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It shares homology with the mating-type protein, Mc, from the fission yeast Schizosaccharomyces pombe and a conserved DNA-binding motif present in the nuclear high-mobility-group proteins HMG1 and HMG2. (nih.gov)
DNA sequences that form the coding region for the viral envelope (env) proteins in retroviruses. (lookformedical.com)
Retroviral proteins, often glycosylated, coded by the envelope (env) gene. (lookformedical.com)
Proteins coded by the retroviral gag gene. (lookformedical.com)
The 37-Mb genome was predicted to contain a total of 12,074 genes encoding proteins with a length greater than 100 amino acid residues (see Methods). (nature.com)
As observed more broadly in angiosperms, ribosomal proteins have been especially prone to gene loss in the S. latifolia lineage. (biomedcentral.com)
Plant mitochondrial genomes contain genes for their own rRNA subunits as well as for some of the ribosomal proteins and tRNAs required for translation (Figure 1 ), but many necessary ribosomal protein and tRNA genes are located in the nuclear genome, so their gene products must be imported into the mitochondrion [ 15 ]. (biomedcentral.com)
N, P, M, G and L share significant sequence homology and/or structural characteristics with the homologous proteins of other rhabdoviruses. (ictv.global)
Our observations support the notion that full LPS response of TNF gene requires both NF-kappaB and non-NF-kappaB nuclear proteins. (ox.ac.uk)
The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
This protein binds to the GCM-motif (A/G)CCCGCAT, a novel sequence among known targets of DNA-binding proteins. (avivasysbio.com)
Sequence alignments and phylogenetic trees of these domains allow us to interpret the evolutionary relationship between these proteins, concluding that spectrin evolved from alpha-actinin by an elongation process that included two duplications of a block of seven repeats. (embl.de)
This four and a half-credit course will present an introduction to the Biophysical Chemistry and Structural Biology of proteins and nucleic acids. (columbia.edu)

Two of the most common uses of the DNA microarrays are genetic analysis and the analysis of gene expression. (ddw-online.com)
These results indicate that the env genes of primary HIV-1 isolates collected worldwide can vary considerably in their genetic, phylogenetic, and biological properties. (duke.edu)
Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species. (bvsalud.org)
Horizontal gene transfer happens when foreign genetic material jumps into genomes, creating new combinations (recombination) of genes, or new genomes. (i-sis.org.uk)
Genetic modification is essentially horizontal gene transfer and recombination, speeded up enormously, and totally unlimited in the source of genetic material recombined to make the GMDNA that's inserted into the genomes plants, animals and livestock to create genetically modified organisms (GMOs). (i-sis.org.uk)
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. (uchicago.edu)

Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans 5 and Aspergillus fumigatus 6 . (nature.com)
Angiosperm mitochondrial genomes also contain numerous introns, some of which have been split such that the resulting gene fragments must be transcribed separately and then trans- spliced together [ 7 ]. (biomedcentral.com)
These inverted repeat structures form the target for telomere resolution events that include sequence-specific cleavage and directed strand exchange to form the hairpin termini of progeny virus genomes. (ox.ac.uk)
To correlate and compare gene structures from related genomes, the first step is to define "orthologous" gene couples. (biomedcentral.com)
Each RBH couple consists of two genes, one from each of the two genome sequences (or genomes) to compare, which display the highest scoring hit in the other data set in a reciprocal manner [ 36 ]. (biomedcentral.com)
Here, we extend our previous analysis to the genomes of low G + C firmicutes and gamma-proteobacteria, and in a second step to all sequenced bacterial genomes. (pasteur.fr)
Smaller biases were found in the genomes of obligatory intracellular bacteria, for which the assignment of essentiality by homology from fast growing free-living bacteria is most problematic. (pasteur.fr)
These results indicate that essentiality plays a fundamental role in the distribution of genes in most bacterial genomes. (pasteur.fr)

Divergence in one region of 18S rRNA appears to be the result of a gene conversion event, in which recombination with a homologous gene of chloroplast origin led to the complete replacement of a helix in this ribosomal RNA. (biomedcentral.com)
Our technique is based on knockout constructs that contain regions homologous to the target gene cloned into vectors carrying dominant drug-resistance markers. (ox.ac.uk)
However, the relevance of homologous sites in the human TNF gene remained a matter of controversy, partly because the high affinity NF-kappaB/Rel site located at -510 in the murine promoter is not conserved in humans. (ox.ac.uk)
In the recently reported partial sequence of the chicken non-muscle alpha-actinin, a repetitive sequence homologous to the internal repeat in spectrin occurs several times. (embl.de)
2006 ). Mice have two homologous genes of MBL i.e. (springeropen.com)
Southern blot analysis of total cell DNA of the transformants shows that the wild type psaC gene has been replaced by the interrupted psaC gene through homologous recombination. (unige.ch)

A 3.6-kb region of the Shope fibroma virus (SFV) BamHI D fragment located in the central region of the viral genome was sequenced. (ox.ac.uk)
Homology scores and assays of viral cores indicate that SFV D3R encodes the large subunit of the SFV mRNA capping enzyme. (ox.ac.uk)
The terminal sequence domain which forms the telomere resolution target (TRT) shares considerable sequence similarity with viral late promoters. (ox.ac.uk)
The proposed model for telomere resolution invokes directed unwinding of the TRT double helix by a transcription initiation complex and processing of the resulting secondary structure by viral late-gene products. (ox.ac.uk)
Our results also demonstrate that CTL pressures help to maintain certain elements of consensus viral sequence, which likely represent viral escape from common HLA-restricted CTL responses. (jenner.ac.uk)

These aberrant transcripts are the products of abnormal RNA splicing and termination owing to the inserted sequence, and transcription initiation within the 3' long terminal repeat (LTR) of the ETn. (essex.ac.uk)
The genome contains a leader region of approximately 59 nt preceding the transcription start of the N gene, and a trailer of about 19 nt following the transcription termination of the L gene. (ictv.global)
Transcription of the TNF gene is rapidly and transiently induced by LPS in cells of monocyte/macrophage lineage. (ox.ac.uk)
Out of these, 4 SNPs from 3′ UTR were found to play role in miRNA binding, 7 SNPs from 5′ near and intronic region were predicted to involve in transcription factor binding and expression of MBL2 gene. (springeropen.com)
In 2007, autosomal dominant mutations in signal transducer and activator of transcription-3 (STAT3) gene were identified as the molecular cause of this disease. (medscape.com)
Dimerized STATs then translocate to the nucleus, where they bind DNA in the promoter sequences of target genes to activate transcription. (medscape.com)

The highest degree of homology in the Cox 1 nucleic acid sequences and predicted amino acid sequences was found between A. agkistrodontis and A. armillatus . (unl.edu)
The degree of homology between target and probe results in stable hybridization. (enzolifesciences.com)

Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context. (ucdenver.edu)
Revealing the architecture of gene regulation: the promise of eQTL studies. (uchicago.edu)
High-resolution mapping of expression-QTLs yields insight into human gene regulation. (uchicago.edu)
Part I covers key laboratory manipulations, including DNA cloning, gene characterization, association of genes with disease, and methods for studying gene regulation and activities of gene products. (columbia.edu)
Whole genome analysis of lung, sampled 24 hours after challenge, showed expression changes of not only genes belonging to several Gene Ontology groups with up-regulation of inflammatory-associated genes and those associated with lung remodeling but also genes involved in downsizing these processes. (cdc.gov)

High frequency intra- and intermolecular recombination among large repeated sequences is the rule, generating a heterogeneous pool of genome configurations within a single individual [ 12 - 14 ]. (biomedcentral.com)
Horizontal gene transfer and recombination go hand in hand. (i-sis.org.uk)
By enhancing both the rate and scope of horizontal gene transfer and recombination, GM has also increased the chance of generating new disease-causing viruses and bacteria [1, 2]. (i-sis.org.uk)
More recently, his group invented tools for cleavage-free large gene insertion via mining microbial recombination protein, and developed single-cell tracking approach for studying cancer biology and cancer immunology. (stanford.edu)

To generate a more representative panel of genetically diverse envelope genes, we PCR amplified, cloned, and sequenced complete gp160 coding regions of 35 primary (peripheral blood mononuclear cell-propagated) HIV-1 isolates collected at major epicenters of the current AIDS pandemic. (duke.edu)
Analysis of their deduced amino acid sequences revealed several important differences from prototypic subtype B strains, including changes in the number and distribution of cysteine residues, substantial length differences in hypervariable regions, and premature truncations in the gp41 domain. (duke.edu)
For most lineages and most regions of the gene, both silent and replacement substitutions have accumulated in a constant, clock-like manner. (ox.ac.uk)
This affinity and complementary sequence allow binding to specific regions of a target sequence of nucleotides. (enzolifesciences.com)
Here we report on a systematic approach to delineate such conserved elements from upstream regions of orthologous gene pairs from man and mouse. (mdc-berlin.de)
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. (uchicago.edu)
1998 ). The MBL2 gene is composed of 7461 bases and lies between the regions 52765380 to 52772841 bp of chromosome no. 10 (NCBI reference sequence number NC_000010.11). (springeropen.com)
2007 ). SNPs of MBL2 gene cover both coding and non-coding regions. (springeropen.com)

a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. (sbgrid.org)
Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments. (cdc.gov)

Scholars@Duke publication: Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID Networks for HIV Isolation and Characterization. (duke.edu)

an interactive perl/tk application that can read common sequence alignment formats that the user can then alter, embellish, markup, etc. to produce the kind of sequence figure commonly found in biochemical articles. (sbgrid.org)
Bit-parallel sequence-to-graph alignment. (cdc.gov)

Gene probes are used in various blotting and in situ hybridization (ISH) techniques for the detection of nucleic acid sequences in food industry, environmental, medical, and veterinary applications to improve the specificity of the analyses. (enzolifesciences.com)
Probes labeled by nick translation can be used in many different hybridization techniques including: chromogenic in situ hybridization (CISH), fluorescent in situ hybridization (FISH), screening gene banks by colony or plaque hybridization, DNA or RNA transfer hybridization, and re-association kinetic studies. (enzolifesciences.com)

The completion of the sequencing of the human genome has uncovered 32,000 to 35,000 predicted genes, offering the prospect for many more drugable targets. (ddw-online.com)
Gene expression levels are a target of recent natural selection in the human genome. (uchicago.edu)

In today's research laboratory, two common ways that gene expression is assessed is by using quantitative polymerase chain reaction techniques (QTPCR) for monitoring expression of smaller numbers of genes, and by employing DNA microarrays for the highly parallel monitoring of thousands of genes (or the whole transcriptome). (ddw-online.com)

Non-coding DNA segments that are conserved between the human and mouse genomic sequence are good indicators of possible regulatory sequences. (mdc-berlin.de)
Sequencing and analysis of Neanderthal genomic DNA. (uchicago.edu)
Genomic Southern analysis demonstrated that jrPPO1 is the sole PPO gene in walnut. (ashs.org)

We have designed the most efficient strategy to knock out genes in fission yeast Schizosaccharomyces pombe on a large scale. (ox.ac.uk)

Many new nucleic acid-based diagnostic tools or assays have been developed that allow analysis of DNA and RNA molecules in clinical samples. (enzolifesciences.com)

Previous data suggested that multiple NF-kappaB/Rel binding sites play a role in the transcriptional response to LPS of the murine gene. (ox.ac.uk)
Topics covered include various high-throughput genomics technologies (genome sequencing, DNA microarrays, proteomics), quantitative modeling of transcriptional and post-transcriptional regulatory networks, synthetic biology, and the world of RNA structure, dynamics, and function. (columbia.edu)
Run-on analysis showed transcriptional attenuation in the normal rat myc gene, similar to the situation in mice and humans. (lu.se)

DNA microarrays take advantage of the major feature of the DNA double helix, the sequence complementarity of the two-paired strands, by using DNA capture probes which are the complement of the expressed target sequence (mRNA, cRNA or cDNA made from the mRNA). (ddw-online.com)
We have devised a method for the selection of genes from cDNA libraries that suppress the block to virus infection, and so restore virus susceptibility. (biomedcentral.com)
We cloned a PPO-encoding gene from a walnut pistillate flower cDNA library and designated the gene jrPPO1 . (ashs.org)

Alpha-1-acid glycoprotein 1 is a protein that in humans is encoded by the ORM1 gene. (wikipedia.org)

Major immune response pathways control the expression of hundreds of genes that represent potential effectors of the immune response. (cnrs.fr)
The identities of these genes provide insights into the mechanism of virus resistance and will help to define new pathways used during retrovirus infection. (biomedcentral.com)
Unsensitized animals challenged with TMA exhibited also an increased number of macrophages in BAL, but gene expression in the above-mentioned gene pathways was unchanged or down-regulated. (cdc.gov)

A DNA probe is a labeled fragment of DNA that contains a nucleotide sequence specific for the gene or chromosomal region of interest. (enzolifesciences.com)
Progress in several laboratories over the past few years including substantial partial peptide and nucleotide sequence determination has greatly enhanced our knowledge of the structural properties of this large molecule (heterodimer = 465,000 daltons). (embl.de)

Spectrin, the major component of the membrane skeleton that provides elasticity to the cell, contains tandemly repeated sequences of 106 amino acid residues. (embl.de)
Information regarding solvent accessibility, molecular dynamics and energy minimization calculations showed that this variant causes clashes with neighboring amino acids residues that must interfere in the normal triple helix formation of trimeric subunit and further with the normal assembly of MBL oligomeric form, hence decrease in stability. (springeropen.com)

His work has led to one of the first CRISPR/Cas9 gene-editing tools for in vivo gene therapy. (stanford.edu)
United States Patent 8,932,814 CRISPR-Cas nickase systems, methods and compositions for sequence manipulation in eukaryotes. (stanford.edu)
SHERLOCK: nucleic acid detection with CRISPR nucleases. (cdc.gov)

The amino acid sequence of the transformer (tra) gene exhibits an extremely rapid rate of evolution among Drosophila species, although the gene performs a critical step in sex determination. (ox.ac.uk)
Sequence evolution was also examined among six species representative of the genus Drosophila. (ox.ac.uk)
Mitochondrial gene loss and functional transfer to the nucleus is an ongoing process in many lineages of plants, resulting in substantial variation across species in mitochondrial gene content. (biomedcentral.com)
That's because each species comes onto the evolutionary stage in its own space and time, and only those species that overlap in space and time could ever exchange genes at all in nature. (i-sis.org.uk)

Analysis of gene expression can include measuring expression levels of a small set of genes to whole genome expression monitoring. (ddw-online.com)
Sequencing of the A. oryzae genome was accomplished using the whole-genome shotgun (WGS) approach. (nature.com)
Optimizing a Whole-Genome Sequencing Data Processing Pipeline for Precision Surveillance of Health Care-Associated Infections. (cdc.gov)
Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci. (cdc.gov)

The restriction analysis and partial sequencing of the gene shows that it contains (1) four alternatively spliced exons previously described in rodent and bovine but not in human tau cDNAs and (2) two CpG islands, one associated with the promoter region, the other with exon 9. (nih.gov)
The sequence analysis of the 32-35,000 predicted genes indicates the there may be as many as 1,000 kinase or kinase-like genes. (ddw-online.com)
Gene expression analysis may uncover or facilitate answers to these questions as well as assist research and development and health care in several other ways. (ddw-online.com)
This report will focus in using DNA microarrays for the analysis of gene expression or expression profiling, and how DNA chips are used for drug discovery and development. (ddw-online.com)
Syntenic analysis of the three aspergilli revealed the presence of syntenic blocks and A. oryzae -specific blocks of sequence (lacking synteny with the two other aspergilli) in a mosaic manner throughout the A. oryzae genome ( Fig. 1 ). (nature.com)
Both levels of analysis of the tra sequence suggest that, although the gene is evolving at a rapid pace, these changes are neutral in function. (ox.ac.uk)
Phylogenetic and cluster analysis were also undertaken, focusing on the 18S rRNA and the Cox1 gene. (unl.edu)
In depth analysis of the predicted gene set revealed some errors involving genes with non-canonical splice sites in their introns. (biomedcentral.com)
We are using genome technology such as gene-editing and data science method/analysis to study immunological and neurological diseases. (stanford.edu)
Protein structural analysis with this amino acid variant was performed by using I-TASSER, RAMPAGE, Swiss-PdbViewer, Chimera and I-mutant. (springeropen.com)
The course includes a series of biophysical research-related topics including practical introductions to the software tools available for the visualization and modeling of biomolecular structures and the bioinformatic analysis of biomolecular sequence and structural homology. (columbia.edu)
Sequence analysis of two tumors failed to reveal any structural changes within exon 1, as found by others in Burkitt's lymphoma. (lu.se)

This method was used to measure the number of copies of repeated genes such as rRNA genes (2) and to measure whether specific genes were under-replicated during the replication process used in forming polytene chromosomes (3). (ddw-online.com)
STARD12 co-expressed genes participated in cell cycle and DNA replication, and STARD14 were enriched in ECM-receptor interaction. (medsci.org)

The genome contains the fewest genes of any angiosperm mitochondrial genome sequenced to date, with intact copies of only 25 of the 41 protein genes inferred to be present in the common ancestor of angiosperms. (biomedcentral.com)
The sprivivirus genome contains five genes in the order 3′- N - P - M - G - L- 5′ encoding a nucleoprotein, polymerase-associated protein, matrix protein, glycoprotein and RNA-directed RNA polymerase, respectively (Figure 1. (ictv.global)

Additionally, in San Diego County, nucleic acid amplification tests (NAATs) are used to test for urethral, pharyngeal, and rectal gonorrhea and chlamydia infections at the county's public health laboratory. (cdc.gov)

In addition, genes encoding 18S and, especially, 5S rRNA exhibit exceptional sequence divergence relative to other plants. (biomedcentral.com)
Based on the 18S rRNA sequence, the shortest hereditary distance was found between A. agkistrodontis and Raillietiella spp. (unl.edu)

The Caryophyllaceae represents one lineage that has experienced a particularly high rate of mitochondrial gene loss relative to other angiosperms. (biomedcentral.com)
In this study, we report the first complete mitochondrial genome sequence from a member of this family, Silene latifolia . (biomedcentral.com)
Even assuming expanded wobble-pairing rules, the mitochondrial genome can support translation of only 17 of the 61 sense codons, which code for only 9 of the 20 amino acids. (biomedcentral.com)
These findings suggest a markedly expanded role for nuclear gene products in the translation of mitochondrial genes in S. latifolia and raise the possibility of altered selective constraints operating on the mitochondrial translational apparatus in this lineage. (biomedcentral.com)
1) "native" tRNAs encoded in the mitochondrial genome and inherited from the α-proteobacterial progenitor of mitochondria, 2) chloroplast-like tRNAs, which are also encoded in the mitochondrial genome but which were acquired by functional gene transfer from the chloroplast genome during land plant evolution, and 3) nuclear-encoded tRNAs imported from the cytosol. (biomedcentral.com)

One of these, derived from a patient with rapid CD4 cell decline, contained an amino acid substitution in a highly conserved endocytosis signal (Y721C), as mediated virus entry with very poor efficiency, although they did not contain sequence changes predicted to alter protein function. (duke.edu)
Gene expression also relies on extensive C-to-U (and sometimes U-to-C) RNA editing, in which substitution of specific pyrimidines in the mRNA sequence restores phylogenetically conserved codons [ 8 ]. (biomedcentral.com)

We focus on orthologous genes in order to maximize our chances to find functionally similar regulatory elements. (mdc-berlin.de)

Adaptations to climate in candidate genes for common metabolic disorders. (uchicago.edu)

Eukaryotic genes are transcribed as a primary transcript that is subsequently converted to a mature mRNA through several processing steps including splicing. (biomedcentral.com)
Provirus 0 domande Duplex DNA sequences in eukaryotic chromosomes, corresponding to the genome of a virus, that are transmitted from one cell generation to the next without causing lysis of the host. (lookformedical.com)

Since non-canonical splice sites are difficult to predict ab initio, we checked for options to improve the annotation by transferring annotation information from the recently released Columbia-0 reference genome sequence annotation Araport11. (biomedcentral.com)
GeneSet_Nd-1_v1.1 contains previously missed non-canonical splice sites in 1256 genes. (biomedcentral.com)
Despite attempts to annotate non-canonical splice sites automatically [ 24 , 25 ], ab initio gene prediction without experimental support from e.g. (biomedcentral.com)
RNA-Seq data ("external hints") does not support the detection and annotation of non-canonical splice sites on genome sequence assemblies at a satisfying level [ 26 , 27 , 28 ]. (biomedcentral.com)

Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation. (nature.com)

The inference of essentiality by homology allows us to show that essential genes are much more frequent in the leading strand than other genes, even when compared with non- essential highly expressed genes. (pasteur.fr)

It is clear that gene expression profiling systems have a role to play in many facets of drug discovery and development, but several questions remain. (ddw-online.com)
We take a look at the use of DNA microarray for gene expression or expression profiling and how DNA chips are used for drug discovery and development as a whole. (ddw-online.com)

The degree of similarity between sequences. (bvsalud.org)
These, however, are sometimes difficult to trace because of low sequence similarity between duplicated segments. (embl.de)

The blocks of A. oryzae -specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. (nature.com)

The genome has also experienced a major reduction in tRNA gene content, including loss of functional tRNAs of both native and chloroplast origin. (biomedcentral.com)

This gene is conserved and Y-specific among a wide range of mammals, and encodes a testis-specific transcript. (nih.gov)
This gene encodes a key acute phase plasma protein. (wikipedia.org)
It encodes a 248 amino acid residue transmembrane protein, MBL (NCBI accession number XP_011538118.1) which is encoded via a 3570 bp long mRNA (NCBI accession number NM_000242.21). (springeropen.com)

The chloroplast gene psaC encoding the iron sulfur protein of photosystem I (PSI) from the green alga Chlamydomonas reinhardtii has been cloned and characterized. (unige.ch)
The present study suggests that any chloroplast gene encoding a component of the photosynthetic apparatus can be disrupted in C. reinhardtii using the strategy described. (unige.ch)

Our data also suggest that the functional activity of a given kappaB site depends on the entire DNA sequence context in the promoter region. (ox.ac.uk)
The present study was carried out to identify and prioritize the SNPs of MBL2 gene for further genotyping and functional studies. (springeropen.com)
MBL1 and MBL2 , but in human the first of them is pseudogene leaving one functional gene MBL2 (Guo et al. (springeropen.com)

In addition, all subtype E and three subtype G viruses initially classified on the basis of partial env sequences were found to cluster in subtype A in the 3' half of their gp41 coding region, suggesting that they are also recombinant. (duke.edu)

Anatomy8

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Chemicals and Drugs75

Analytical, Diagnostic and Therapeutic Techniques and Equipment33

Phenomena and Processes86

Disciplines and Occupations4

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Proteins13

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Genomes8

Homologous6

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Transcription6

Degree of homology2

Regulation5

Recombination4

Regions8

Multiple sequence alignments2

Publication1

Alignment2

Hybridization2

Human genome2

Polymerase Chain Re1

Genomic3

Fission yeast Schizosaccharomyces pombe1

Assays1

Transcriptional3

CDNA3

Humans1

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Nucleotide sequence2

Residues2

CRISPR3

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Whole genome4

Analysis12

Replication2

Genome contains2

Amplification1

RRNA2

Mitochondrial5

Substitution2

Orthologous1

Candidate genes1

Eukaryotic2

Splice sites4

Transporters1

Inference1

Expression Profiling2

Similarity2

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TRNA1

Encodes3

Chloroplast gene2

Functional3

Partial1