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Results for “genomic sequence”

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At least 1,621 records · Page 90Linked to original sources
PubMed2003

The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida--evidence for close relationship to the T7 group.

The genome of the lytic Pseudomonas putida bacteriophage gh-1 is linear double-stranded DNA containing 37,359 bp with 216-bp direct terminal repeats. Like other members of the T7 group, the gh-1 genome contains regions of high homology to T7 interspersed with nonhomologous regions that contain small open reading frames of unknown function. The genome shares 31 genes in common with other members of the T7 group, including RNA polymerase, and an additional 12 unique putative genes. A major difference between gh-1 and other members of this group is the absence of any open reading frames between the left direct terminal repeat and gene 1. Sequence analysis of the gh-1 genome also revealed the presence of 10 putative phage promoters with a consensus sequence similar to the promoters of T3 and phiYeO3-12 (consensus: TAAAAACCCTCACTRTGGCHSCM). P. putida mutants resistant to gh-1 were demonstrated to have an altered lipopolysaccharide structure, indicating that members of this group use lipopolysaccharide as their cellular receptor.

Amino Acid Sequence↗
PubMed2026

The genome sequence of the lesser white-fronted goose, Anser erythropus (Linnaeus, 1758) (Anseriformes: Anatidae).

We present a genome assembly from an individual female Anser erythropus (lesser white-fronted goose; Chordata; Aves; Anseriformes; Anatidae). The assembly contains two haplotypes with total lengths of 1 339.88 megabases and 1 168.02 megabases. Most of haplotype 1 (88.67%) is scaffolded into 41 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.74 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Anser erythropus↗
PubMed1999

Isolation and characterization of genomic sequences involved in the regulation of the human reduced folate carrier gene (RFC1).

Decreased reduced folate carrier (RFC) activity has been associated with MTX resistance in experimental models of transport-mediated MTX resistance, and has been attributed to changes in the expression of RFC1, the gene that encodes a protein with this activity. RNA transcripts of RFC1 may contain any one of four distinct 5' untranslated regions (UTRs). We cloned a human genomic DNA fragment upstream from the RFC1 translation start site and determined the nucleotide sequence of a 4.8kb region that contained the exons corresponding to each of the reported UTRs. To identify regulatory elements that may be involved in RFC1 transcription, we first developed a semi-quantitative RT-PCR assay using primers specific for each of the 5' UTRs to amplify RNA transcripts containing each of the RFC1 5' exons, and found evidence for differential transcription of RFC1 non-coding exons in tissues, during development, and in MTX-resistant, transport-deficient cells. We also found that RFC1 RNA levels are cell cycle regulated and peak at the G1 to S transition. Then, using a series of RFC1 promoter-reporter fusion constructs, we identified genomic sequences that may be involved in the regulation of expression of exons 1b and 1c of the RFC1 gene. These studies therefore identify regulatory regions of RFC1 promoters and potential models of regulation in which these regions may exert control.

5' Untranslated Regions↗
PubMed2005

Comparison of the complete genome sequence between C1 and G4 isolates of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus.

The complete nucleotide sequence of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus isolate C1 (HearSNPV-C1) was determined and analyzed by comparing with the genome of HearSNPV-G4 isolate. C1 and G4 isolates occurred in the same host species and geographic location but showed different virulence. The HearSNPV-C1 genome consisted of 130,759 bp and 137 putative open reading frames larger than 150 nucleotides were identified. The two genomes shared 98.1% nucleotide sequence identity, with a total number of 555 bp substitutions, 1354 bp deletions, and 710 bp insertions in HearSNPV-C1. Comparison of ORFs and homologous repeat (hr) regions of the two genomes showed that there were four highly variable regions hr1, hr4, hr5, and bro-b, all in repeat regions. These results suggest that baculovirus strain heterogeneity may be often caused by SNPs and changes in the hrs and bro genes.

Animals↗
PubMed2005

Rickettsia felis, from culture to genome sequencing.

Rickettsia felis has been recently cultured in XTC2 cells. This allows production of enough bacteria to create a genomic bank and to sequence it. The chromosome of R. felis is longer than that of previously sequenced rickettsiae and it possess 2 plasmids. Microscopically, this bacterium exhibits two forms of pili: one resembles a conjugative pilus and another forms hair-like projections that may play a role in pathogenicity. R. felis also exhibits several copies of ankyrin-repeat genes and tetratricopeptide encoding gene that are specifically linked to pathogenic host-associated bacteria. It also contains toxin-antitoxin system encoding genes that are extremely rare in intracellular bacteria and may be linked to plasmid maintenance.

Animals↗
PubMed1995

Genomic sequence analysis identifies Jembrana disease virus as a new bovine lentivirus.

Jembrana disease virus, the cause of an acute, severe disease in Bali (Bos javanicus) cattle in Indonesia was recently identified as a retrovirus, and possibly a lentivirus. We have produced sequence data representing 598 bp of the pol gene, amplified by PCR from viral cDNA using broadly reactive universal primers for retroviruses and more specific genus-reactive primers for lentiviruses. When the sequence data were compared with that of known lentiviruses and other bovine retroviruses, the closest alignment was with bovine immunodeficiency-like lentivirus (BIV), showing 74% nucleotide sequence identity. This confirmed that JDV is a lentivirus and that it is distinguishable from BIV. The pathogenesis of Jembrana disease is most unusual for a lentivirus infection and differs markedly from that reported for BIV infection.

Amino Acid Sequence↗
PubMed2003

Complete genome sequence of the Q-fever pathogen Coxiella burnetii.

The 1,995,275-bp genome of Coxiella burnetii, Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular acidophile that is highly adapted for life within the eukaryotic phagolysosome. Genome analysis revealed many genes with potential roles in adhesion, invasion, intracellular trafficking, host-cell modulation, and detoxification. A previously uncharacterized 13-member family of ankyrin repeat-containing proteins is implicated in the pathogenesis of this organism. Although the lifestyle and parasitic strategies of C. burnetii resemble that of Rickettsiae and Chlamydiae, their genome architectures differ considerably in terms of presence of mobile elements, extent of genome reduction, metabolic capabilities, and transporter profiles. The presence of 83 pseudogenes displays an ongoing process of gene degradation. Unlike other obligate intracellular bacteria, 32 insertion sequences are found dispersed in the chromosome, indicating some plasticity in the C. burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation.

Bacterial Adhesion↗
PubMed2025

The genome sequence of the de Prunner's Ringlet, Erebia triaria von Prunner, 1798 (Lepidoptera: Nymphalidae).

We present a genome assembly from a female specimen of Erebia triaria (de Prunner's Ringlet; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The assembly contains two haplotypes with total lengths of 521.30 megabases and 412.03 megabases. Most of haplotype 1 (99.7%) is scaffolded into 17 chromosomal pseudomolecules, including the Z 1, Z 2, and W sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.26 kilobases.

Erebia triaria↗
PubMed1989

The mouse homologue of hst/k-FGF: sequence, genome organization and location relative to int-2.

We have located and sequenced the murine homologue of the hst/k-FGF oncogene in genomic DNA clones that extend 3' from int-2 on mouse chromosome 7. The two genes are in the same transcriptional orientation, less than 20 kilobase pairs (kb) apart, and presumably evolved by tandem duplication of a common ancestral gene. RNase mapping and primer extension analyses indicated that the major 3.2 kb hst transcript expressed in undifferentiated embryonal carcinoma (EC) cell lines initiates at a unique cap site downstream from an obvious TATA-box. The 3' end of the transcript as identified in multiple cDNA clones occurs at an appropriate distance from a variant polyadenylation signal, ATTAAA. Translation of the major open reading frame would yield a 202 amino acid protein that is 82% homologous to human HST but lacking 4 residues at the presumed signal peptide cleavage site.

Amino Acid Sequence↗
PubMed1998

Genomic organization of the human mucin gene MUC5B. cDNA and genomic sequences upstream of the large central exon.

The complete structure of the DNA encoding the polypeptide chain of human mucin MUC5B has been determined. In this paper, we report the full-length cDNA (3886 bp) and genomic (15,143 bp) sequences upstream of the unusually large central exon of the human mucin gene MUC5B. This region, composed of 29 exons, encodes 1283 amino acid residues. Exon sizes vary from 44 to 262 bp, and intron sizes range from 87 to 1703 bp. We determined the 5'-end of MUC5B by performing rapid amplification of cDNA ends-polymerase chain reaction experiments leading to the same length of the amplified product and by using primer extension experiments. A putative translation start site was found at nucleotide +37. We compared the amino-terminal region of MUC5B with those of pro-von Willebrand Factor, MUC2 and MUC5AC, and animal mucins, RMuc2, PSM, and FIM-B.1. The primary amino acid sequence with a high content of cysteine residues demonstrates a high degree of similarity with other members of the 11p15 mucin gene family, particularly MUC5AC. The complete genomic organization and both full-length genomic and cDNA sequences of MUC5B have been elucidated. This gene contains 48 exons and encodes 5662 amino acid residues to give a polypeptide with a Mr approximately 600,000.

Amino Acid Sequence↗
PubMed2026

The genome sequence of the Shepherd's Fritillary, Boloria pales (Denis & Schiffermüller), 1775 (Lepidoptera: Nymphalidae).

We present a genome assembly from a female specimen of Boloria pales (Shepherd's Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The assembly contains two haplotypes with total lengths of 382.99 megabases and 364.88 megabases. Most of haplotype 1 (99.96%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.17 kilobases. Gene annotation of this assembly on Ensembl identified 12,117 protein-coding genes.

Boloria pales↗
PubMed1996

Genomic sequence of the DAX1 gene: an orphan nuclear receptor responsible for X-linked adrenal hypoplasia congenita and hypogonadotropic hypogonadism.

The gene responsible for X-linked adrenal hypoplasia congenita, DAX1, encodes a member of the nuclear hormone receptor superfamily. We sequenced 8851 bp that contained the DAX1 genomic region. The DAX gene was composed of two exons and one 3.4-kilobase intron. Putative TATA and GC boxes and a putative steroidogenic factor 1 response element were present in the 5'-flanking region. Two potentially polymorphic short tandem repeats were identified. The first exon encoded two putative novel zinc finger motifs within a putative DNA binding domain and part of the ligand binding domain, and the second exon encoded the remainder of the ligand binding domain. Although the putative DNA binding domain of DAX1 does not contain substantial sequence similarity to other nuclear hormone receptor superfamily members, the putative ligand binding domain had remarkable similarity to other family members. Single-strand conformational polymorphism analysis permitted identification of three new mutations in DAX1. In conclusion, single-strand conformational polymorphism analysis facilitates identification of mutations in the DAX1 gene, and the short tandem repeats may permit linkage analysis in families in which mutations are not yet identified. We speculate that DAX1 may be the most primitive member of the nuclear hormone receptor superfamily identified in mammals.

Adrenal Insufficiency↗