Nucleotide sequence of the corrected DQB1*06011 allele

The DQB1*06011 allele first classified and registered with the codon ACC at position 51(1) was recently corrected to ACG by Dr. Akinori Kimura (2) and in independently confirmed in our laboratory (3). The correct nucleotide sequence for this allele is shown below. The DQB1*06011 allele was found in two sisters of Turkish nationality who had been serologically typed for class I as HLA-A11, A33, B44, B52, Cw4. Nucleotide sequencing based typing of HLA class II alleles disclosed DRB1*0701, *15021, DRB4*01011/*0103, DRB5*0102, DQA1*0103, *0201, DQB1*02, *06011, DPB1*0401,*11011.     

Nucleotide sequence of exons 2 and 3 of the novel HLA-Cw*12032 allele

A novel HLA-C nucleotide sequence was discovered in an individual of Pacific Island, Tongan ethnicity using sequencing based typing. The sequence was given an official allele designation HLA-Cw*12032 by the WHO Nomenclature Committee for Factors of the HLA System. The novel sequence has 2 bp substitutions compared to the HLA-Cw*1203 at codon 134 "T" to "C" and codon 135 "C" to "G". However, when converted to amino acid sequences HLA-Cw*1203 and HLA-Cw*12032 are identical and would not have direct clinical implications.     

Nucleotide sequence of a new HLA-DQB1 allele, DQB1*03033

HLA-genotyping by sequencing of the corresponding polymerase chain reaction (PCR) product allow the identification of a new HLA-DQB1 allele, DQB1*03033. To confirm the finding the entire exon 2 was sequenced.     

我国彝族另一新的DR15(2)等位基因的核苷酸序列分析

目的对在用ＰＣＲ／ＳＳＯ方法作我国彝族群体样本ＨＬＡＤ区寡核苷酸分型中发现的１例ＤＲＢ１的杂合子进行等位基因序列分析。方法用ＤＲＢ基因类引物扩增该特殊的ＤＲＢ１杂合子细胞基因组的ＤＲＢ基因的第二外显子。扩增产物经纯化转染大肠杆菌ＪＭ１０１,克隆后再经酚／氯仿抽提后得到单链Ｍ１３ＤＮＡ。利用ＡＢＩ３７７测序仪自动测序。结果彝族这一特殊的ＤＲＢ１杂合子细胞的ＤＲＢ１基因阳性克隆,经序列分析证实了该ＤＲＢ１杂合子中一个等位基因确为ＤＲＢ１＊１２０２,与ＰＣＲ／ＳＳＯ分型一致;另一个新等位基因ＤＲＢ１＊１５Ｙ２（暂定）等位基因在第二外显子的４７位由编码苯丙氨酸的ＴＴＣ（ＤＲＢ１＊１５０２）变为编码酪氨酸的ＴＡＣ。结论在云南彝族样本中发现的ＤＲＢ１＊１５Ｙ２,其４７位由ＴＡＣ（酪氨酸）置换了相应于ＤＲＢ１＊１５０２的ＴＴＣ（苯丙氨酸）。在我国这样一个多民族国家中,就ＨＬＡ系统而言,可能还有更多新等位基因有待鉴定。这样有助于完善群体遗传资料     

Conservation of the c-myc coding sequence in transduced feline v-myc genes

We have cloned the normal feline c-myc locus and determined the nucleotide sequence of all three exons. The feline c-myc gene shows close homology to other mammalian c-myc genes, particularly human c-myc. The feline and human sequences are colinear within the open reading frame for the putative c-myc product but show insertions and deletions relative to each other outside this domain. We have also analyzed a cloned FeLV provirus, CT4, which contains the host-derived myc gene. In this provirus the v-myc sequences are located at the 3' end of the pol gene, replacing pol and env sequences. Nucleotide sequence analysis of CT4 shows an open reading frame for a v-myc gene product which may be expressed without fusion to any viral protein sequences. This contrasts with another FeLV v-myc (LC), in which myc and gag sequences were found to be fused. Unlike previously identified avian v-myc genes, the feline v-myc genes contain exon 1-derived sequences, but these have been truncated or internally deleted. The FeLV CT4 v-myc sequence shows very few coding changes relative to c-myc and the FeLV LC v-myc coding sequence is unchanged relative to c-myc apart from fusion to gag. These results are discussed in relation to the mechanism of transduction and activation of myc by FeLV.     

Nucleotide sequence of a new Fc gamma receptor IIIB allele that codes for a neutrophil antigen

A new allele of the human neutrophil antigen (HNA) system (tentatively called NA2M) was discovered and its nucleotide sequence was determined. NA2M differs in a single nucleotide (193G-->A) from FCGR3B*2(NA2), resulting in an amino acid change (54Glu-->Lys). The frequency of the NA2M gene in the Japanese population was estimated to be 0.008. Granulocytes of individuals possessing NA2M reacted with HNA-1b(NA2)-specific monoclonal antibody (TAG2) in the GIFT assay.     

DNA sequence analysis of the HLA-DRw12 allele

The complete DNA sequence of a DR beta chain cDNA encoding the DRw12 allele has been determined. The sequence of this DRB1 allele reveals a structural relationship to the group of other DRB1 genes found on DRw52 haplotypes, such as DR3, -w11, -w13, -w14, and -w8. The structural similarities among this group of alleles are particularly evident in the first hypervariable as well as in the 3' untranslated region. The second hypervariable region contains a unique sequence not identified in any other DRB1 allele. The third hypervariable region appears to have arisen by gene conversion events involving two DRB1 chain genes, DR7 and DR1 or DR2/Dw21.     

Nucleotide sequence of the vaccinia virus hemagglutinin gene

Vaccinia virus hemagglutinin (HA) is expressed at late time of infection cycle, and it is nonessential for virus growth. Location of the HA structural gene was determined by hybrid-arrested and hybrid-selected translation methods at the right terminus of the HindIII A fragment. The position of the HA gene was confirmed by the production of the complete HA protein in the cells transfected with the plasmid containing that region. Examination of this nucleotide sequence revealed the positions of cleavage sites for a number of restriction endonucleases. The deduced amino acid sequence revealed that the HA protein is a member of typical surface membrane glycoproteins. Comparison of the nucleotide sequence upstream of the HA coding region with corresponding region of other late genes suggested the existence of the consensus decanucleotides TTCATTTa/tGT between 34 to 18 bp upstream to the initiation codon followed by a cluster of A or T, a unique feature of the late genes of vaccinia virus. These results in conjunction with the ease of isolating HA- mutants provide a basis for a new site suitable for inserting foreign genes.     

Complete sequence analysis of the A*1103 allele

Here we report the full-length sequence of a novel A*11 variant. The variant was identified by ARMS-PCR and serology, the sequence was confirmed by cloning and subsequent sequencing. This variant, A*1103, found in a family of oriental origin, resembles the A*1101 sequence in exon 2 but differs in exon 3 with regard to codons 151 and 152. The polymorphism's result in two amino acid substitutions (one conserved (His->Arg), one introducing a negative charge (Ala->Glu)) located in the alpha2 helical region. The arginine at amino acid position 151 is rare amongst Alocus alleles and is besides A*1103 only observed in A*29 variants, the glutamine at amino acid position 152 is shared with A*0301, A*25, *26, *34 variants and the A*02 subtypes A*0203, *0213 and *0226. In fact, the amino acid motif comprising codons 151 and 152 is unique to A*1103 among Alocus alleles, but is common to C-locus alleles.     

Nucleotide sequence of the genome of eggplant mosaic tymovirus

The sequence of the RNA genome of an isolate of eggplant mosaic tymovirus from Trinidad (EMV-Trin) has been determined. The genome is 6330 nucleotide residues in length and contains three open reading frames; two overlapping genes, whose initiation codons are separated by seven nucleotide residues (nucleotide residues 102-2051 and 109-5628) near the 5' terminus, and the virion protein gene, which is near the 3' terminus (nucleotide residues 5633-6199). The genomes of EMV-Trin and turnip yellow mosaic tymovirus have the same genomic organization and similar nucleotide and encoded amino acid sequences. The nucleotide residues adjacent to the initiation codons of tymoviral overlapping genes have closely similar sequences which may form a weak stem-loop secondary structure that regulates their translation.     

Nucleotide sequence of the ononis yellow mosaic tymovirus genome

The nucleotide sequence of the genome of ononis yellow mosaic tymovirus (OYMV) has been determined. The genome is single-stranded RNA, 6211 nucleotides long, and has three main open reading frames (ORFs), two of them overlapping. The largest ORF (nucleotides 179-5509) encodes a polyprotein of 1776 amino acid residues that has sequence similarities with polymerases of other viruses with RNA genomes. The smaller overlapping ORF (nucleotides 172-1965) encodes a protein of 597 amino acids of unknown function. The third ORF located at the 3' end of the genome (nucleotides 5487-6065) is the virion protein gene, and it overlaps by 20 nucleotides the 3' terminus of the largest ORF. The organization of the OYMV genome, its sequence, and the sequences of the protein it encodes are clearly similar to those of two other tymoviruses, turnip yellow mosaic virus and eggplant mosaic virus. The 5' terminal noncoding region of the OYMV genome is much longer than the same region of other tymoviral genomes and includes a direct duplication of a sequence of 21-23 nucleotides.     

Nucleotide sequence of the geminivirus chloris striate mosaic virus

The genome of chloris striate mosaic virus (CSMV) comprises a single circular DNA as determined by analyses on virion single-stranded (ss) DNA and virus-specific covalently closed circular (ccc) DNA isolated from infected plants. The nucleotide sequence of CSMV DNA was determined from cccDNA and the data were accommodated into one DNA circle of 2750 nucleotides. Comparison of the nucleotide sequence with those of maize streak virus (MSV), wheat dwarf virus (WDV), and digitaria streak virus (DSV) showed 49, 47, and 48% DNA homology, respectively. The sequence has four potential open reading frames for proteins of greater than 10,000 mol wt, two in the viral (+) sense and two in the complementary (-) sense. Three of these potential coding regions have homologous counterparts, by comparison of the amino acid sequences, among the open reading frames reported for MSV, WDV, and DSV. CSMV encapasidates primer molecules able to prime the synthesis in vitro of a complementary strand to virion DNA, initiating this reaction at one site on the genome. The CSMV primer comprising approximately 88 nucleotides was located within the smaller of two intergenic or noncoding regions.     

Complementary DNA sequence of the HLA-B*3924 allele.

We have isolated the complete coding region of HLA-B*39 from a Spanish Caucasoid, using a new PCR primer for its 5' untranslated region. The cDNA matched partial genomic sequences of B*3924, an allele whose distribution appears to be restricted to Mediterranean and Arabian Caucasoids. A single amino acid change exclusive to B*3924 (threonine-98) distinguishes it from B*3903.