Homologous sequences sequence homology nucleic acid. Medical search. Frequent questions

And the cell achieves the target gene editing through non-homologous end joint (NHEJ) or homology directed repair (HDR). (cd-genomics.com)
For genotyping applications, dPCR can capture rare allele or copy number variation, be used for liquid biopsy analysis, identify homology directed repair (HDR) or non-homologous end joining (NHEJ) induced by CRISPR-based genome editing, and assess DNA quality for next generation sequencing (NGS). (idtdna.com)
Precise removal of introns, preferential removal of smaller introns and presence of at least 2 bp of microhomology flanking most introns indicated that intron loss may have predominantly occurred through non-homologous end-joining (NHEJ) repair of double strand breaks. (biomedcentral.com)
Two main mechanisms for intron loss have been proposed, that is reverse transcription (RT)-mediated intron loss and intron deletion triggered by repair of double strand breaks (DSBs) via non-homologous end joining (NHEJ). (biomedcentral.com)
A signature of genomic deletion of introns via NHEJ is the presence of 2-8 bp of micro-homology. (biomedcentral.com)

Retroviruses have been shown to efficiently delete sequences between repeats as a consequence of the template switching ability of the viral reverse transcriptase. (peerj.com)
Although HIV-1 based gene transfer vectors lack most of the viral coding sequences, it retains a small portion of the gag sequence, and also contains a 5′ splice donor site upstream of gag and frequently a 3′ splice acceptor site further downstream. (peerj.com)
The present article is based on the large amount of sequence data accumulated in these years and focuses on the viral nucleic acids and proteins and their function. (pdfroom.com)
Mutational analysis of several of these amino acids both in pUL105 and pUL70, proved that they are crucial for viral replication. (frontiersin.org)
The J. Craig Venter Institute (JCVI) has been involved in viral sequencing and analysis for more than 25 years, and coronavirus research for more than 15. (jcvi.org)
DNA sequences that form the coding region for the viral envelope (env) proteins in retroviruses. (lookformedical.com)

These, however, are sometimes difficult to trace because of low sequence similarity between duplicated segments. (embl.de)
Including such artifacts can result in similarity between non-homologous sequences. (berkeley.edu)
The degree of similarity between sequences. (bvsalud.org)
OTEs are undesired changes to genomic DNA sequences with some sequence similarity to the target site. (idtdna.com)
OTEs occur when the Cas enzyme is directed to the wrong site by the gRNA due to such sequence similarity. (idtdna.com)

Furthermore, AtRAD54, which performs an important role in the homologous recombination repair pathway, was involved in the pairing of homologous loci with γ-irradiation. (nature.com)
Orthologous to human MCM8 (minichromosome maintenance 8 homologous recombination repair factor). (nih.gov)

N, P, M, G and L share significant sequence homology and/or structural characteristics with the homologous proteins of other rhabdoviruses. (ictv.global)
The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. (uni-marburg.de)
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)
The Structural Classification of Proteins - extended ( SCOPe ) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst all proteins of known structure, along with resources for analyzing the protein structures and their sequences. (berkeley.edu)
By providing a broad survey of protein folds and authoritative information about relatives of proteins, particularly those too ancient to be readily recognized from sequence, SCOPe is a framework for future research and classification. (berkeley.edu)
RecA family proteins are responsible for homology search and strand exchange. (ibpc.fr)
While all coronaviruses contains these proteins, a subset (HEV, HCV-OC43 and BCV) is now recognized to possess an additional glycopolypeptide (gp65), which is unrelated to S or M. N protein The number of amino acids in the N protein has been determined by cloning and sequencing for MHV strains A59 (Armstrong et al. (pdfroom.com)

DNA sequences that form secondary structures or bind protein complexes are known barriers to replication and potential inducers of genome instability. (uthscsa.edu)
We show that the Srs2 protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a protein-bound repeat. (uthscsa.edu)
In one embodiment, the present invention relates to a recombinant protein having a protein comprising at least a portion of the amino acid sequence set forth in SEQ ID NO:2. (justia.com)
In some embodiments, the present invention provides a protein which consists of the amino acid sequence shown in SEQ ID NO: 2 having a deletion, substitution, or addition of at least one amino acid and which has neurogenesis inducing activity. (justia.com)
The present invention also relates to a gene which hybridizes with the neurogenesis inducing gene encoding for a protein comprising at least a portion of the amino acid sequence set forth in SEQ ID NO:2. (justia.com)
In another embodiment, the present invention relates to an isolated nucleic acid encoding a protein having at least a portion of the amino acid sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 42 and in SEQ ID NO: 44. (justia.com)
Prediction of protein antigenic determinants from amino acid sequences. (scirp.org)
Taxonomy and function of C1 protein kinase C homology domains. (embl-heidelberg.de)
secretase" which cleaves between amino acids 16 and 17 of the protein. (justia.com)
amyloid precursor protein (.beta.APP), which is expressed in differently spliced forms of 695, 751, and 770 amino acids. (justia.com)
A proportion of these will alter protein sequences, the most common of which is the non-synonymous single nucleotide polymorphism (nsSNP). (biomedcentral.com)
For over 40% of the nsSNPs, structure-based methods predicted which of these sequence changes are likely to either disrupt the structure of the protein or interfere with the function or interactions of the protein. (biomedcentral.com)
The most identifiable category of SNP is the small proportion (less than 1%) that change protein sequence, the most common of which is the non-synonymous SNP. (biomedcentral.com)
We identify the main binding sites of a catalytically inactive Cas9 (dCas9) protein in bovine fetal fibroblast cells (BFFs) with chromatin immunoprecipitation sequencing (ChIP-seq). (biomedcentral.com)
The env genes contain a cis-acting RNA target sequence for the rev protein (= GENE PRODUCTS, REV ), termed the rev-responsive element (RRE). (lookformedical.com)
Collation and analyses of DNA-binding protein domain families from sequence and structural databanks. (ncbs.res.in)

It was revealed that homologous loci kept a constant distance in nuclei of A. thaliana roots in general growth. (nature.com)
We also found that DNA double-strand breaks (DSBs) induce the approach of the homologous loci with γ-irradiation. (nature.com)
These results suggest that homologous loci approach each other to repair DSBs and AtRAD54 mediates these phenomena. (nature.com)
Here, we examined chromatin dynamics and arrangement in living roots of A. thaliana with DNA damage, focusing our attention on the distance between homologous loci using the lacO /LacI-EGFP system. (nature.com)
We revealed that the homologous loci kept a constant three-dimensional distance in the nucleus using live-cell imaging with a bacterial operator/repressor system. (nature.com)
Moreover, the distance between two homologous loci in the interphase nucleus was shortened by γ-irradiation, which induces DNA double-strand breaks (DSBs). (nature.com)
We found that AtRAD54, which performs an important role in the homologous recombination (HR) repair pathway, was involved in the approach of two homologous loci under γ-irradiation. (nature.com)
Our results suggest that the transient reduction in inter-allelic distance and increase in pairing frequency of homologous loci after DSB result in partial chromatin reorganisation of interphase nuclei and that AtRAD54 contributes to the subcellular movement of homologous loci in the HR repair pathway. (nature.com)
All loci therefore have common sequences. (ox.ac.uk)
Loci concerned with the alpha phenotype (MAT alpha and HML alpha) contain and 850 bp alpha-specific sequence, whereas loci concerned with the a phenotype (MATa and HMRa) contain a 700 bp a-specific sequence. (ox.ac.uk)
The a- or alpha-specific sequences are surrounded by DNA sequences that are common to all loci. (ox.ac.uk)
the invention also provides non-human animals and cells comprising a transgene encoding an APP comprising the Swedish mutation and further comprising functionally disrupted endogenous APP gene loci, transgenes and targeting constructs used to produce such transgenic cells and animals, transgenes encoding human Swedish mutation APP polypeptide sequences, and methods for using the transgenic animals in pharmaceutical screening and as commercial research animals for modeling neurodegenerative diseases (e.g. (justia.com)
Following crRNA and tracrRNA hybridization, SpCas9 is targeted to genomic loci matching a 20-nt guide sequence within the crRNA, immediately upstream of a required 5′-NGG protospacer adjacent motif (PAM) 11 . (cdc.gov)
Although an sgRNA design consisting of a truncated crRNA and tracrRNA had been previously shown to mediate efficient cleavage in vitro 12 , it failed to achieve detectable cleavage at several loci that were efficiently modified by crRNA-tracrRNA duplexes bearing identical guide sequences 1 . (cdc.gov)

CRISPR screening is a large-scale genetic loss-of-function screen approach that generates and screens a population of mutant cells to facilitate the discovery of key genes or genetic sequences in a particular cell type. (cd-genomics.com)
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)
each has drawbacks, especially when the sequences of the interested genes are truncated, contain gaps or are low quality [ 9 ]. (biomedcentral.com)
While the size of the introns, number of introns per gene and the number of intron-containing genes can vary greatly between sequenced eukaryotic genomes, the structure of a gene with reference to intron presence and positions is typically conserved in closely related species. (biomedcentral.com)
In the present report we have compared and contrasted structure- and sequence-based methods of prediction to over 5500 genes carrying nearly 24,000 nsSNPs, by employing an automatic comparative modelling procedure to build models for the genes. (biomedcentral.com)

By using sequence alignment of herpesviruses homologs, we identified conserved amino acids in the putative pUL105 ATP binding site and in the putative pUL70 zinc finger pattern. (frontiersin.org)

We can therefore amplify nucleotide sequences from infinitesimal amounts of DNA extract. (intechopen.com)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)

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)
The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. (embl-heidelberg.de)

Fortunately, with the availability of several fully sequenced plant genomes, studies of genome evolution and organization become possible in part by detecting syntenies and colinearities or clustering and ordering of neighboring matching gene pairs [ 3 ]. (biomedcentral.com)
Our analysis enables the accurate detection of sequencing errors, small insertions and deletions (indels), and structural variants, including large reciprocal indels and copy number variants, from comparisons between the resequenced and reference genomes. (psu.edu)

When DSBs are repaired by homologous recombination, DNA ends can undergo extensive processing, producing long stretches of single-stranded DNA (ssDNA). (uthscsa.edu)

Hybridization studies have shown that the 700 bp sequence is present at HMLa but absent at HMR alpha alleles. (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)
Despite the gene's repetitive and GC-rich sequences, 13% of RPGR gene copies showed mutation correction and conversion to the wild-type allele. (nature.com)
However, the presence of repetitive sequences and structural variants can lead to false positives in the identification of polymorphic alleles. (psu.edu)

In this study, chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq) was performed to identify the AmtR regulon in C. glutamicum ATCC 14067. (frontiersin.org)

The recent sequencing of the human genome has provided a wealth of information detailing several million genetic variations between individuals. (biomedcentral.com)

Its principle is based on the use of DNA polymerase which is an in vitro replication of specific DNA sequences. (intechopen.com)
S. G. Kamita, S. Maeda, Hammock, B. D. (2003) High-fre-quency homologous recombination between baculoviruses in-volves DNA replication. (scirp.org)

The iPSCs were transduced with CRISPR guide RNAs, Cas9 endonuclease and a donor homology template. (nature.com)
The uncertainty of when the enzyme is expressed may be problematic for experiments that require other manipulations such as timed drug delivery or delivery of a donor template for homology-directed recombination (HDR). (idtdna.com)

To evaluate this approach for deriving safety-modified lentiviral vectors, we created HIV-1 vectors engineered to delete the Rev-response element (RRE) during reverse-transcription by sandwiching the RRE between two non-functional hygromycin phosphotransferase sequences. (peerj.com)
All gene transfer vectors also contain cis -sequences for encapsidation, reverse-transcription, and integration. (peerj.com)
HIV-1 based vectors also contain the RRE sequence. (peerj.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)
C1 domains are compact alpha/beta structural units of about 50 amino acids which tightly bind two zinc ions. (embl-heidelberg.de)

However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. (biomedcentral.com)
To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses. (cdc.gov)
We performed northern blot analyses for the guide RNA truncations and found increased levels of expression for the longer tracrRNA sequences, suggesting that improved target cleavage was at least partially due to higher sgRNA expression or stability ( Fig. 1c ). (cdc.gov)

However the gag/pol coding sequence serves as an intron and is spliced out for expression of Env. (peerj.com)
2020. Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species. . (ncbs.res.in)

By combining CRISPR/Cas9 genomic screening technology and single-cell sequencing, the expression of sgRNA can be accurately captured, and the changes of gene transcription level in cells can be measured. (cd-genomics.com)
Because the major difference between this sgRNA design and the native crRNA-tracrRNA duplex is the length of the tracrRNA sequence, we tested whether extension of the tracrRNA tail would improve SpCas9 activity. (cdc.gov)

At its center, each locus contains one of two apparently nonhomologous sequences. (ox.ac.uk)

E. B. Carstens, A. Krebs, Gallerneault, C. E. (1986) Identifica-tion of an amino acid essential to the normal assembly of Auto-grapha californica nuclear polyhedrosis virus polyhedra. (scirp.org)

Our analysis revealed a high level of gene retention and colinearity, as well as high gene structure and sequence conservation, with an average sequence divergence of 4% for exons. (gnpannot.org)
The colinearity of homologous pairs is controlled by a statistical distance function. (biomedcentral.com)

To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. (biomedcentral.com)

In competition with bacteriophages, bacteria and archaea have evolved unique ways of defending, which include the CRISPR/Cas systems, the immune systems of bacteria and archaea to resist the invasion of foreign DNAs or RNAs, recognize the foreign invading nucleic acids, and cleave them for immune defense. (cd-genomics.com)
The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. (degruyter.com)

Evolutionary loss and gain of introns in genomic sequence data may provide a mechanism by which organisms diversify gene expression and gene function. (biomedcentral.com)

CRISPR gRNAs were selected to minimize the off-target profile and to maximize the degree of homology with a target sequence directly centered on the mutation site. (nature.com)

The order of amino acids as they occur in a polypeptide chain. (lookformedical.com)

The traditional phylogenetic principles and methods are based on amino acid or nucleotide sequence to assess homology, determine orthology and paralogy, and deduce relationships within gene families and/or reconstruct gene evolutionary events. (biomedcentral.com)
They are pairing this with a rapid, modular reverse genetic system to assess genomic variants identified in the wealth of global sequencing data, develop and test vaccine candidates, and generate needed reagents, including fluorescent and tagged virus strains. (jcvi.org)

The genome sequence of the multinucleocapsid nucleo-polyhedrovirus of the Chinese oak silkworm Antheraea pernyi. (scirp.org)

Oct. 26, 1993, Abstract No. 15.4, Anaheim, Calif.) which contains more of the .beta.AP sequence carboxy terminal to that form described by Esch et al. (justia.com)

Consequently, we determined the feasibility of using Cas9n-induced SSB to stimulate homology-directed repair (HDR) and therefore provided a safe alternative for gene insertion and transgenic animal generation. (biomedcentral.com)

The newly described crystallographic structures of two consecutive homologous repeats of human alpha-actinin, a member of the spectrin superfamily, shed new light on alpha-actinin interchain binding properties. (embl.de)

CCCVd have a sequence of 246 nucleotides, 44 of which are common with most viroids. (wikipedia.org)
The Open reading frame (ORF) of the AnpeNPV consists of 738 nucleotides encoding 245 amino acids with molecular masses of 29 kDa. (scirp.org)

There is inverse complementarity between the 3′-leader and 5′-trailer sequences. (ictv.global)
Each of these sequences are designed to have sequence complementarity to the target gene/DNA of interest. (idtdna.com)

As with any genomic analysis, a sample of nucleic acid must be obtained. (idtdna.com)
The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. (biomedcentral.com)
The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis. (biomedcentral.com)
W. B. Wang, S. Y. Zhu, L. Q. Wang, F. Yu, Shen W. D. (2005) Cloning and sequence analysis of the Antheraea pernyi nucleo-polyhedrovirus gp64 gene. (scirp.org)
S. Gomi, K. Majima, Maeda S. (1999) Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. (scirp.org)
E. A. van Strien, D. Zuidema, R.W. Goldbach, Vlak, J. M. (1992) Nucleotide sequence and transcriptional analysis of the polyhedrin gene of Spodoptera exigua nuclear polyhedrosis vi-rus. (scirp.org)
By combining analysis of 54 C1 domain sequences with information from previously reported solution and crystal structure determinations and site-directed mutagenesis, profiles are derived and used to classify C1 domains. (embl-heidelberg.de)

This ability of the RT to 'jump' is likely responsible for elimination of direct repeats, and sequences inserted between the repeats during reverse transcription. (peerj.com)

In order to investigate the genome dynamics in this highly polyploid context, we sequenced and compared seven hom(oe)ologous haplotypes (bacterial artificial chromosome clones). (gnpannot.org)

The sequence and structure prediction of CCCVd has been documented. (wikipedia.org)

We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the mutated conserved amino acids in this domain could be involved in ATP hydrolysis. (frontiersin.org)

Studies on the GM process have shown that the foreign gene inserts invariably damages the genome, scrambling and rearranging DNA sequences, resulting in inappropriate gene expression that can trigger cancer [3, 4]. (i-sis.org.uk)
Studies have shown that non-coding sequences play a pivotal role in the regulation of gene expression, tumorigenesis, immune regulation, ontogenesis, and many other biological processes. (cd-genomics.com)

He also noted concern regarding delays in referring specimens to the laboratory for testing, and emphasized the need for improvement in timeliness of reporting and tracking of the viruses referred for genomic sequencing. (who.int)

Digital PCR (dPCR) quantifies the absolute number of copies of a target genomic or complementary DNA (cDNA) sequence from a sample and can be used for a variety of applications [1-3] . (idtdna.com)
As with qPCR, the primers anneal to the outer regions of the target sequence (typically 60-150 bp in length). (idtdna.com)
This method can generate tens of billions of copies of a particular DNA fragment (the sequence of interest, DNA of interest, or target DNA) from a DNA extract (DNA template). (intechopen.com)
We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. (cdc.gov)

We also present data suggesting that an initial homology test of 8 contiguous bases rejects most interactions containing more than 1/8 mismatches without forming a detectable 20 bp product. (ibpc.fr)
We offer an alternative interpretation of the sequencing data of meiotic products, including the number and type of recombination events, to illustrate the potential for mistakes in single-nucleotide polymorphism calling. (psu.edu)
Using these examples, we propose that the detection of DNA polymorphisms using resequencing data needs to account for nonallelic homologous sequences. (psu.edu)

In another embodiment, the present invention relates to a gene comprising a DNA sequence having at least a portion of the nucleotide sequence set forth in SEQ ID NO: 1. (justia.com)
In preferred embodiments, the present invention provides a nucleic acid encoding a neurogenesis inducing gene (e.g., early neurogenesis inducing gene). (justia.com)
Indeed, if the sequence of interest is present in the DNA extract, it is possible to selectively replicate it (we speak of amplification) in very large numbers. (intechopen.com)
HMRa lacks an extensive (700 bp) DNA sequence to the right of the large right-hand homologous region, and possibly also a small (90 bp) sequence to the left of the small left-hand homologous region, both of which are present at HML alpha, MATa and MAT alpha. (ox.ac.uk)

IDT offers a variety of different products to support your dPCR experiments, including PrimeTime™ qPCR Probes , PrimeTime qPCR Probe Assays , and Affinity Plus™ qPCR Probes with locked nucleic acids. (idtdna.com)
We speculate that once the initial test is passed, the mismatch insensitive binding in the heteroduplex allows short mismatched regions to be incorporated in otherwise homologous strand exchange products even though sequences with less homology are eventually rejected. (ibpc.fr)

Anatomy11

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Diseases2

Chemicals and Drugs73

Analytical, Diagnostic and Therapeutic Techniques and Equipment39

Phenomena and Processes113

Disciplines and Occupations3

Information Science15

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NHEJ5

Viral6

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Recombination repair2

Proteins7

Protein16

Loci14

Genes5

Homologs1

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Amino acid residues2

Genomes2

DSBs1

Hybridization1

Repetitive3

Chromatin1

Human genome1

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Structural2

Analyses3

Intron2

SgRNA2

Locus1

19861

Colinearity2

Species1

RNAs2

Genomic Sequence1

Mutation1

Polypeptide1

Assess2

Genome sequence1

Abstract1

Repair1

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