum homology. In B. mori Hsp 20.8 and Hsp 90 is encoded by single gene without intron. Specific primers were used to amplify the Hsp 20.8 gene and Hsp 90 variable region from genomic DNA by using the PCR. Obtained products were 216 bp in Hsp 20.8 and 437 bp in Hsp 90. There was no variation found in the six silkworm races PCR products size of contrasting response to thermal tolerance. The comparison of the sequenced nucleotide variations through multiple sequence alignment analysis of Hsp 90 variable region products of three races not showed any differences respect to their thermotolerance and formed the clusters among the voltinism. The comparison of aminoacid sequences of B. mori Hsps with dipteran and other insect taxa revealed high percentage of identity growing with phylogenetic relatedness of species. The conserved domains of B. mori Hsps predicted, in which the Hsp 20.8 possesses ${\alpha}-crystallin$ domain and Hsp 90 holds HATPase and Hsp 90 domains.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.7
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• pp.1019-1025
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• 2011

Toll-like receptors (TLRs) play an important role in the recognition of invading pathogens and the modulation of innate immune responses in mammals. The TLR4 and TLR7 are well known to recognize the bacterial lipopolysaccharide (LPS) and single stranded (ssRNA) ligands, respectively and play important role in host defense against Gram-negative bacteria and ssRNA viruses. In the present study, coding exon fragments of these two TLRs were identified, cloned, sequenced and analyzed in terms of insertion-deletion polymorphism, within bovine TLRs 4 and 7, thereby facilitating future TLR signaling and association studies relevant to bovine innate immunity. Comparative sequence analysis of TLR 4 exons revealed that this gene is more variable, particularly the coding frame (E3P1), while other parts showed percent identity of 95.7% to 100% at nucleotide and amino acid level, respectivley with other Bos indicus and Bos taurus breeds from different parts of the world. In comparison to TLR4, sequence analysis of TLR7 showed more conservation among different B. indicus and B. taurus breeds, except single point mutation at 324 nucleotide position (AAA to AAM) altering a single amino acid at 108 position (K to X). Percent identity of TLR7 sequences (all 3 exons) was between 99.2% to 100% at nucleotide and amino acid level, when compared with available sequence database of B. indicus and B. taurus. Simple Modular Architecture Research Tool (SMART) analysis showed variations in the exon fragments located in the Leucine Rich Repeat (LRR) region, which is responsible for binding with the microbial associated molecular patterns and further, downstream signaling to initiate anti-microbial response. Considering importance of TLR polymorphism in terms of innate immunity, further research is warranted.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.11
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• pp.4513-4518
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• 2014

The prevalence of BRCA1 gene mutations in breast cancer differs between diverse ethnic groups. Relatively little information is known about patterns of BRCA1 mutations in early-onset breast cancer in women of Uighur or Han descent, the major ethnic populations of the Xinjiang region in China. The aim of this study was to identify BRCA1 mutations in Uighur and Han patients with early-onset (age <35 years), and sporadic breast cancer for genetic predisposition to breast cancer. For detection of BRCA1 mutations, we used a polymerase chain reaction single-stranded conformation polymorphism approach, followed by direct DNA sequencing in 22 Uighur and 13 Han women with early-onset sporadic breast cancer, and 32 women with benign breast diseases. The prevalence of BRCA1 mutations in this population was 22.9% (8/35) among early-onset sporadic breast cancer cases. Of these, 31.8% (7/22) of Uighur patients and 7.69% (1/13) of Han patients were found to have BRCA1 mutations. In 7 Uighur patients with BRCA1 mutations, there were 11 unique sequence alterations in the BRCA1 gene, including 4 clearly disease-associated mutations on exon 11 and 3 variants of uncertain clinical significance on exon 11, meanwhile 4 neutral variants on intron 20 or 2. None of the 11 BRCA1 mutations identified have been previously reported in the Breast Cancer Information Core database. These findings reflect the prevalence of BRCA1 mutations in Uighur women with early-onset and sporadic breast cancer, which will allow for provision of appropriate genetic counseling and treatment for Uighur patients in the Xinjiang region.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3503-3507
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• 2013

Background: Although the majority of investigations concerned with TP53 and its protein have focused on coding regions, recently a set of studies highlighted significant roles of regulatory elements located in p53 mRNA, especially 5'UTR. The wrap53${\alpha}$ transcript is one of those that acts as a natural antisense agent, forming RNA-RNA hybrids with p53 mRNA and protecting it from degradation. Materials and Methods: In this study, we focused on the mutation status of exon $1{\alpha}$ of the WRAP53 gene (according to exon 1 of p53) in 160 breast tumor tissue samples and conducted a bioinformatics search for probable miRNA binding site in the p53/wrap53 overlapping region. Mutations were detected, using single stranded conformation polymorphism (SSCP) and sequencing. We applied the miRBase database for prediction of miRNAs which target overlapping region of p53/wrap53 transcripts. Results: Our results showed all samples to have wild type alleles in exon 1 of TP53 gene. We could detect a novel and unreported intronic mutation (IVS1+56, G>C) outside overlapping regions of p53/wrap53 genes in breast cancer tissues and also predict the presence of a binding site for miR-4732-5p in the 5'UTR of Wrap53 mRNA. Conclusions: From our findings we propose designing further studies focused on overexpression of miRNA-4732-5p and introducing different mutations in the overlapping region of wrap53 and p53 genes in order to study their effects on p53 and its ${\Delta}N$ isoform (${\Delta}$40p53) expression. The results may provide new pieces in the p53 targeting puzzle for cancer therapy.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.3
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• pp.449-456
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• 2018

Objective: Nanog, a homeodomain protein, has been investigated in humans and mice using embryonic stem cells (ESCs). Because of the limited availability of ESCs, few studies have reported the function and role of Nanog in porcine ESCs. Therefore, in this study, we investigated the location of the porcine Nanog chromosome and its basal promoter activity, which might have potential applications in development of ESCs specific marker as well as understanding its operating systems in the porcine. Methods: To characterize the porcine Nanog promoter, the 5'-flanking region of Nanog was isolated from cells of mini-pig ears. BLAST database search showed that there are two porcine Nanog genomic loci, chromosome 1 and 5, both of which contain an exon with a start codon. Deletion mutants from the 5'-flanking region of both loci were measured using the Dual-Luciferase Reporter Assay System, and a fluorescence marker, green fluorescence protein. Results: Promoter activity was detected in the sequences of chromosome 5, but not in those of chromosome 1. We identified the sequences from -99 to +194 that possessed promoter activity and contained transcription factor binding sites from deletion fragment analysis. Among the transcription factor binding sites, a Sp1 was found to play a crucial role in basal promoter activity, and point mutation of this site abolished its activity, confirming its role in promoter activity. Furthermore, gel shift analysis and chromatin immunoprecipitation analysis confirmed that Sp1 transcription factor binds to the Sp1 binding site in the porcine Nanog promoter. Taken together, these results show that Sp1 transcription factor is an essential element for porcine Nanog basal activity the same as in human and mouse. Conclusion: We showed that the porcine Nanog gene is located on porcine chromosome 5 and its basal transcriptional activity is controlled by Sp1 transcription factor.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.3
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• pp.328-333
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• 2007

Carboxypeptidase E (CPE) plays an important role in the regulation of the body fat content. Therefore, it has been suggested as candidate gene for traits related to meat quality in beef cattle. This study was conducted to identify single nucleotide polymorphisms (SNPs) in the CPE gene and to investigate association of SNP marker with carcass and meat quality traits in Korean cattle. Three SNPs were identified in the intron 4 (A309G SNP and C445T SNP) and exon 5 (C601T SNP) of the CPE gene by sequence analyses of CPE cDNA and genomic DNA samples. The sequences have been deposited in GenBank database with accession numbers AY970664 and AY970663. Genotyping of the gene-specific SNP marker was carried out using the PCR-RFLP with restriction enzymes DdeI for C445T SNP and NlaIII for C601T SNP. The frequencies of C and T alleles were 0.43 and 0.57 for C445T SNP and 0.42 and 0.58 for C601T SNP, respectively. Statistical analysis indicated that the C445T SNP showed a significant effect (p<0.05) on marbling score (MS) and breeding value of backfat thickness (BF-EBV), respectively. Animals with the CT genotype showed higher marbling score and backfat thickness than those with the TT genotype. This marker also showed a significant dominance effect for the MS and BF-EBV (p<0.05). However, no significant associations were observed between C601T SNP genotypes and all traits examined. The results suggest that the CPE gene may be used as a marker for carcass traits in Korean cattle.

• Journal of Animal Science and Technology
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• v.63 no.2
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• pp.248-261
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• 2021

Attributable to their major function in pathogen recognition, the use of bovine leukocyte antigens (BoLA) as disease markers in immunological traits in cattle is well established. However, limited report exists on polymorphism of the BoLA gene in zebu cattle breeds by high resolution typing methods. Thus, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 100 animals (Boran, n = 13; Sheko, n = 20; Fogera, n = 16; Horro, n = 19), Hanwoo cattle (n = 18) and Bangladesh Red Chittagong zebu (n = 14). Out of the 59 detected alleles, 43 were already deposited under the Immuno Polymorphism Database for major histocompatibility complex (IPD-MHC) while 16 were unique to this study. Assessment of the level of genetic variability at the population and sequence levels with genetic distance in the breeds considered in this study showed that Zebu breeds had a gene diversity score greater than 0.752, nucleotide diversity score greater than 0.152, and mean number of pairwise differences higher than 14, being very comparable to those investigated for other cattle breeds. Regarding neutrality tests analyzed, we investigated that all the breeds except Hanwoo had an excess number of alleles and could be expected from a recent population expansion or genetic hitchhiking. Howbeit, the observed heterozygosity was not significantly (p < 0.05) higher than the expected heterozygosity. The Hardy Weinberg equilibrium (HWE) analysis revealed non-significant excess of heterozygote animals, indicative of plausible over-dominant selection. The pairwise FST values suggested a low genetic variation among all the breeds (FST = 0.056; p < 0.05), besides the rooting from the evolutionary or domestication history of the cattle. No detached clade was observed in the evolutionary divergence study of the BoLA-DRB3 gene, inferred from the phylogenetic tree based on the maximum likelihood model. The investigation herein indicated the clear differences in BoLA-DRB3 gene variability between African and Asian cattle breeds.