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1.
2.
MHCDB: database of the human MHC (release 2) 总被引:2,自引:0,他引:2
The second release of the human major histocompatibility complex (MHC) database is now publicly available. It contains an
updated physical map and considerably more genomic sequence. cDNA sequences of all current alleles are accessible as individual
sequence entries. The variability of different genes is displayed graphically as static and dynamic images accessible from
the database. Known disease-serotype associations have also been incorporated, together with data from the MHCPEP database
of eluted peptides.
Received: 13 February 1996 / Revised: 12 August 1996 相似文献
3.
Laurent Pichon Annie Hampe Thierry Giffon Gwenaelle Carn Jean Yves Legall Veronique David 《Immunogenetics》1996,44(4):259-267
In an effort to initiate steps designed to characterize the idiopathic hemochromatosis disease gene, the HLA-A/HLA-F region where this gene is in disequilibrium linkage with some polymorphic markers has been overlapped by a yeast artificial
chromosome (YAC) contig. In order to achieve the physical mapping of these YACs and of the corresponding genomic region, we
subcloned one of the YACs involved. A computer-assisted analysis of the sequence of one subclone led to the isolation of a
potential exon that proved to belong to a new expressed messenger named HCGIX. After Southern blot analysis, the corresponding cDNA clone was found to belong to a new multigene family whose members are
dispersed throughout the HLA class I region and are closely associated with members of another recently described multigene family designated PERB11. The data reported here suggest that these two multigene families form a cluster that have been dispersed together throughout
the telomeric part of the major histocompatibility complex and have been involved in the genesis of this human class I region.
Received: 23 February 1996 / Revised: 23 April 1996 相似文献
4.
The XIST gene plays an essential role in X Chromosome (Chr) inactivation during the early development of female humans. It
is believed that the XIST gene, not encoding a protein, functions as an RNA. The XIST cDNA is unusually long, as its full
length is reported to be 16.5 kilobase pairs (kb). Here, comparison of sequences from the genomic interval downstream to the
3′ end of the human XIST gene against the human EST database brought to light a number of human EST sequences that are mapped
to the region. Furthermore, PCR amplification of human cDNA libraries and RNA fluorescence in situ hybridization (RNA-FISH)
demonstrate that the human XIST gene has additional 2.8 kb downstream sequences which have not been documented as a part of
the gene. These data show that the full-length XIST cDNA is, in fact, 19.3 kb, not 16.5 kb as previously reported. The newly
defined region contains an intron that may be alternatively spliced and seven polyadenylation signal sequences. Sequences
in the newly defined region show overall sequence similarity with the 3′ terminal region of mouse Xist, and three subregions exhibit quite high sequence conservation. Interestingly, the new intron spans the first two subregions
that are absent in one of the two isoforms of mouse Xist. Taken together, we revise the structure of human XIST cDNA and compare cDNA structures between human and mouse XIST/Xist.
Received: 3 August 1999 / Accepted: 15 November 1999 相似文献
5.
Cecilie Boysen Christopher Carlson Eran Hood Leroy Hood Deborah A. Nickerson 《Immunogenetics》1996,44(2):121-127
The T-cell receptor (TCR) is a highly variable molecule composed of two polypeptide chains that recognize antigenic peptides
in the context of major histocompatibility complex (MHC) molecules. In this study, we describe a sequence-based search for
germline polymorphisms in the variable (V) gene segments of the human TCRA/D locus. Thirty different V gene segments were amplified from six to eight unrelated individuals and sequenced from low melting point agarose. Twenty-seven
polymorphisms were identified in 15 V gene segments. These polymorphisms are mainly single nucleotide substitutions, but an insertion/deletion polymorphism and
a single dinucleotide repeat with variable length were also seen. Of the 15 sequence variations found in the coding regions,
six are silent and nine encode amino acid changes. All of the amino acid changes are found at non-conserved residues, frequently
in the hypervariable regions, where they may influence MHC and/or peptide recognition. Therefore, it is possible that germline
variations in TCR genes could influence an individual’s immune response, and may also contribute to susceptibility to diseases such as autoimmunity.
Received: 9 January 1996 / Revised: 22 February 1996 相似文献
6.
7.
Genome and expressed sequence tag information of Xenopus tropicalis suggested that short-consensus repeat (SCR)-containing proteins are encoded by three genes that are mapped within a 300-kb
downstream of PFKFB2, which is a marker gene for the regulator of complement activation (RCA) loci in human and chicken. Based on this observation,
we cloned the three cDNAs of these proteins using 3′- or 5′-RACE technique. Since their primary structures and locations of
the proximity to the PFKFB2 locus, we named them amphibian RCA protein (ARC) 1, 2, and 3. Expression in human HEK293 or CHO cells suggested that ARC1
is a soluble protein of Mr ∼67 kDa, ARC2 is a membrane protein with Mr 44 kDa, and ARC3 a secretary protein with a putative
transmembrane region. They were N-glycosylated during maturation. In human and chicken RCA clusters, the order in which genes for soluble, GPI-anchored, and
membrane forms of SCR proteins are arranged is from the distant to proximity to the PFKFB2 gene. However, the amphibian ARC1, 2, and 3 resembled one another and did not reflect the same order found in human and chicken
RCA genes. This may be due to self-duplication of ARCs to form a family, and it evolved after the amphibia separated from
the ancestor of the amniotes, which possessed soluble, GPI-anchored, and membrane forms of SCR protein members. Taken together,
frog possesses a RCA locus, but the constitution of the ARC proteins differs from that of the amniotes with a unique self-resemblance. 相似文献
8.
Exact Tandem Repeats Analyzer 1.0 (E-TRA) combines sequence motif searches with keywords such as ‘organs’, ‘tissues’, ‘cell
lines’ and ‘development stages’ for finding simple exact tandem repeats as well as non-simple repeats. E-TRA has several advanced
repeat search parameters/options compared to other repeat finder programs as it not only accepts GenBank, FASTA and expressed
sequence tags (EST) sequence files, but also does analysis of multiple files with multiple sequences. The minimum and maximum
tandem repeat motif lengths that E-TRA finds vary from one to one thousand. Advanced user defined parameters/options let the
researchers use different minimum motif repeats search criteria for varying motif lengths simultaneously. One of the most
interesting features of genomes is the presence of relatively short tandem repeats (TRs). These repeated DNA sequences are
found in both prokaryotes and eukaryotes, distributed almost at random throughout the genome. Some of the tandem repeats play
important roles in the regulation of gene expression whereas others do not have any known biological function as yet. Nevertheless,
they have proven to be very beneficial in DNA profiling and genetic linkage analysis studies. To demonstrate the use of E-TRA,
we used 5,465,605 human EST sequences derived from 18,814,550 GenBank EST sequences. Our results indicated that 12.44% (679,800)
of the human EST sequences contained simple and non-simple repeat string patterns varying from one to 126 nucleotides in length.
The results also revealed that human organs, tissues, cell lines and different developmental stages differed in number of
repeats as well as repeat composition, indicating that the distribution of expressed tandem repeats among tissues or organs
are not random, thus differing from the un-transcribed repeats found in genomes. 相似文献
9.
10.
A high-resolution map of the regulator of the complement activation gene cluster on 1q32 that integrates new genes and markers 总被引:1,自引:1,他引:0
Damián Heine-Suñer M. A. Díaz-Guillén Fernando Pardo-Manuel de Villena Mercedes Robledo Javier Benítez Santiago Rodríguez C de Córdoba 《Immunogenetics》1997,45(6):422-427
Sixteen microsatellite markers, including two described here, were used to construct a high-resolution map of the 1q32 region
encompassing the regulator of the complement activation (RCA) gene cluster. The RCA genes are a group of related genes coding for plasma and membrane associated proteins that collectively control activation
of the complement component C3. We provide here the location of two new genes within the RCA gene cluster. These genes are PFKFB2 that maps 15 kilobases (kb) upstream of the C4BPB gene, and a gene located 4 kb downstream of C4BP
A, which seems to code for the 72 000 M
r
component of the signal recognition particle (SRP72). Neither of these two genes is related structurally or functionally to the RCA genes. In addition, our map shows the centromere-telomere orientation of the C4BPB/MCP linkage group, which is: centromere-PFKFB2-C4BPB-C4BPA-SRP72-C4BPAL1-C4BPAL2-telomere, and outlines an interval with a significant female-male recombination difference which suggests the presence of
a female-specific hotspot(s) of recombination.
Received: 12 December 1996 / Revised: 23 December 1996 相似文献
11.
J. M. Crous I. S. Pretorius W. H. van Zyl 《Applied microbiology and biotechnology》1996,46(3):256-260
First-strand cDNA was prepared from mRNA of Aspergillus niger MRC11624 induced on oat spelts xylan. Using the cDNA as a template, the α-L-arabinofuranosidase gene (abf B) was amplified with the polymerase chain reaction technique. The abf B DNA fragment was inserted between the yeast phosphoglycerate kinase I gene promoter (PGK1
P
) and terminator (PGK1
T
) sequences on a multicopy episomal plasmid. The resulting construct PGK1
P
-abf B-PGK1
T
was designated ABF2. The ABF2 gene was expressed successfully in Saccharomyces cerevisiae and functional α-L-arabinofuranosidase was secreted from the yeast cells. The ABF2 nucleotide sequence was determined and verified to encode a 449-amino-acid protein (Abf 2) that is 94% identical to the α-L-arabinofuranosidase B of A. niger N400. Maximum α-L-arabinofuranosidase activities of 0.020 U/ml and 1.40 U/ml were obtained with autoselective recombinant S. cerevisiae strains when grown for 48 h in synthetic and complex medium respectively.
Received: 29 January 1996/Received revision: 3 May 1996/Accepted: 9 May 1996 相似文献
12.
David M. Hwang Adam Dempsey Kiat-Tsong Tan Choong-Chin Liew 《Journal of molecular evolution》1996,43(5):536-540
HnifU, a gene exhibiting similarity tonifU genes of nitrogen fixation gene clusters, was identified in the course of expressed sequence tag (EST) generation from a
human fetal heart cDNA library. Northern blot of human tissues and polymerase chain reaction (PCR) using human genomic DNA
verified that the hnifU gene represented a human gene rather than a microbial contaminant of the cDNA library. Conceptual translation of the hnifU cDNA yielded a protein product bearing 77% and 70% amino acid identity to NifU-like hypothetical proteins fromHaemophilus influenzae andSaccharomyces cerevisiae, respectively, and 40–44% identity to the N-terminal regions of NifU proteins from several diazatrophs (i.e., nitrogen-fixing
organisms). Pairwise determination of amino acid identities between the NifU-like proteins of nondiazatrophs showed that these
NifU-like proteins exhibited higher sequence identity to each other (63–77%) than to the diazatrophic NifU proteins (40–48%).
Further, the NifU-like proteins of non-nitrogenfixing organisms were similar only to the N-terminal region of diazatrophic
NifU proteins and therefore identified a novel modular domain in these NifU proteins. These findings support the hypothesis
that NifU is indeed a modular protein. The high degree of sequence similarity between NifU-like proteins from species as divergent
as humans andH. influenzae suggests that these proteins perform some basic cellular function and may be among the most highly conserved proteins.
Correspondence to: C.-C. Liew 相似文献
13.
Characterization of EST-SSRs in loblolly pine and spruce 总被引:3,自引:0,他引:3
Yanik Bérubé Jun Zhuang Dainis Rungis Steven Ralph Jörg Bohlmann Kermit Ritland 《Tree Genetics & Genomes》2007,3(3):251-259
In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases
were characterized for EST-SSRs. One database was from “interior spruce” (white and Engelmann spruce in Southern British Columbia)
and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce,
respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs
differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one
EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class
in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered
in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in conifers
could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for
in-silico approaches for marker development. 相似文献
14.
Complement is an efficient defense mechanism of innate immunity. Factor H is the central complement regulator of the alternative pathway, acting in the fluid-phase and on self surfaces. Pigs are considered a suitable source for xenotransplantation and thus several membrane-bound pig complement regulators with importance for the acute rejection phase have been investigated. However, pig fluid-phase regulators have not been described so far. We report the cloning, expression and functional characterization of pig factor H. After constructing a pig liver cDNA library, a full-length factor H cDNA was isolated and sequenced. The predicted protein is organized in 20 short consensus repeat (SCR) domains and has an overall identity of 62% to the human protein. For functional characterization, three deletion constructs of pig factor H were expressed in insect cells. Pig factor H construct SCR 1–4 has cofactor activity for factor I-mediated cleavage of human C3b, which is similar to the human regulator. In addition, this N-terminal construct binds to human C3b, while a construct consisting of SCR 15–20 showed a weaker binding to human C3b/C3d. Pig factor H has two major binding sites for heparin, as the two constructs representing SCR 1–7 and SCR 15–20 proteins, but not the SCR 1–4 protein, bind heparin. The C-terminal construct is able to bind to human endothelial cells, as assayed by FACS. We show that pig and human factor H share functional characteristics in complement regulation and cell surface binding. Possible consequences of using pig livers for xenotransplantation are discussed.The nucleotide sequence data reported are available in the EMBL database (accession number AJ278470) 相似文献
15.
Toshi Foster Chris Kirk William T. Jones Andrew C. Allan Richard Espley Sakuntala Karunairetnam Jasna Rakonjac 《Tree Genetics & Genomes》2007,3(3):187-197
The hormone gibberellic acid (GA) regulates growth and development throughout the plant life cycle. DELLA proteins are key
components of the GA signalling pathway and act to repress GA responses. The “DELLA” amino acid motif is highly conserved
among diverse species and is essential for GA-induced destruction of DELLA proteins, which relieves repression. Six genes
encoding the DELLA motif were identified within an apple expressed sequence tag (EST) database. Full-length cDNA clones were
obtained by RACE and these were designated MdRGL1a/b, MdRGL2a/b, and MdRGL3a/b. Sequence alignment of the predicted proteins indicates that the MdDELLAs are 37–93% homologous to one another and 44–65%
to the Arabidopsis DELLAs. The MdDELLAs cluster into three pairs, which reflect the presumed allopolyploid origins of the Maloideae. Expression analysis using quantitative real-time PCR indicates that all three pairs of MdDELLA mRNAs are expressed at the highest levels in summer arrested shoot tips and in autumn vegetative buds. Transgenic Arabidopsis expressing MdRGL2a have smaller leaves and shorter stems, take longer to flower in short days, and exhibit a reduced response to exogenous GA3, indicating significant conservation of gene function between DELLA proteins from apple and Arabidopsis.
Electronic supplementary material Supplementary material is available for this article at and is accessible for authorized users. 相似文献
16.
Michelle Goldsworthy Anuradha Sampath J. M. Wilkinson S. H. Powis 《Immunogenetics》1997,46(3):206-212
Although many human major histocompatibility genes have been identified, relatively few have been localized to the class
I region. We searched for new class I region genes by sample sequencing, a process in which short stretches of random genomic
sequence are generated from cosmids and then compared with sequences deposited in nucleotide databases. Four class I region
cosmids were isolated for sample sequencing by screening a chromosome 6 specific cosmid library with probes derived from specific
class I region genes or with overlapping class I region yeast artificial chromosomes. Cosmids were sonnicated to produce fragments
of 0.5 – 1 kilobases, subcloned, and sequenced using an automated sequencer. Sequences were then compared with nucleotide
sequences deposited in the GenBank databases using the BLASTN algorithm. A number of potential new class I region genes were
identified, including a cDNA with similarity to the tre oncogene, the trans-activating factor SC1 (TCF19), and a member of the interferon inducible 1 – 8 gene family. These observations suggest that sample sequencing is an efficient method for identifying new class I region
genes, which can be applied to other regions of the genome and to other species, and support previous observations that the
class I region contains a variety of genes other than those encoding HLA antigens.
Received: 10 December 1996 / Revised: 7 January 1997 相似文献
17.
Horse (Equus caballus) immunoglobulin mu chain-encoding (IgM) variable, joining, and constant gene segments were cloned and characterized. Nucleotide sequence analyses of 15 cDNA clones
from a mesenteric lymph node library identified 7 unique variable gene segments, 5 separate joining segments, and a single
constant region. Based on comparison with human sequences, horse variable segments could be grouped into either family 1 of
immunoglobulin (Ig) clan I or family 4 of Ig clan II subclan IV. All horse sequences had a relatively conserved 16 base pair (bp) segment in framework 3 which was recognized
with high specificity in polymerase chain reaction by a degenerate oligonucleotide primer. Horse complementarity determining
regions (CDR) had considerable variability in predicted amino acid content and length but also included the presence of relatively
conserved residues and several canonical sequences that may be necessary in formation of the β chain main structure and conformation
of antigen-binding sites through interaction with light chain CDR. Sequence analysis of joining regions revealed the presence
of nearly invariant 3′ regions similar to those found in human and mouse genes. A single horse IgM constant region comprising 1472 bp and encoding 451 residues was also identified. Direct comparison of the horse constant
region predicted amino acid sequence with those from eleven other species revealed the presence of 53 invariant residues with
particularly conserved sequences within the third and fourth exons. Phylogenetic analysis using a neighbor-joining algorithm
showed closest similarity of the horse mu chain-encoding constant region gene to human and dog sequences. Together, these
findings provide insights into the comparative biology of IgM as well as data for additional detailed studies of the horse immune system and investigation of immune-related diseases.
Received: 14 October 1996 / Revised: 10 December 1996 相似文献
18.
S. E. Harrington H. F. J. Bligh W. D. Park C. A. Jones S. R. McCouch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(5):564-568
The chromosomal position of Starch Branching Enzyme III (SBEIII) was determined via linkage to RFLP markers on an existing
molecular map of rice (Oryza sativa L.). A cDNA of 890 bp was generated using specific PCR primers designed from available SBEIII sequence data and used as a
probe in Southern analysis. The SBEIII cDNA hybridized to multiple restriction fragments, but these fragments mapped to a
single locus on rice chromosome 2, flanked by CDO718 and RG157. The detection of a multiple-copy hybridization pattern suggested the possibility of a tandemly duplicated gene at this
locus. The map location of orthologous SBE genes in maize, wheat, and oat were predicted based on previously published genetic
studies and comparative maps of the grass family.
Received : 5 August 1996 / Accepted : 13 September 1996 相似文献
19.
20.
Nomura M Tsujimura A Shida K Matsumoto M Matsuda Y Toyoshima K Seya T 《Immunogenetics》1999,50(5-6):245-254
A cDNA encoding a new secretory form of mouse membrane cofactor protein (MCP, CD46) was identified additionally to the membrane
form cDNA. The secretory MCP, predicted from the cDNA sequence, consisted of the conserved four short consensus repeats (SCRs)
plus a four amino acid-stretch. Unlike human MCP which comprises many isoforms, mouse MCP cDNA predicted a single isoform
of membrane MCP with cytoplasmic tail 1 (CYT1) and serine/threonine-rich domain C (STC). To clarify the genomic origin and monomorphic alteration of these cDNAs, we cloned and analyzed a mouse genomic DNA harboring
the full coding sequence of MCP from a 129/SV mouse genomic library. The mouse Mcp was a single gene ∼50 kilobases long. Eleven of the 14 coding exons of the human MCP gene and intron-exon boundary sequences were found to be conserved in the mouse gene. The STC homologue but not the STA or STB homologue in the mouse exons was functional: the latter being due to deletions and lack of consensus sequences for splicing.
The sequence equivalent to cytoplasmic tail 2 (CYT2) has not been identified in the Mcp genome. Thus, the three exons (STA, STB, and probably CYT2) responsible for the polymorphism of human MCP by differential splicing were missing in the mouse Mcp gene. Unlike the case in humans, no Mcp-related genes or pseudogenes were observed in the mouse genome. The single mouse Mcp gene was mapped to the R-positive H5 band of mouse Chromosome 1 by FISH. Strikingly, one alternative exon with 73 base pairs
(encoding the four new amino acids and a TGA stop codon) was discovered between the SCRIV and the STC exons; alternative splicing causes the generation of the secretory form of mouse MCP. These results on mouse MCP, together
with the information concerning other mouse SCR proteins, infer that the regulator of complement activation (RCA) gene cluster
is genetically diverged between humans and mice.
Received: 22 April 1999 / Revised: 21 June 1999 相似文献